diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index fdee6325d0f65c04fa76eec1cfa58ee90012c8c9..b91e58a83f43476d985fc513a98a77c943ce8789 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -9,13 +9,51 @@ lib/kokkos/* @stanmoore1 lib/molfile/* @akohlmey lib/qmmm/* @akohlmey lib/vtk/* @rbberger +lib/kim/* @ellio167 -# packages -src/KOKKOS @stanmoore1 -src/USER-CGSDK @akohlmey -src/USER-COLVARS @giacomofiorin -src/USER-OMP @akohlmey -src/USER-QMMM @akohlmey +# whole packages +src/COMPRESS/* @akohlmey +src/GPU/* @ndtrung81 +src/KOKKOS/* @stanmoore1 +src/KIM/* @ellio167 +src/LATTE/* @cnegre +src/SPIN/* @julient31 +src/USER-CGDNA/* @ohenrich +src/USER-CGSDK/* @akohlmey +src/USER-COLVARS/* @giacomofiorin +src/USER-DPD/* @timattox +src/USER-INTEL/* @wmbrownintel +src/USER-MANIFOLD/* @Pakketeretet2 +src/USER-MEAMC/* @martok +src/USER-MOFFF/* @hheenen +src/USER-MOLFILE/* @akohlmey +src/USER-NETCDF/* @pastewka +src/USER-PHONON/* @lingtikong +src/USER-OMP/* @akohlmey +src/USER-QMMM/* @akohlmey +src/USER-REAXC/* @hasanmetin +src/USER-TALLY/* @akohlmey +src/USER-UEF/* @danicholson +src/USER-VTK/* @rbberger + +# individual files in packages +src/GPU/pair_vashishta_gpu.* @andeplane +src/KOKKOS/pair_vashishta_kokkos.* @andeplane +src/MANYBODY/pair_vashishta_table.* @andeplane +src/USER-MISC/fix_bond_react.* @jrgissing +src/USER-MISC/*_grem.* @dstelter92 # tools tools/msi2lmp/* @akohlmey +tools/emacs/* @HaoZeke + +# cmake +cmake/* @junghans @rbberger + +# python +python/* @rbberger + +# docs +doc/utils/*/* @rbberger +doc/Makefile @rbberger +doc/README @rbberger diff --git a/README b/README index a258a335e934743df088d3e36cb1bc756377096b..784b1cb13ea9abfc852cf790b1ed40c579305619 100644 --- a/README +++ b/README @@ -25,7 +25,7 @@ The LAMMPS distribution includes the following files and directories: README this file LICENSE the GNU General Public License (GPL) bench benchmark problems -couple code coupling examples using LAMMPS as a library +cmake CMake build system doc documentation examples simple test problems lib libraries LAMMPS can be linked with diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 3a7e5dace641642186364f9ddf01c3295c0d4db2..d51108ba7aed1aae0a6040e7bda6f9d8dab20555 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -2,15 +2,17 @@ # CMake build system # This file is part of LAMMPS # Created by Christoph Junghans and Richard Berger -cmake_minimum_required(VERSION 3.1) +cmake_minimum_required(VERSION 2.8.12) -project(lammps) +project(lammps CXX) set(SOVERSION 0) -set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src) -set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib) -set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib) +get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE) +get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE) +get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE) +get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE) -#To not conflict with old Makefile build system, we build everything here + +# To avoid conflicts with the conventional Makefile build system, we build everything here file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp) file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES}) @@ -23,13 +25,23 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) -# remove any style headers in the src dir -file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h) -if(SRC_STYLE_FILES) - file(REMOVE ${SRC_STYLE_FILES}) -endif() - -enable_language(CXX) +# check for files auto-generated by make-based buildsystem +# this is fast, so check for it all the time +message(STATUS "Running check for auto-generated files from make-based build system") +file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h) +list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h) +foreach(_SRC ${SRC_AUTOGEN_FILES}) + get_filename_component(FILENAME "${_SRC}" NAME) + if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME}) + message(FATAL_ERROR "\n########################################################################\n" + "Found header file(s) generated by the make-based build system\n" + "\n" + "Please run\n" + "make -C ${LAMMPS_SOURCE_DIR} purge\n" + "to remove\n" + "########################################################################") + endif() +endforeach() ###################################################################### # compiler tests @@ -41,28 +53,80 @@ if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") endif() +# GNU compiler features +if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + option(ENABLE_COVERAGE "Enable code coverage" OFF) + mark_as_advanced(ENABLE_COVERAGE) + if(ENABLE_COVERAGE) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + endif() + option(ENABLE_SANITIZE_ADDRESS "Enable address sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_ADDRESS) + if(ENABLE_SANITIZE_ADDRESS) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address") + endif() + option(ENABLE_SANITIZE_UNDEFINED "Enable undefined behavior sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_UNDEFINED) + if(ENABLE_SANITIZE_UNDEFINED) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=undefined") + endif() + option(ENABLE_SANITIZE_THREAD "Enable thread sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_THREAD) + if(ENABLE_SANITIZE_THREAD) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread") + endif() +endif() + ######################################################################## # User input options # ######################################################################## -option(BUILD_SHARED_LIBS "Build shared libs" OFF) -if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg - set(CMAKE_POSITION_INDEPENDENT_CODE ON) +option(BUILD_EXE "Build lmp binary" ON) +if(BUILD_EXE) + set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically") + mark_as_advanced(LAMMPS_MACHINE) + if(LAMMPS_MACHINE) + set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") + endif() +endif() + +option(BUILD_LIB "Build LAMMPS library" OFF) +if(BUILD_LIB) + option(BUILD_SHARED_LIBS "Build shared library" OFF) + if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg + set(CMAKE_POSITION_INDEPENDENT_CODE ON) + endif() + set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file") + mark_as_advanced(LIB_SUFFIX) + if(LIB_SUFFIX) + set(LIB_SUFFIX "_${LIB_SUFFIX}") + endif() endif() + +if(NOT BUILD_EXE AND NOT BUILD_LIB) + message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE") +endif() + +option(DEVELOPER_MODE "Enable developer mode" OFF) +mark_as_advanced(DEVELOPER_MODE) +option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) include(GNUInstallDirs) set(LAMMPS_LINK_LIBS) set(LAMMPS_DEPS) set(LAMMPS_API_DEFINES) -option(ENABLE_MPI "Build MPI version" OFF) -if(ENABLE_MPI) + +find_package(MPI QUIET) +option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) +if(BUILD_MPI) find_package(MPI REQUIRED) - include_directories(${MPI_C_INCLUDE_PATH}) + include_directories(${MPI_CXX_INCLUDE_PATH}) list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES}) option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF) if(LAMMPS_LONGLONG_TO_LONG) add_definitions(-DLAMMPS_LONGLONG_TO_LONG) endif() else() + enable_language(C) file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c) add_library(mpi_stubs STATIC ${MPI_SOURCES}) include_directories(${LAMMPS_SOURCE_DIR}/STUBS) @@ -83,12 +147,6 @@ if(LAMMPS_EXCEPTIONS) set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS") endif() -set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically") -mark_as_advanced(LAMMPS_MACHINE) -if(LAMMPS_MACHINE) - set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") -endif() - option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF) option(ENABLE_TESTING "Enable testing" OFF) @@ -96,70 +154,75 @@ if(ENABLE_TESTING) enable_testing() endif(ENABLE_TESTING) -option(ENABLE_ALL "Build all default packages" OFF) -set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR - KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ - REAX REPLICA RIGID SHOCK SNAP SRD) -set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE - USER-ATC USER-AWPMD USER-CGDNA USER-MESO - USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF - USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC +set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR + KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP + SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS + USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE + USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) +set(OTHER_PACKAGES CORESHELL QEQ) foreach(PKG ${DEFAULT_PACKAGES}) - option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL}) + option(PKG_${PKG} "Build ${PKG} Package" OFF) endforeach() foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) - option(ENABLE_${PKG} "Build ${PKG} Package" OFF) + option(PKG_${PKG} "Build ${PKG} Package" OFF) endforeach() macro(pkg_depends PKG1 PKG2) - if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2}) + if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2})) message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}") endif() endmacro() +# "hard" dependencies between packages resulting +# in an error instead of skipping over files pkg_depends(MPIIO MPI) -pkg_depends(QEQ MANYBODY) pkg_depends(USER-ATC MANYBODY) -pkg_depends(USER-H5MD MPI) pkg_depends(USER-LB MPI) -pkg_depends(USER-MISC MANYBODY) pkg_depends(USER-PHONON KSPACE) -if(ENABLE_BODY AND ENABLE_POEMS) - message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time") -endif() - ###################################################### # packages with special compiler needs or external libs ###################################################### -if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE) +if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE) enable_language(Fortran) - include(CheckFortranCompilerFlag) - check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE) endif() -if(ENABLE_KOKKOS OR ENABLE_MSCG) - # starting with CMake 3.1 this is all you have to do to enforce C++11 - set(CMAKE_CXX_STANDARD 11) # C++11... - set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required... - set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11 +if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM) + enable_language(C) endif() -if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL) +find_package(OpenMP QUIET) +option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) +if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL) find_package(OpenMP REQUIRED) set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") endif() -if(ENABLE_KSPACE) - set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package") - set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2) +if(PKG_KSPACE) + option(FFT_SINGLE "Use single precision FFT instead of double" OFF) + set(FFTW "FFTW3") + if(FFT_SINGLE) + set(FFTW "FFTW3F") + add_definitions(-DFFT_SINGLE) + endif() + find_package(${FFTW} QUIET) + if(${FFTW}_FOUND) + set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package") + else() + set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package") + endif() + set_property(CACHE FFT PROPERTY STRINGS KISSFFT ${FFTW} MKL) if(NOT FFT STREQUAL "KISSFFT") find_package(${FFT} REQUIRED) - add_definitions(-DFFT_${FFT}) + if(NOT FFT STREQUAL "FFTW3F") + add_definitions(-DFFT_FFTW) + else() + add_definitions(-DFFT_${FFT}) + endif() include_directories(${${FFT}_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES}) endif() @@ -170,28 +233,23 @@ if(ENABLE_KSPACE) endif() endif() -if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE) +if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) find_package(LAPACK) if(NOT LAPACK_FOUND) enable_language(Fortran) - file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f) + file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF]) add_library(linalg STATIC ${LAPACK_SOURCES}) - include(CheckFortranCompilerFlag) - check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE) - if(FC_HAS_NO_SECOND_UNDERSCORE) - target_compile_options(linalg PRIVATE -fno-second-underscore) - endif() set(LAPACK_LIBRARIES linalg) endif() endif() -if(ENABLE_PYTHON) +if(PKG_PYTHON) find_package(PythonInterp REQUIRED) find_package(PythonLibs REQUIRED) add_definitions(-DLMP_PYTHON) include_directories(${PYTHON_INCLUDE_DIR}) list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY}) - if(BUILD_SHARED_LIBS) + if(BUILD_LIB AND BUILD_SHARED_LIBS) if(NOT PYTHON_INSTDIR) execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))" @@ -201,16 +259,25 @@ if(ENABLE_PYTHON) endif() endif() -find_package(JPEG) -if(JPEG_FOUND) +find_package(JPEG QUIET) +option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND}) +if(WITH_JPEG) + find_package(JPEG REQUIRED) add_definitions(-DLAMMPS_JPEG) include_directories(${JPEG_INCLUDE_DIR}) list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES}) endif() -find_package(PNG) -find_package(ZLIB) +find_package(PNG QUIET) +find_package(ZLIB QUIET) if(PNG_FOUND AND ZLIB_FOUND) + option(WITH_PNG "Enable PNG support" ON) +else() + option(WITH_PNG "Enable PNG support" OFF) +endif() +if(WITH_PNG) + find_package(PNG REQUIRED) + find_package(ZLIB REQUIRED) include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES}) add_definitions(-DLAMMPS_PNG) @@ -218,113 +285,194 @@ endif() find_program(GZIP_EXECUTABLE gzip) find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE) -if(GZIP_FOUND) +option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND}) +if(WITH_GZIP) + if(NOT GZIP_FOUND) + message(FATAL_ERROR "gzip executable not found") + endif() add_definitions(-DLAMMPS_GZIP) endif() find_program(FFMPEG_EXECUTABLE ffmpeg) find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE) -if(FFMPEG_FOUND) +option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND}) +if(WITH_FFMPEG) + if(NOT FFMPEG_FOUND) + message(FATAL_ERROR "ffmpeg executable not found") + endif() add_definitions(-DLAMMPS_FFMPEG) endif() -if(ENABLE_VORONOI) - find_package(VORO REQUIRED) #some distros +if(PKG_VORONOI) + option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF) + if(DOWNLOAD_VORO) + include(ExternalProject) + ExternalProject_Add(voro_build + URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz + URL_MD5 2338b824c3b7b25590e18e8df5d68af9 + CONFIGURE_COMMAND "" BUILD_IN_SOURCE 1 INSTALL_COMMAND "" + ) + ExternalProject_get_property(voro_build SOURCE_DIR) + set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a) + set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src) + list(APPEND LAMMPS_DEPS voro_build) + else() + find_package(VORO) + if(NOT VORO_FOUND) + message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it") + endif() + endif() include_directories(${VORO_INCLUDE_DIRS}) list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES}) endif() -if(ENABLE_LATTE) - find_package(LATTE QUIET) - if(NOT LATTE_FOUND) +if(PKG_LATTE) + option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF) + if(DOWNLOAD_LATTE) message(STATUS "LATTE not found - we will build our own") include(ExternalProject) ExternalProject_Add(latte_build - URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz - URL_MD5 5137e28cb1a64444bd571c98c98a6eee + URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz + URL_MD5 85ac414fdada2d04619c8f936344df14 SOURCE_SUBDIR cmake CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ) ExternalProject_get_property(latte_build INSTALL_DIR) set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a) list(APPEND LAMMPS_DEPS latte_build) + else() + find_package(LATTE) + if(NOT LATTE_FOUND) + message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it") + endif() endif() - list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES}) endif() -if(ENABLE_USER-MOLFILE) +if(PKG_USER-MOLFILE) add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile) target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) list(APPEND LAMMPS_LINK_LIBS molfile) endif() -if(ENABLE_USER-NETCDF) +if(PKG_USER-NETCDF) find_package(NetCDF REQUIRED) include_directories(NETCDF_INCLUDE_DIR) list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY}) add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020) endif() -if(ENABLE_USER-SMD) - find_package(Eigen3 REQUIRED) +if(PKG_USER-SMD) + option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF) + if(DOWNLOAD_Eigen3) + include(ExternalProject) + ExternalProject_Add(Eigen3_build + URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz + URL_MD5 1a47e78efe365a97de0c022d127607c3 + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + ) + ExternalProject_get_property(Eigen3_build SOURCE_DIR) + set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR}) + list(APPEND LAMMPS_DEPS Eigen3_build) + else() + find_package(Eigen3) + if(NOT Eigen3_FOUND) + message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it") + endif() + endif() include_directories(${EIGEN3_INCLUDE_DIR}) endif() -if(ENABLE_USER-QUIP) +if(PKG_USER-QUIP) find_package(QUIP REQUIRED) - list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES}) endif() -if(ENABLE_USER-QMMM) +if(PKG_USER-QMMM) + message(WARNING "Building QMMM with CMake is still experimental") find_package(QE REQUIRED) include_directories(${QE_INCLUDE_DIRS}) - list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES}) endif() -if(ENABLE_USER-VTK) +if(PKG_USER-VTK) find_package(VTK REQUIRED NO_MODULE) include(${VTK_USE_FILE}) add_definitions(-DLAMMPS_VTK) list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES}) endif() -if(ENABLE_KIM) - find_package(KIM REQUIRED) +if(PKG_KIM) + option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF) + if(DOWNLOAD_KIM) + include(ExternalProject) + ExternalProject_Add(kim_build + URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz + URL_MD5 9f66efc128da33039e30659f36fc6d00 + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND /configure --prefix= + ) + ExternalProject_get_property(kim_build INSTALL_DIR) + set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1) + set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so) + list(APPEND LAMMPS_DEPS kim_build) + else() + find_package(KIM) + if(NOT KIM_FOUND) + message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it") + endif() + endif() list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES}) include_directories(${KIM_INCLUDE_DIRS}) endif() -if(ENABLE_MSCG) +if(PKG_MSCG) find_package(GSL REQUIRED) - set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg) - set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip) - set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src) - if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR}) - if(NOT EXISTS ${MSCG_TARBALL}) - message(STATUS "Downloading ${MSCG_TARBALL}") - file(DOWNLOAD - https://github.com/uchicago-voth/MSCG-release/archive/master.zip - ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master + option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF) + if(DOWNLOAD_MSCG) + include(ExternalProject) + if(NOT LAPACK_FOUND) + set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a") + endif() + ExternalProject_Add(mscg_build + URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz + URL_MD5 8c45e269ee13f60b303edd7823866a91 + SOURCE_SUBDIR src/CMake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS} + BUILD_COMMAND make mscg INSTALL_COMMAND "" + ) + ExternalProject_get_property(mscg_build BINARY_DIR) + set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a) + ExternalProject_get_property(mscg_build SOURCE_DIR) + set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src) + list(APPEND LAMMPS_DEPS mscg_build) + if(NOT LAPACK_FOUND) + file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS}) + add_dependencies(mscg_build linalg) + endif() + else() + find_package(MSCG) + if(NOT MSCG_FOUND) + message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it") endif() - message(STATUS "Unpacking ${MSCG_TARBALL}") - execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL} - WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg) endif() - file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp) - add_library(mscg STATIC ${MSCG_SOURCES}) - list(APPEND LAMMPS_LINK_LIBS mscg) - target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1) - target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR}) - target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES}) + include_directories(${MSCG_INCLUDE_DIRS}) +endif() + +if(PKG_COMPRESS) + find_package(ZLIB REQUIRED) + include_directories(${ZLIB_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES}) endif() ######################################################################## # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## -include(CheckIncludeFile) +include(CheckIncludeFileCXX) foreach(HEADER math.h) - check_include_file(${HEADER} FOUND_${HEADER}) + check_include_file_cxx(${HEADER} FOUND_${HEADER}) if(NOT FOUND_${HEADER}) message(FATAL_ERROR "Could not find needed header - ${HEADER}") endif(NOT FOUND_${HEADER}) @@ -333,6 +481,9 @@ endforeach(HEADER) set(MATH_LIBRARIES "m" CACHE STRING "math library") mark_as_advanced( MATH_LIBRARIES ) include(CheckLibraryExists) +if (CMAKE_VERSION VERSION_LESS "3.4") + enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4 +endif() foreach(FUNC sin cos) check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES}) if(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) @@ -350,25 +501,16 @@ RegisterStyles(${LAMMPS_SOURCE_DIR}) ############################################## # add sources of enabled packages ############################################ -foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES}) +foreach(PKG ${DEFAULT_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) - # ignore PKG files which were manually installed in src folder - # headers are ignored during RegisterStyles file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp) file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h) - foreach(PKG_FILE in ${${PKG}_SOURCES}) - get_filename_component(FNAME ${PKG_FILE} NAME) - list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME}) - endforeach() - - foreach(PKG_FILE in ${${PKG}_HEADERS}) - get_filename_component(FNAME ${PKG_FILE} NAME) - DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME}) - endforeach() + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) - if(ENABLE_${PKG}) + if(PKG_${PKG}) # detects styles in package and adds them to global list RegisterStyles(${${PKG}_SOURCES_DIR}) @@ -377,12 +519,23 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES}) endif() endforeach() +# dedicated check for entire contents of accelerator packages +foreach(PKG ${ACCEL_PACKAGES}) + set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) + + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h) + + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) +endforeach() + ############################################## # add lib sources of (simple) enabled packages ############################################ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-QMMM) - if(ENABLE_${SIMPLE_LIB}) + if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") string(TOLOWER "${PKG_LIB}" PKG_LIB) file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F @@ -403,40 +556,61 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD endif() endforeach() -if(ENABLE_USER-AWPMD) +if(PKG_USER-AWPMD) target_link_libraries(awpmd ${LAPACK_LIBRARIES}) endif() -if(ENABLE_USER-ATC) +if(PKG_USER-ATC) target_link_libraries(atc ${LAPACK_LIBRARIES}) endif() -if(ENABLE_USER-H5MD) +if(PKG_USER-H5MD) find_package(HDF5 REQUIRED) target_link_libraries(h5md ${HDF5_LIBRARIES}) target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS}) endif() -if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE) - foreach(FSRC ${meam_SOURCES}) - string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}") - list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX) - if(FINDEX GREATER -1) - set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore") - endif() - endforeach() -endif() - -if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE) - target_compile_options(reax PRIVATE -fno-second-underscore) -endif() - ###################################################################### # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### -if(ENABLE_USER-OMP) +if(PKG_CORESHELL) + set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL) + set(CORESHELL_SOURCES) + set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}") + + # detects styles which have a CORESHELL version + RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES) + + get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES) + + list(APPEND LIB_SOURCES ${CORESHELL_SOURCES}) + include_directories(${CORESHELL_SOURCES_DIR}) +endif() + +# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed +if(PKG_QEQ) + set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ) + file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h) + file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp) + + if(NOT PKG_MANYBODY) + list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h) + list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp) + endif() + set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}") + + foreach(MY_HEADER ${QEQ_HEADERS}) + AddStyleHeader(${MY_HEADER} FIX) + endforeach() + + get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES) + list(APPEND LIB_SOURCES ${QEQ_SOURCES}) + include_directories(${QEQ_SOURCES_DIR}) +endif() + +if(PKG_USER-OMP) set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP) set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp ${USER-OMP_SOURCES_DIR}/thr_omp.cpp @@ -447,13 +621,32 @@ if(ENABLE_USER-OMP) # detects styles which have USER-OMP version RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) + get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) + # manually add package dependent source files from USER-OMP that do not provide styles + + if(PKG_RIGID) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp) + endif() + + if(PKG_USER-REAXC) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp) + endif() + list(APPEND LIB_SOURCES ${USER-OMP_SOURCES}) include_directories(${USER-OMP_SOURCES_DIR}) endif() -if(ENABLE_KOKKOS) +if(PKG_KOKKOS) set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos) add_definitions(-DLMP_KOKKOS) @@ -489,7 +682,7 @@ if(ENABLE_KOKKOS) RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h) - if(ENABLE_USER-DPD) + if(PKG_USER-DPD) get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES) list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp) RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h) @@ -502,7 +695,7 @@ if(ENABLE_KOKKOS) include_directories(${KOKKOS_PKG_SOURCES_DIR}) endif() -if(ENABLE_OPT) +if(PKG_OPT) set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT) set(OPT_SOURCES) set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}") @@ -516,7 +709,34 @@ if(ENABLE_OPT) include_directories(${OPT_SOURCES_DIR}) endif() -if(ENABLE_USER-INTEL) +if(PKG_USER-INTEL) + if(NOT DEVELOPER_MODE) + if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler") + endif() + if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) + message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") + endif() + endif() + option(INJECT_KNL_FLAG "Inject flags for KNL build" OFF) + if(INJECT_KNL_FLAG) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xMIC-AVX512") + endif() + option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON) + if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512") + else() + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost") + endif() + include(CheckCXXCompilerFlag) + foreach(_FLAG -qopenmp -qno-offload -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high) + check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG}) + if(COMPILER_SUPPORTS${_FLAG}) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_FLAG}") + endif() + endforeach() + endif() set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL) set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h ${USER-INTEL_SOURCES_DIR}/intel_buffers.h @@ -540,7 +760,10 @@ if(ENABLE_USER-INTEL) include_directories(${USER-INTEL_SOURCES_DIR}) endif() -if(ENABLE_GPU) +if(PKG_GPU) + if (CMAKE_VERSION VERSION_LESS "3.1") + message(FATAL_ERROR "For the GPU package you need at least cmake-3.1") + endif() set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU) set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h ${GPU_SOURCES_DIR}/fix_gpu.h @@ -563,8 +786,7 @@ if(ENABLE_GPU) endif() option(CUDPP_OPT "Enable CUDPP_OPT" ON) - set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture") - set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60) + set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)") file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu) @@ -637,7 +859,7 @@ if(ENABLE_GPU) add_library(gpu STATIC ${GPU_LIB_SOURCES}) target_link_libraries(gpu ${OpenCL_LIBRARIES}) target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS}) - target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT) + target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT) target_compile_definitions(gpu PRIVATE -DUSE_OPENCL) list(APPEND LAMMPS_LINK_LIBS gpu) @@ -673,60 +895,231 @@ GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR}) include_directories(${LAMMPS_SOURCE_DIR}) include_directories(${LAMMPS_STYLE_HEADERS_DIR}) +###################################### +# Generate lmpinstalledpkgs.h +###################################### +set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n") +set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n") +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) + if(PKG_${PKG}) + set(temp "${temp} \"${PKG}\",\n") + endif() +endforeach() +set(temp "${temp} NULL\n};\n#endif\n\n") +message(STATUS "Generating lmpinstalledpkgs.h...") +file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" ) +execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h") + ########################################### # Actually add executable and lib to build ############################################ -add_library(lammps ${LIB_SOURCES}) -target_link_libraries(lammps ${LAMMPS_LINK_LIBS}) -if(LAMMPS_DEPS) - add_dependencies(lammps ${LAMMPS_DEPS}) +get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) +list (FIND LANGUAGES "Fortran" _index) +if (${_index} GREATER -1) + list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) endif() -set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE}) -if(BUILD_SHARED_LIBS) - set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) - install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) - install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) - configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY) - install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) +list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS) +if(BUILD_LIB) + add_library(lammps ${LIB_SOURCES}) + target_link_libraries(lammps ${LAMMPS_LINK_LIBS}) + if(LAMMPS_DEPS) + add_dependencies(lammps ${LAMMPS_DEPS}) + endif() + set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX}) + if(BUILD_SHARED_LIBS) + set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) + install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) + configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + endif() +else() + list(APPEND LMP_SOURCES ${LIB_SOURCES}) endif() -add_executable(lmp ${LMP_SOURCES}) -target_link_libraries(lmp lammps) -set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE}) -install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) -if(ENABLE_TESTING) - add_test(ShowHelp lmp${LAMMPS_MACHINE} -help) +if(BUILD_EXE) + add_executable(lmp ${LMP_SOURCES}) + if(BUILD_LIB) + target_link_libraries(lmp lammps) + else() + target_link_libraries(lmp ${LAMMPS_LINK_LIBS}) + if(LAMMPS_DEPS) + add_dependencies(lmp ${LAMMPS_DEPS}) + endif() + endif() + + set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE}) + install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) + if(ENABLE_TESTING) + add_test(ShowHelp lmp${LAMMPS_MACHINE} -help) + endif() +endif() + +############################################################################### +# Build documentation +############################################################################### +option(BUILD_DOC "Build LAMMPS documentation" OFF) +if(BUILD_DOC) + include(ProcessorCount) + ProcessorCount(NPROCS) + find_package(PythonInterp 3 REQUIRED) + + set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv) + + file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt) + file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt) + list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES}) + + add_custom_command( + OUTPUT docenv + COMMAND ${VIRTUALENV} docenv + ) + + set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin) + + add_custom_command( + OUTPUT requirements.txt + DEPENDS docenv + COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt + COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade + COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters + ) + + set(RST_FILES "") + set(RST_DIR ${CMAKE_BINARY_DIR}/rst) + file(MAKE_DIRECTORY ${RST_DIR}) + foreach(TXT_FILE ${DOC_SOURCES}) + get_filename_component(FILENAME ${TXT_FILE} NAME_WE) + set(RST_FILE ${RST_DIR}/${FILENAME}.rst) + list(APPEND RST_FILES ${RST_FILE}) + add_custom_command( + OUTPUT ${RST_FILE} + DEPENDS requirements.txt docenv ${TXT_FILE} + COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE} + ) + endforeach() + + add_custom_command( + OUTPUT html + DEPENDS ${RST_FILES} + COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR} + COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html + ) + + add_custom_target( + doc ALL + DEPENDS html + SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES} + ) + + install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR}) +endif() + +############################################################################### +# Install potential files in data directory +############################################################################### +set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) +install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials) + +configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) +configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) +install( + FILES ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh + ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh + DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d +) + +############################################################################### +# Testing +# +# Requires latest gcovr (for GCC 8.1 support):# +# pip install git+https://github.com/gcovr/gcovr.git +############################################################################### +if(ENABLE_COVERAGE) + find_program(GCOVR_BINARY gcovr) + find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY) + + if(GCOVR_FOUND) + get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE) + + add_custom_target( + gen_coverage_xml + COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMENT "Generating XML Coverage Report..." + ) + + add_custom_target( + gen_coverage_html + COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMENT "Generating HTML Coverage Report..." + ) + endif() endif() -################################## +############################################################################### # Print package summary -################################## -foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES}) - if(ENABLE_${PKG}) +############################################################################### +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) + if(PKG_${PKG}) message(STATUS "Building package: ${PKG}") endif() endforeach() string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) +get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS) +include(FeatureSummary) +feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND) message(STATUS "<<< Build configuration >>> Build type ${CMAKE_BUILD_TYPE} Install path ${CMAKE_INSTALL_PREFIX} Compilers and Flags: C++ Compiler ${CMAKE_CXX_COMPILER} Type ${CMAKE_CXX_COMPILER_ID} - C++ Flags ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}") + Version ${CMAKE_CXX_COMPILER_VERSION} + C++ Flags ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} + Defines ${CPPFLAGS}") get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) -if(LANGUAGES MATCHES ".*Fortran.*") +list (FIND LANGUAGES "Fortran" _index) +if (${_index} GREATER -1) message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} Type ${CMAKE_Fortran_COMPILER_ID} + Version ${CMAKE_Fortran_COMPILER_VERSION} Fortran Flags ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}") endif() -message(STATUS "Linker flags: +list (FIND LANGUAGES "C" _index) +if (${_index} GREATER -1) + message(STATUS "C Compiler ${CMAKE_C_COMPILER} + Type ${CMAKE_C_COMPILER_ID} + Version ${CMAKE_C_COMPILER_VERSION} + C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}") +endif() +if(CMAKE_EXE_LINKER_FLAGS) + message(STATUS "Linker flags: Executable ${CMAKE_EXE_LINKER_FLAGS}") + endif() if(BUILD_SHARED_LIBS) - message(STATUS "Shared libries ${CMAKE_SHARED_LINKER_FLAGS}") + message(STATUS "Shared libraries ${CMAKE_SHARED_LINKER_FLAGS}") else() - message(STATUS "Static libries ${CMAKE_STATIC_LINKER_FLAGS}") + message(STATUS "Static libraries ${CMAKE_STATIC_LINKER_FLAGS}") endif() message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}") - +if(BUILD_MPI) + message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}") +endif() +if(PKG_GPU) + message(STATUS "GPU Api: ${GPU_API}") + if(GPU_API STREQUAL "CUDA") + message(STATUS "GPU Arch: ${GPU_ARCH}") + elseif(GPU_API STREQUAL "OpenCL") + message(STATUS "OCL Tune: ${OCL_TUNE}") + endif() + message(STATUS "GPU Precision: ${GPU_PREC}") +endif() +if(PKG_KOKKOS) + message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") +endif() +if(PKG_KSPACE) + message(STATUS "Using ${FFT} as FFT") +endif() diff --git a/cmake/Modules/FindFFTW2.cmake b/cmake/Modules/FindFFTW2.cmake deleted file mode 100644 index c77e6cf8e9d126d5ebb4223e6e7cf53ef25b60b2..0000000000000000000000000000000000000000 --- a/cmake/Modules/FindFFTW2.cmake +++ /dev/null @@ -1,22 +0,0 @@ -# - Find fftw2 -# Find the native FFTW2 headers and libraries. -# -# FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc. -# FFTW2_LIBRARIES - List of libraries when using fftw2. -# FFTW2_FOUND - True if fftw2 found. -# - -find_path(FFTW2_INCLUDE_DIR fftw.h) - -find_library(FFTW2_LIBRARY NAMES fftw) - -set(FFTW2_LIBRARIES ${FFTW2_LIBRARY}) -set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR}) - -include(FindPackageHandleStandardArgs) -# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE -# if all listed variables are TRUE - -find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR) - -mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY ) diff --git a/cmake/Modules/FindFFTW3F.cmake b/cmake/Modules/FindFFTW3F.cmake new file mode 100644 index 0000000000000000000000000000000000000000..92d1e85e791ec362a15909bd09dccdc046efc2a5 --- /dev/null +++ b/cmake/Modules/FindFFTW3F.cmake @@ -0,0 +1,25 @@ +# - Find fftw3f +# Find the native FFTW3F headers and libraries. +# +# FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc. +# FFTW3F_LIBRARIES - List of libraries when using fftw3f. +# FFTW3F_FOUND - True if fftw3f found. +# + +find_package(PkgConfig) + +pkg_check_modules(PC_FFTW3F fftw3f) +find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS}) + +find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS}) + +set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY}) +set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR}) + +include(FindPackageHandleStandardArgs) +# handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE +# if all listed variables are TRUE + +find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR) + +mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY ) diff --git a/cmake/Modules/FindMSCG.cmake b/cmake/Modules/FindMSCG.cmake new file mode 100644 index 0000000000000000000000000000000000000000..311ff7803836aa43c2c48bd4040a60686b1803db --- /dev/null +++ b/cmake/Modules/FindMSCG.cmake @@ -0,0 +1,22 @@ +# - Find mscg +# Find the native MSCG headers and libraries. +# +# MSCG_INCLUDE_DIRS - where to find mscg.h, etc. +# MSCG_LIBRARIES - List of libraries when using mscg. +# MSCG_FOUND - True if mscg found. +# + +find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg) + +find_library(MSCG_LIBRARY NAMES mscg) + +set(MSCG_LIBRARIES ${MSCG_LIBRARY}) +set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR}) + +include(FindPackageHandleStandardArgs) +# handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE +# if all listed variables are TRUE + +find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR) + +mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY ) diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index c6f580f4632d92fabc4fe6d2b95464b18a5c9487..29ea3725972ce2e1166ef70297c3d6067e90c769 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -45,14 +45,10 @@ function(FindStyleHeadersExt path style_class extension headers sources) endfunction(FindStyleHeadersExt) function(CreateStyleHeader path filename) - math(EXPR N "${ARGC}-2") - set(temp "") - if(N GREATER 0) - math(EXPR ARG_END "${ARGC}-1") - - foreach(IDX RANGE 2 ${ARG_END}) - list(GET ARGV ${IDX} FNAME) + if(ARGC GREATER 2) + list(REMOVE_AT ARGV 0 1) + foreach(FNAME ${ARGV}) get_filename_component(FNAME ${FNAME} NAME) set(temp "${temp}#include \"${FNAME}\"\n") endforeach() @@ -107,35 +103,6 @@ function(RegisterStyles search_path) FindStyleHeaders(${search_path} REGION_CLASS region_ REGION ) # region ) # domain endfunction(RegisterStyles) -function(RemovePackageHeader headers pkg_header) - get_property(hlist GLOBAL PROPERTY ${headers}) - list(REMOVE_ITEM hlist ${pkg_header}) - set_property(GLOBAL PROPERTY ${headers} "${hlist}") -endfunction(RemovePackageHeader) - -function(DetectAndRemovePackageHeader fname) - RemovePackageHeader(ANGLE ${fname}) - RemovePackageHeader(ATOM_VEC ${fname}) - RemovePackageHeader(BODY ${fname}) - RemovePackageHeader(BOND ${fname}) - RemovePackageHeader(COMMAND ${fname}) - RemovePackageHeader(COMPUTE ${fname}) - RemovePackageHeader(DIHEDRAL ${fname}) - RemovePackageHeader(DUMP ${fname}) - RemovePackageHeader(FIX ${fname}) - RemovePackageHeader(IMPROPER ${fname}) - RemovePackageHeader(INTEGRATE ${fname}) - RemovePackageHeader(KSPACE ${fname}) - RemovePackageHeader(MINIMIZE ${fname}) - RemovePackageHeader(NBIN ${fname}) - RemovePackageHeader(NPAIR ${fname}) - RemovePackageHeader(NSTENCIL ${fname}) - RemovePackageHeader(NTOPO ${fname}) - RemovePackageHeader(PAIR ${fname}) - RemovePackageHeader(READER ${fname}) - RemovePackageHeader(REGION ${fname}) -endfunction(DetectAndRemovePackageHeader) - function(RegisterStylesExt search_path extension sources) FindStyleHeadersExt(${search_path} ANGLE_CLASS ${extension} ANGLE ${sources}) FindStyleHeadersExt(${search_path} ATOM_CLASS ${extension} ATOM_VEC ${sources}) @@ -181,3 +148,21 @@ function(GenerateStyleHeaders output_path) GenerateStyleHeader(${output_path} READER reader ) # read_dump GenerateStyleHeader(${output_path} REGION region ) # domain endfunction(GenerateStyleHeaders) + +function(DetectBuildSystemConflict lammps_src_dir) + if(ARGC GREATER 1) + list(REMOVE_AT ARGV 0) + foreach(SRC_FILE ${ARGV}) + get_filename_component(FILENAME ${SRC_FILE} NAME) + if(EXISTS ${lammps_src_dir}/${FILENAME}) + message(FATAL_ERROR "\n########################################################################\n" + "Found package(s) installed by the make-based build system\n" + "\n" + "Please run\n" + "make -C ${lammps_src_dir} no-all purge\n" + "to uninstall\n" + "########################################################################") + endif() + endforeach() + endif() +endfunction(DetectBuildSystemConflict) diff --git a/cmake/README.md b/cmake/README.md index cc67cceb52ec7b40327af88b52709eda7a6c1416..b6644ffda959c45faec16e89e0a6a3275725c796 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -1,19 +1,1663 @@ -cmake-buildsystem ------------------ +# Building LAMMPS using CMake -To use the cmake build system instead of the make-driven one, do: +LAMMPS recently acquired support for building with CMake thanks to the efforts +of Christoph Junghans (LANL) and Richard Berger (Temple U). One of the key +strengths of CMake is that it can generate the necessary build system files of +your own personal preference. It also enables using common development IDEs such +as Eclipse, Visual Studio, QtCreator, Xcode and many more for LAMMPS +development. + +CMake can both be used as a command-line (CLI) utility `cmake` or through one of +its GUIs. `ccmake` is a text-based ui to configure and build CMake projects. +`cmake-gui` is a graphical frontend for running CMake operations that works on +Linux desktop environments, Windows and MacOS X. + +The following is a tutorial-style introduction in using the CMake system. It +should give you the necessary foundation to understand how to do the most common +tasks, act as a reference and provide examples of typical use cases. + +## Table of Contents + + * [Quick Start for the Impatient](#quick-start-for-the-impatient) + * [Building LAMMPS using cmake](#building-lammps-using-cmake-1) + * [Prerequisites](#prerequisites) + * [Build directory vs. Source Directory](#build-directory-vs-source-directory) + * [Defining and using presets](#defining-and-using-presets) + * [Reference](#reference) + * [Common CMAKE Configuration Options](#common-cmake-configuration-options) + * [LAMMPS Configuration Options](#lammps-configuration-options) + * [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages) + * [Default Packages](#default-packages) + * [Other Packages](#other-packages) + * [User Packages](#user-packages) + * [Package-Specific Configuration Options](#package-specific-configuration-options) + * [KSPACE Package](#kspace-package) + * [MKL](#mkl) + * [FFTW2](#fftw2) + * [FFTW3](#fftw3) + * [LAPACK](#lapack) + * [PYTHON Package](#python-package) + * [GPU Package](#gpu-package) + * [VORONOI Package](#voronoi-package) + * [USER-SMD Package](#user-smd-package) + * [Optional Features](#optional-features) + * [zlib support](#zlib-support) + * [JPEG support](#jpeg-support) + * [PNG support](#png-support) + * [GZIP support](#gzip-support) + * [FFMPEG support](#ffmpeg-support) + * [Compilers](#compilers) + * [Building with GNU Compilers](#building-with-gnu-compilers) + * [Building with Intel Compilers](#building-with-intel-compilers) + * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers) + * [Examples](#examples) + + +## Quick Start for the Impatient +If you want to skip ahead and just run the compilation using `cmake`, please +find a minimal example below. Together with the options reference below, this +should get you started. + +```bash +git clone https://github.com/lammps/lammps.git +mkdir lammps/build +cd lammps/build +cmake ../cmake [-DOPTION_A=VALUE_A -DOPTION_B=VALUE_B ...] +make +``` + +# Building LAMMPS using `cmake` + +## Prerequisites +This tutorial assumes you are running in a command-line environment using a +shell like Bash. + +* Linux: any terminal window will work +* MacOS X: launch the Terminal app +* Windows 10: install and run "Bash on Windows" (aka Ubuntu on Windows) + +Before we start, please download the latest and greatest version of LAMMPS from +GitHub. You can either download it as a tarball or ZIP file, or via git. When +you start with a fresh lammps directory, the contents should look like this: + +```bash +$ ls +bench doc lib potentials README tools +cmake examples LICENSE python src +``` + +## Build directory vs. Source Directory + +By using CMake we separate building LAMMPS into multiple phases: + +1. **Configuration**: define which features we want to enable/disable and how it should be compiled +2. **Compilation**: compile each source file and generate binaries and libraries based on the configuration +3. **Installation** (Optional): finally we can install the generated binaries on our system + +In the GNU Make based build system of LAMMPS, configuration occurs by running +special make targets like `make yes-MOLECULAR`. These targets modify the +**source directory** (`src/`) directory by copying package files and patching +Makefile. In some cases you are force to manually edit Makefiles to add compiler +options and/or correct include directory and library paths. + +These edits and copy operations are no longer necessary when compiling with +CMake. The source directory stays untouched, so you compile LAMMPS in many +different variants using the same source code checkout. It enables true +**out-of-source** builds. + +When using Cmake, you can compile in **any** folder outside of the source +directory. Any working directory you choose becomes a so-called **build +directory**. All configuration files and compilation results are stored in this +folder. We recommend calling it something like `build/`. + +Let's have a look a quick example, where we get the greatest and latest version +of LAMMPS from GitHub via git: +```bash +git clone https://github.com/lammps/lammps.git +``` + +We then create a new `build` folder and make it our current working directory: +``` +mkdir lammps/build +cd lammps/build +``` + +To configure LAMMPS we run `cmake` inside of this folder. However it requires at +least one argument. `cmake` needs to read the LAMMPS `CMakeLists.txt` file to +know what to do. This file is located in the `cmake/` subdirectory of the +lammps checkout. To run `cmake` add the relative or absolute path to the `cmake/` +directory as first argument. + +E.g., if the current working directory is `lammps/build` you can specify the +relative path to `lammps/cmake` as follows: ``` -cmake /path/to/lammps/source/cmake +cmake ../cmake ``` -(please note the cmake directory as the very end) -To enable package, e.g. GPU do +You could also specify the absolute path: ``` -cmake /path/to/lammps/source/cmake -DENABLE_GPU=ON +cmake /path/to/my/lammps/folder/cmake ``` -cmake has many many options, do get an overview use the curses-based cmake interface, ccmake: +Please note: **This does NOT compile the code!** Running cmake only configures +the next build. It generates the necessary files to compile the code. On +Unix/Linux it defaults to generating Makefiles. You can also choose other output +formats to generate files for Eclipse, Xcode or Visual Studio which are +supported on other platorms. + +To compile LAMMPS once the Makefiles are generated, simply type `make` in the +build directory. + ``` -ccmake /path/to/lammps/source/cmake +make ``` -(Don't forget to press "g" for generate once you are done with configuring) +# Defining and using presets + +The CMake build exposes a lot of different options. In the old build system +some of the package selections were possible by using special make target like +`make yes-std` or `make no-lib`. Achieving the same result with cmake requires +specifying all options manually. This can quickly become a very long command +line that is hard to handle. While these could be stored in a simple script +file, there is another way of defining "presets" to compile LAMMPS in a certain +way. + +A preset is a regular CMake script file that can use constructs such as +variables, lists and for-loops to manipulate configuration options and create +an [*initial cache*](https://cmake.org/cmake/help/v3.12/manual/cmake.1.html). +Options must be set with the `CACHE` and `FORCE` flag to ensure they are +considered even during a second cmake run. + +Such a file can then be passed to cmake via the `-C` flag. Several examples of +presets can be found in the `cmake/presets` folder. + +```bash +# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package +mkdir build +cd build +cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on +``` + +# Reference + +## Common CMAKE Configuration Options + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
CMAKE_INSTALL_PREFIXInstall location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do. +
CMAKE_BUILD_TYPEControls if debugging symbols are added to the generated binaries +
+
Release (default)
+
Debug
+
+
+ + +## LAMMPS Configuration Options + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
LAMMPS_SIZE_LIMITControls the integer sizes used by LAMMPS internally +
+
LAMMPS_SMALLBIG (default)
+
32bit , 64bit
+
LAMMPS_SMALLSMALL
+
32bit , 32bit
+
LAMMPS_BIGBIG
+
64bit , 64bit
+
+
LAMMPS_MEMALIGNcontrols the alignment of blocks of memory allocated by LAMMPS +
+
64 (default)
+
+
LAMMPS_EXCEPTIONScontrols whether LAMMPS dies after an error or throws a C++ exception. This is particularly useful when running through the C library interface, since an error + in LAMMPS then doesn't kill the parent process +
+
off (default)
+
on
+
+
LAMMPS_MACHINEallows appending a machine suffix to the generate LAMMPS binary +
+
*none* (default)
+
+
BUILD_SHARED_LIBScontrol whether to build LAMMPS as a shared-library +
+
off (default)
+
on
+
+
BUILD_DOCcontrol whether to build LAMMPS documentation +
+
off (default)
+
on
+
+
LAMMPS_LONGLONG_TO_LONGWorkaround if your system or MPI version does not recognize long long data types +
+
off (default)
+
on
+
+
+ +## Parallelization and Accelerator Packages + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
BUILD_MPIcontrol whether to build LAMMPS with MPI support. This will look for + `mpicxx` in your path and use this MPI implementation. +
+
off (default)
+
on
+
+
BUILD_OMPcontrol whether to build LAMMPS with OpenMP support. +
+
off (default)
+
on
+
+
PKG_OPT + A handful of pair styles which are optimized for improved CPU performance on + single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials. + +
+
off (default)
+
on
+
+
PKG_USER-OMP + Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace + styles which are altered to enable threading on many-core CPUs via OpenMP + directives. + +
+
off (default)
+
on
+
+
PKG_USER-INTEL + Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which + are optimized for Intel CPUs and KNLs (Knights Landing). + +
+
off (default)
+
on
+
+
PKG_GPU + Dozens of pair styles and a version of the PPPM long-range Coulombic solver + optimized for GPUs. All such styles have a “gpu†as a suffix in their style + name. The GPU code can be compiled with either CUDA or OpenCL, however the + OpenCL variants are no longer actively maintained and only the CUDA versions + are regularly tested. + +
+
off (default)
+
on
+
+
PKG_KOKKOSDozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. +
+
off (default)
+
on
+
+
+ +## Default Packages + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
PKG_ASPHEREComputes, time-integration fixes, and pair styles for aspherical particle models including ellipsoids, 2d lines, and 3d triangles. +
+
off (default)
+
on
+
+
PKG_BODYBody-style particles with internal structure. Computes, time-integration fixes, pair styles, as well as the body styles themselves. +
+
off (default)
+
on
+
+
PKG_CLASS2Bond, angle, dihedral, improper, and pair styles for the COMPASS CLASS2 molecular force field. +
+
off (default)
+
on
+
+
PKG_COLLOIDCoarse-grained finite-size colloidal particles. Pair styles and fix wall styles for colloidal interactions. Includes the Fast Lubrication Dynamics (FLD) method for hydrodynamic interactions, which is a simplified approximation to Stokesian dynamics. +
+
off (default)
+
on
+
+
PKG_COMPRESSCompressed output of dump files via the zlib compression library, using dump styles with a “gz†in their style name. +
+
off (default)
+
on
+
+
PKG_CORESHELLCompute and pair styles that implement the adiabatic core/shell model for polarizability. The pair styles augment Born, Buckingham, and Lennard-Jones styles with core/shell capabilities. The compute temp/cs command calculates the temperature of a system with core/shell particles. +
+
off (default)
+
on
+
+
PKG_DIPOLEAn atom style and several pair styles for point dipole models with short-range or long-range interactions. +
+
off (default)
+
on
+
+
PKG_GRANULARPair styles and fixes for finite-size granular particles, which interact with each other and boundaries via frictional and dissipative potentials. +
+
off (default)
+
on
+
+
PKG_KSPACEA variety of long-range Coulombic solvers, as well as pair styles which compute the corresponding short-range pairwise Coulombic interactions. These include Ewald, particle-particle particle-mesh (PPPM), and multilevel summation method (MSM) solvers. +
+
off (default)
+
on
+
+
PKG_MANYBODY + A variety of manybody and bond-order potentials. These include (AI)REBO, BOP, + EAM, EIM, Stillinger-Weber, and Tersoff potentials. + +
+
off (default)
+
on
+
+
PKG_MC + Several fixes and a pair style that have Monte Carlo (MC) or MC-like + attributes. These include fixes for creating, breaking, and swapping bonds, + for performing atomic swaps, and performing grand-canonical MC (GCMC) in + conjuction with dynamics. + +
+
off (default)
+
on
+
+
PKG_MEAM +

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

+ +

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

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

FFT library for KSPACE package

+

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

+ 		+
+
KISSFFT
+
FFTW3
+
FFTW2
+
MKL
+
+
PACK_ARRAYOptimization for FFT +
+
PACK_ARRAY
+
PACK_POINTER
+
PACK_MEMCPY
+
+
+ +### MKL + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
MKL_INCLUDE_DIRS +
MKL_LIBRARIES +
+ +TODO static vs dynamic linking + +### FFTW2 + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
FFTW2_INCLUDE_DIRS +
FFTW2_LIBRARIES +
+ +### FFTW3 + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
FFTW3_INCLUDE_DIRS +
FFTW3_LIBRARIES +
+ +### LAPACK +TODO + +### PYTHON Package + + +### GPU Package +The GPU package builds a support library which can either use OpenCL or CUDA as +target API. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
GPU_APIAPI used by GPU package +
+
OpenCL (default)
+
CUDA
+
+
GPU_PRECPrecision size used by GPU package kernels +
+
SINGLE_DOUBLE
+
SINGLE_SINGLE
+
DOUBLE_DOUBLE
+
+
OCL_TUNE (OpenCL only)Tuning target for OpenCL driver code +
+
GENERIC (default)
+
INTEL (Intel CPU)
+
PHI (Intel Xeon Phi)
+
FERMI (NVIDIA)
+
KEPLER (NVIDIA)
+
CYPRESS (AMD)
+
+
GPU_ARCH (CUDA only)CUDA SM architecture targeted by GPU package +
+
sm_20 (Fermi)
+
sm_30 (Kepler)
+
sm_50 (Maxwell)
+
sm_60 (Pascal)
+
sm_70 (Volta)
+
+
CUDPP_OPT (CUDA only)Enable CUDA Performance Primitives Optimizations +
+
on (default)
+
off
+
+
+ +### VORONOI Package + +TODO + +### USER-SMD Package + +Requires a Eigen3 installation + + + + + + + + + + + + + + + + +
OptionDescriptionValues
EIGEN3_INCLUDE_DIR +
+ +## Optional Features + +### zlib support + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
ZLIB_INCLUDE_DIR +
ZLIB_LIBRARIES +
+ +### JPEG support + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
JPEG_INCLUDE_DIR +
JPEG_LIBRARIES +
+ +### PNG support +(requires zlib support) + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
PNG_INCLUDE_DIR +
PNG_LIBRARIES +
+ +### GZIP support + +requires `gzip` to be in your `PATH` + + + + + + + + + + + + + + + + +
OptionDescriptionValues
GZIP_EXECUTABLE +
+ +### FFMPEG support + +requires `ffmpeg` to be in your `PATH` + + + + + + + + + + + + + + + + +
OptionDescriptionValues
FFMPEG_EXECUTABLE +
+ + +## Compilers + +By default, `cmake` will use your environment C/C++/Fortran compilers for a build. It uses the `CC`, `CXX` and `FC` environment variables to detect which compilers should be used. However, these values +will be cached after the first run of `cmake`. Subsequent runs of `cmake` will ignore changes in these environment variables. To ensure the correct values are used you avoid the cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`, `CMAKE_Fortran_COMPILER` options directly. + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionDefault
CMAKE_C_COMPILERC Compiler which should be used by CMakevalue of `CC` environment variable at first `cmake` run
CMAKE_CXX_COMPILERC++ compiler which should be used by CMake + value of `CXX` environment variable at first `cmake` run +
CMAKE_Fortran_COMPILERC++ compiler which should be used by CMake + value of `FC` environment variable at first `cmake` run +
+ +### Building with GNU Compilers + +```bash +cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran +``` + +### Building with Intel Compilers + +```bash +cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort +``` + + +### Building with LLVM/Clang Compilers + +```bash +cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang +``` + + +## Examples diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in new file mode 100644 index 0000000000000000000000000000000000000000..def49bf75c0112503f7286dbb68843a258e993f3 --- /dev/null +++ b/cmake/etc/profile.d/lammps.csh.in @@ -0,0 +1,2 @@ +# set environment for LAMMPS executables to find potential files +if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in new file mode 100644 index 0000000000000000000000000000000000000000..acd75fa0cff7bae7013d8c32d8453e2083dc217d --- /dev/null +++ b/cmake/etc/profile.d/lammps.sh.in @@ -0,0 +1,2 @@ +# set environment for LAMMPS executables to find potential files +export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in index c5e17017825c01bb59ec02597dd5a43957a69bba..400b7593cff4034539df766111dd53d6fbbeaac9 100644 --- a/cmake/pkgconfig/liblammps.pc.in +++ b/cmake/pkgconfig/liblammps.pc.in @@ -13,6 +13,6 @@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library URL: http://lammps.sandia.gov Version: Requires: -Libs: -L${libdir} -llammps@LAMMPS_MACHINE@ +Libs: -L${libdir} -llammps@LIB_SUFFIX@@ Libs.private: -lm Cflags: -I${includedir} @LAMMPS_API_DEFINES@ diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake new file mode 100644 index 0000000000000000000000000000000000000000..f7e90ddbb44153f12af59cf4f51f64afe0c3317a --- /dev/null +++ b/cmake/presets/all_off.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake new file mode 100644 index 0000000000000000000000000000000000000000..2c6f67904e6d50ff785ccb67664a4136fb737470 --- /dev/null +++ b/cmake/presets/all_on.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/manual_selection.cmake b/cmake/presets/manual_selection.cmake new file mode 100644 index 0000000000000000000000000000000000000000..6c03d983f6e9989e50883d974973fd08323acb8e --- /dev/null +++ b/cmake/presets/manual_selection.cmake @@ -0,0 +1,69 @@ +set(PKG_ASPHERE OFF CACHE BOOL "" FORCE) +set(PKG_BODY OFF CACHE BOOL "" FORCE) +set(PKG_CLASS2 OFF CACHE BOOL "" FORCE) +set(PKG_COLLOID OFF CACHE BOOL "" FORCE) +set(PKG_COMPRESS OFF CACHE BOOL "" FORCE) +set(PKG_CORESHELL OFF CACHE BOOL "" FORCE) +set(PKG_DIPOLE OFF CACHE BOOL "" FORCE) +set(PKG_GPU OFF CACHE BOOL "" FORCE) +set(PKG_GRANULAR OFF CACHE BOOL "" FORCE) +set(PKG_KIM OFF CACHE BOOL "" FORCE) +set(PKG_KOKKOS OFF CACHE BOOL "" FORCE) +set(PKG_KSPACE OFF CACHE BOOL "" FORCE) +set(PKG_LATTE OFF CACHE BOOL "" FORCE) +set(PKG_LIB OFF CACHE BOOL "" FORCE) +set(PKG_MANYBODY OFF CACHE BOOL "" FORCE) +set(PKG_MC OFF CACHE BOOL "" FORCE) +set(PKG_MEAM OFF CACHE BOOL "" FORCE) +set(PKG_MISC OFF CACHE BOOL "" FORCE) +set(PKG_MOLECULE OFF CACHE BOOL "" FORCE) +set(PKG_MPIIO OFF CACHE BOOL "" FORCE) +set(PKG_MSCG OFF CACHE BOOL "" FORCE) +set(PKG_OPT OFF CACHE BOOL "" FORCE) +set(PKG_PERI OFF CACHE BOOL "" FORCE) +set(PKG_POEMS OFF CACHE BOOL "" FORCE) +set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE) +set(PKG_QEQ OFF CACHE BOOL "" FORCE) +set(PKG_REAX OFF CACHE BOOL "" FORCE) +set(PKG_REPLICA OFF CACHE BOOL "" FORCE) +set(PKG_RIGID OFF CACHE BOOL "" FORCE) +set(PKG_SHOCK OFF CACHE BOOL "" FORCE) +set(PKG_SNAP OFF CACHE BOOL "" FORCE) +set(PKG_SRD OFF CACHE BOOL "" FORCE) +set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE) + +set(PKG_USER OFF CACHE BOOL "" FORCE) +set(PKG_USER-ATC OFF CACHE BOOL "" FORCE) +set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE) +set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE) +set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE) +set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE) +set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE) +set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-DPD OFF CACHE BOOL "" FORCE) +set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE) +set(PKG_USER-EFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-FEP OFF CACHE BOOL "" FORCE) +set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE) +set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE) +set(PKG_USER-LB OFF CACHE BOOL "" FORCE) +set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE) +set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE) +set(PKG_USER-MESO OFF CACHE BOOL "" FORCE) +set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE) +set(PKG_USER-MISC OFF CACHE BOOL "" FORCE) +set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE) +set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE) +set(PKG_USER-OMP OFF CACHE BOOL "" FORCE) +set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE) +set(PKG_USER-QTB OFF CACHE BOOL "" FORCE) +set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE) +set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE) +set(PKG_USER-SMD OFF CACHE BOOL "" FORCE) +set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE) +set(PKG_USER-SPH OFF CACHE BOOL "" FORCE) +set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE) +set(PKG_USER-UEF OFF CACHE BOOL "" FORCE) +set(PKG_USER-VTK OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake new file mode 100644 index 0000000000000000000000000000000000000000..cd603aa80450f29a6da3906188d711f8ae755404 --- /dev/null +++ b/cmake/presets/nolib.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${PACKAGES_WITH_LIB}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/std.cmake b/cmake/presets/std.cmake new file mode 100644 index 0000000000000000000000000000000000000000..36da89795756de1890c2a7b19e39cab56ea2daea --- /dev/null +++ b/cmake/presets/std.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${STANDARD_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/std_nolib.cmake b/cmake/presets/std_nolib.cmake new file mode 100644 index 0000000000000000000000000000000000000000..9bffefcbe00f205aa5aaa3d3724f958147fda38d --- /dev/null +++ b/cmake/presets/std_nolib.cmake @@ -0,0 +1,26 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${STANDARD_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() + +foreach(PKG ${PACKAGES_WITH_LIB}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/user.cmake b/cmake/presets/user.cmake new file mode 100644 index 0000000000000000000000000000000000000000..cb81b6755836871025e5438c978e0eb8b673d8c4 --- /dev/null +++ b/cmake/presets/user.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${USER_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/doc/Makefile b/doc/Makefile index 0a5dbe1e7d64be21628f6e85e0e72a7468752d57..81f362349950be2123d2da4bd14255e7f9f27739 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -9,6 +9,7 @@ TXT2RST = $(VENV)/bin/txt2rst ANCHORCHECK = $(VENV)/bin/doc_anchor_check PYTHON = $(shell which python3) +VIRTUALENV = virtualenv HAS_PYTHON3 = NO HAS_VIRTUALENV = NO @@ -16,7 +17,13 @@ ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0) HAS_PYTHON3 = YES endif +ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0) +VIRTUALENV = virtualenv-3 +HAS_VIRTUALENV = YES +endif + ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0) +VIRTUALENV = virtualenv HAS_VIRTUALENV = YES endif @@ -42,11 +49,11 @@ help: # ------------------------------------------ -clean-all: +clean-all: clean rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe clean: - rm -rf $(RSTDIR) html + rm -rf $(RSTDIR) html old epub rm -rf spelling clean-spelling: @@ -150,7 +157,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST) @(\ mkdir -p $(RSTDIR) ; \ . $(VENV)/bin/activate ;\ - txt2rst $< > $@ ;\ + txt2rst -v $< > $@ ;\ deactivate ;\ ) @@ -158,7 +165,7 @@ $(VENV): @if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @( \ - virtualenv -p $(PYTHON) $(VENV); \ + $(VIRTUALENV) -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ pip install Sphinx; \ pip install sphinxcontrib-images; \ diff --git a/doc/src/Developer/developer.tex b/doc/src/Developer/developer.tex index 3ba9018fb90ccdc29a23965e86f396c240b95529..8852f441680eb4921a010fe5399f21b865e29585 100644 --- a/doc/src/Developer/developer.tex +++ b/doc/src/Developer/developer.tex @@ -449,15 +449,15 @@ Writing fixes is a flexible way of extending LAMMPS. Users can implement many things using fixes: \begin{itemize} -\item changing particles attributes (positions, velocities, forces, etc.). +\item changing particles attributes (positions, velocities, forces, etc.). Example: FixFreeze. \item reading/writing data. Example: FixRestart. \item implementing boundary conditions. Example: FixWall. -\item saving information about particles for future use (previous positions, +\item saving information about particles for future use (previous positions, for instance). Example: FixStoreState. \end{itemize} -All fixes are derived from class Fix and must have constructor with the +All fixes are derived from class Fix and must have constructor with the signature: FixMine(class LAMMPS *, int, char **). Every fix must be registered in LAMMPS by writing the following lines @@ -476,9 +476,9 @@ is the name of the class. This code allows LAMMPS to find your fix when it parses input script. In addition, your fix header must be included in the file "style\_fix.h". In case if you use LAMMPS make, this file is generated automatically - all files starting with prefix -fix\_ are included, so call your header the same way. Otherwise, donÕt +fix\_ are included, so call your header the same way. Otherwise, don't forget to add your include into "style\_fix.h". - + Let's write a simple fix which will print average velocity at the end of each timestep. First of all, implement a constructor: @@ -487,11 +487,11 @@ of each timestep. First of all, implement a constructor: FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (narg < 4) + if (narg < 4) error->all(FLERR,"Illegal fix print command"); - + nevery = atoi(arg[3]); - if (nevery <= 0) + if (nevery <= 0) error->all(FLERR,"Illegal fix print command"); } \end{verbatim} @@ -545,7 +545,7 @@ void FixPrintVel::end_of_step() { // for add3, scale3 using namespace MathExtra; - + double** v = atom->v; int nlocal = atom->nlocal; double localAvgVel[4]; // 4th element for particles count @@ -559,7 +559,7 @@ void FixPrintVel::end_of_step() MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world); scale3(1.0 / globalAvgVel[3], globalAvgVel); if (comm->me == 0) { - printf("\%e, \%e, \%e\n", + printf("\%e, \%e, \%e\n", globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]); } } @@ -607,14 +607,15 @@ this situation there are several methods which should be implemented: \begin{itemize} \item \verb|double memory_usage| - return how much memory fix uses -\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays +\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays in your fix -\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information - to j-th. Used when atoms sorting is performed +\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle + information to j-th. Used when atoms sorting is performed. if delflag is set + and atom j owns a body, move the body information to atom i. \item \verb|void set_arrays(int i)| - sets i-th particle related information to zero \end{itemize} -Note, that if your class implements these methods, it must call add calls of +Note, that if your class implements these methods, it must call add calls of add\_callback and delete\_callback to constructor and destructor: \begin{center} @@ -654,7 +655,7 @@ void FixSavePos::grow_arrays(int nmax) memory->grow(this->x, nmax, 3, "FixSavePos:x"); } -void FixSavePos::copy_arrays(int i, int j) +void FixSavePos::copy_arrays(int i, int j, int delflag) { memcpy(this->x[j], this->x[i], sizeof(double) * 3); } @@ -670,7 +671,7 @@ int FixSavePos::pack_exchange(int i, double *buf) buf[m++] = x[i][0]; buf[m++] = x[i][1]; buf[m++] = x[i][2]; - + return m; } diff --git a/doc/src/Eqs/dihedral_table_cut.jpg b/doc/src/Eqs/dihedral_table_cut.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c124184c1773c60fe2564d8cabce2f6c7d7883c0 Binary files /dev/null and b/doc/src/Eqs/dihedral_table_cut.jpg differ diff --git a/doc/src/Eqs/dihedral_table_cut.tex b/doc/src/Eqs/dihedral_table_cut.tex new file mode 100644 index 0000000000000000000000000000000000000000..3cc1d331a8978d76e668de3f83cf0d4264be3301 --- /dev/null +++ b/doc/src/Eqs/dihedral_table_cut.tex @@ -0,0 +1,11 @@ +\documentclass[12pt]{article} +\pagestyle{empty} +\begin{document} + +\begin{eqnarray*} + f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ + f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 +\end{eqnarray*} + +\end{document} + diff --git a/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg b/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg new file mode 100644 index 0000000000000000000000000000000000000000..9cd8214b4c2be66334502ddb3fa8d2cc607b02c9 Binary files /dev/null and b/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg differ diff --git a/doc/src/Eqs/fix_integration_spin_stdecomposition.tex b/doc/src/Eqs/fix_integration_spin_stdecomposition.tex new file mode 100644 index 0000000000000000000000000000000000000000..8c7baf296d1773a8e5371133c5a35a92615424da --- /dev/null +++ b/doc/src/Eqs/fix_integration_spin_stdecomposition.tex @@ -0,0 +1,40 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm,tikz} +\usetikzlibrary{automata,arrows,shapes,snakes} +\begin{document} +\begin{varwidth}{50in} +\begin{tikzpicture} + +%Global +\node (v1) at (0,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ }; +\node (s1) at (0,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ }; +\node (r) at (0,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{r} \leftarrow \bm{r}+L_r.\Delta t$ }; +\node (s2) at (0,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ }; +\node (v2) at (0,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ }; + +\draw[line width=2pt, ->] (v1) -- (s1); +\draw[line width=2pt, ->] (s1) -- (r); +\draw[line width=2pt, ->] (r) -- (s2); +\draw[line width=2pt, ->] (s2) -- (v2); + +%Spin +\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ }; +\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$}; +\node (sN) at (6,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N} \leftarrow \bm{s}_{\rm N}+L_{s_{\rm N}}.\Delta t/2$ }; +\node (sN2) at (6,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$}; +\node (s02) at (6,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ }; + +\draw[line width=2pt,dashed, ->] (s01) -- (sN1); +\draw[line width=2pt, ->] (sN1) -- (sN); +\draw[line width=2pt, ->] (sN) -- (sN2); +\draw[line width=2pt,dashed, ->] (sN2) -- (s02); + +%from Global to Spin +\draw[line width=2pt, dashed, ->] (s1) -- (s01.west); +\draw[line width=2pt, dashed, ->] (s1) -- (s02.west); + +\end{tikzpicture} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/fix_langevin_spin_sLLG.jpg b/doc/src/Eqs/fix_langevin_spin_sLLG.jpg new file mode 100644 index 0000000000000000000000000000000000000000..f83aadd9eb1f61a70f34ab91ca89bfb32a9d7930 Binary files /dev/null and b/doc/src/Eqs/fix_langevin_spin_sLLG.jpg differ diff --git a/doc/src/Eqs/fix_langevin_spin_sLLG.tex b/doc/src/Eqs/fix_langevin_spin_sLLG.tex new file mode 100644 index 0000000000000000000000000000000000000000..346dde9cec587b7d409ac42fb062d253b04e9b99 --- /dev/null +++ b/doc/src/Eqs/fix_langevin_spin_sLLG.tex @@ -0,0 +1,14 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \frac{d \vec{s}_{i}}{dt} = \frac{1}{\left(1+\lambda^2 \right)} \left( \left( + \vec{\omega}_{i} +\vec{\eta} \right) \times \vec{s}_{i} + \lambda\, \vec{s}_{i} + \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right), \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/force_spin_aniso.jpg b/doc/src/Eqs/force_spin_aniso.jpg new file mode 100644 index 0000000000000000000000000000000000000000..8bc9d7421c23853dcce1601df6b8ffc459a37605 Binary files /dev/null and b/doc/src/Eqs/force_spin_aniso.jpg differ diff --git a/doc/src/Eqs/force_spin_aniso.tex b/doc/src/Eqs/force_spin_aniso.tex new file mode 100644 index 0000000000000000000000000000000000000000..d6abfd580d1d848dad55515ad037ac32cb5b4ce0 --- /dev/null +++ b/doc/src/Eqs/force_spin_aniso.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{aniso} = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/force_spin_zeeman.jpg b/doc/src/Eqs/force_spin_zeeman.jpg new file mode 100644 index 0000000000000000000000000000000000000000..14fb5500cf3328480bd30dc352de699575201bf8 Binary files /dev/null and b/doc/src/Eqs/force_spin_zeeman.jpg differ diff --git a/doc/src/Eqs/force_spin_zeeman.tex b/doc/src/Eqs/force_spin_zeeman.tex new file mode 100644 index 0000000000000000000000000000000000000000..d623ef85ae32cbb4dab12d51c2370ca41820e335 --- /dev/null +++ b/doc/src/Eqs/force_spin_zeeman.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_body_rounded.jpg b/doc/src/Eqs/pair_body_rounded.jpg new file mode 100644 index 0000000000000000000000000000000000000000..e7136ddd20c2acea0e89fa8412497333f15cb541 Binary files /dev/null and b/doc/src/Eqs/pair_body_rounded.jpg differ diff --git a/doc/src/Eqs/pair_body_rounded.tex b/doc/src/Eqs/pair_body_rounded.tex new file mode 100644 index 0000000000000000000000000000000000000000..54e095340f1ab3ae13d672d35797a56faeee927a --- /dev/null +++ b/doc/src/Eqs/pair_body_rounded.tex @@ -0,0 +1,13 @@ +\documentstyle[12pt]{article} + +\begin{document} + +\begin{eqnarray*} + F_n &=& k_n \delta_n - c_n v_n, \qquad \delta_n \le 0 \\ + &=& -k_{na} \delta_n - c_n v_n, \qquad 0 < \delta_n \le r_c \\ + &=& 0 \qquad \qquad \qquad \qquad \delta_n > r_c \\ + F_t &=& \mu k_n \delta_n - c_t v_t, \qquad \delta_n \le 0 \\ + &=& 0 \qquad \qquad \qquad \qquad \delta_n > 0 +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/pair_entropy.jpg b/doc/src/Eqs/pair_entropy.jpg new file mode 100644 index 0000000000000000000000000000000000000000..44161e6aa0e74a05544f8f29aab3ca942ef305a5 Binary files /dev/null and b/doc/src/Eqs/pair_entropy.jpg differ diff --git a/doc/src/Eqs/pair_entropy.tex b/doc/src/Eqs/pair_entropy.tex new file mode 100644 index 0000000000000000000000000000000000000000..304c9d6138500061a55df40a6d8fb9b7863b45d7 --- /dev/null +++ b/doc/src/Eqs/pair_entropy.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_entropy2.jpg b/doc/src/Eqs/pair_entropy2.jpg new file mode 100644 index 0000000000000000000000000000000000000000..db3dcb0ca75f444a6640e704c61326d7c8c598a9 Binary files /dev/null and b/doc/src/Eqs/pair_entropy2.jpg differ diff --git a/doc/src/Eqs/pair_entropy2.tex b/doc/src/Eqs/pair_entropy2.tex new file mode 100644 index 0000000000000000000000000000000000000000..c91004840fee1a3998702a2ce61cd14c85048b71 --- /dev/null +++ b/doc/src/Eqs/pair_entropy2.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_entropy3.jpg b/doc/src/Eqs/pair_entropy3.jpg new file mode 100644 index 0000000000000000000000000000000000000000..0d5e0025b7200f9ca4255c48bd2bbabb291553a2 Binary files /dev/null and b/doc/src/Eqs/pair_entropy3.jpg differ diff --git a/doc/src/Eqs/pair_entropy3.tex b/doc/src/Eqs/pair_entropy3.tex new file mode 100644 index 0000000000000000000000000000000000000000..b0b3c763585dc98de3a66cde754a2bcd90db91f3 --- /dev/null +++ b/doc/src/Eqs/pair_entropy3.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + \bar{s}_S^i = \frac{\sum_j s_S^j + s_S^i}{N + 1} , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_spin_dmi_forces.jpg b/doc/src/Eqs/pair_spin_dmi_forces.jpg new file mode 100644 index 0000000000000000000000000000000000000000..fba6a91cbf6fdb6ee6736073a114d08c907d6d3c Binary files /dev/null and b/doc/src/Eqs/pair_spin_dmi_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_dmi_forces.tex b/doc/src/Eqs/pair_spin_dmi_forces.tex new file mode 100644 index 0000000000000000000000000000000000000000..1c0c246db4c70852212f86c9a7ab7e6b518c323c --- /dev/null +++ b/doc/src/Eqs/pair_spin_dmi_forces.tex @@ -0,0 +1,14 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) + ~~{\rm and}~~ + \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) + , \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.jpg b/doc/src/Eqs/pair_spin_dmi_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..3eb24c67e3b26f97c362fd05982ead5fb0f5c150 Binary files /dev/null and b/doc/src/Eqs/pair_spin_dmi_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.tex b/doc/src/Eqs/pair_spin_dmi_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..79f63a333a6c823258f5d9012fa40561e00fb9cb --- /dev/null +++ b/doc/src/Eqs/pair_spin_dmi_interaction.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} + \left( \vec{e}_{ij} \times \vec{D} \right) + \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), + \nonumber + \end{equation} +\end{varwidth} +\end{document} + \vec{D}\left(r_{ij}\right) + {\rm ~and~} \vec{D}\left(r_{ij}\right) = \vec{e}_{ij} \times \vec{D} diff --git a/doc/src/Eqs/pair_spin_exchange_forces.jpg b/doc/src/Eqs/pair_spin_exchange_forces.jpg new file mode 100644 index 0000000000000000000000000000000000000000..b312a9ccdaaf44b7647f2c444c7d79a740cea88c Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_forces.tex b/doc/src/Eqs/pair_spin_exchange_forces.tex new file mode 100644 index 0000000000000000000000000000000000000000..ac5ef682f3ca9d9532ff6d258cb1012529058636 --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_forces.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} + \left(r_{ij} \right)\,\vec{s}_{j} + ~~{\rm and}~~ + \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ + \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij} + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_exchange_function.jpg b/doc/src/Eqs/pair_spin_exchange_function.jpg new file mode 100644 index 0000000000000000000000000000000000000000..d9a7ed3ce0ba64ef054f9ca7c2115ab971d003e5 Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_function.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_function.tex b/doc/src/Eqs/pair_spin_exchange_function.tex new file mode 100644 index 0000000000000000000000000000000000000000..054c6992f0136c814dbdafdd88cb2934681ece21 --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_function.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} + \right)^2 }\Theta (R_c - r_{ij}) \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.jpg b/doc/src/Eqs/pair_spin_exchange_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c70d8a6554003e37472d648c1944a13ee9d3f859 Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..f20b3e5740ce2db9cb86a70910ca2b80f263fe4f --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_interaction.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_me_forces.jpg b/doc/src/Eqs/pair_spin_me_forces.jpg new file mode 100644 index 0000000000000000000000000000000000000000..d9ae440fb577c5f33d23029ff187175ba7163ac4 Binary files /dev/null and b/doc/src/Eqs/pair_spin_me_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_me_forces.tex b/doc/src/Eqs/pair_spin_me_forces.tex new file mode 100644 index 0000000000000000000000000000000000000000..f9462fc3d50480294787f063048b9a7acba118b8 --- /dev/null +++ b/doc/src/Eqs/pair_spin_me_forces.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{F}^{i} = -\sum_{j}^{Neighbor} \left( \vec{s}_{i}\times \vec{s}_{j} \right) + \times \vec{E} ~~{\rm and}~~ \vec{\omega}^{i} = -\frac{1}{\hbar} + \sum_{j}^{Neighbor} \vec{s}_j \times \left(\vec{E}\times r_{ij} \right),\nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_me_interaction.jpg b/doc/src/Eqs/pair_spin_me_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..8ecddc959226c0e94fa533f36ad84f3afced6ba6 Binary files /dev/null and b/doc/src/Eqs/pair_spin_me_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_me_interaction.tex b/doc/src/Eqs/pair_spin_me_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..64501e9c2fa44243c2859c7ca096003d0b22653b --- /dev/null +++ b/doc/src/Eqs/pair_spin_me_interaction.tex @@ -0,0 +1,12 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times\vec{D}(r_{ij}) ~~{\rm and}~~ + \vec{F}_i = -\sum_{j}^{Neighb} \frac{\partial D(r_{ij})}{\partial r_{ij}} \left(\vec{s}_{i}\times \vec{s}_{j} \right) \cdot \vec{r}_{ij}, \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_neel_functions.jpg b/doc/src/Eqs/pair_spin_neel_functions.jpg new file mode 100644 index 0000000000000000000000000000000000000000..57023634bf9de762613994e44174702f83c630d0 Binary files /dev/null and b/doc/src/Eqs/pair_spin_neel_functions.jpg differ diff --git a/doc/src/Eqs/pair_spin_neel_functions.tex b/doc/src/Eqs/pair_spin_neel_functions.tex new file mode 100644 index 0000000000000000000000000000000000000000..ead5a2b87a2fc879c1b3739b627f74b90f05dddf --- /dev/null +++ b/doc/src/Eqs/pair_spin_neel_functions.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{eqnarray} + g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\ + q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\ + q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber + \end{eqnarray} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_neel_interaction.jpg b/doc/src/Eqs/pair_spin_neel_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c30600d840e56bd04d994a0d16d73c80ddf760dd Binary files /dev/null and b/doc/src/Eqs/pair_spin_neel_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_neel_interaction.tex b/doc/src/Eqs/pair_spin_neel_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..8b4ac33e732cccf30e83e56269617dac780e7cac --- /dev/null +++ b/doc/src/Eqs/pair_spin_neel_interaction.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij} + \cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right) + +q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right) + \left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right) + + q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot + {\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bc520c19dbacc86aaa7a1bd4083f884bde53752 --- /dev/null +++ b/doc/src/Errors.txt @@ -0,0 +1,37 @@ +"Previous Section"_Python.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Section_history.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Errors :h2 + +These doc pages describe the errors you can encounter when using +LAMMPS. The common problems include conceptual issues. The messages +and warnings doc pages give complete lists of all the messages the +code may generate (except those generated by USER packages), with +additional details for many of them. + + + + + +"Common problems"_Errors_common.html +"Reporting bugs"_Errors_bugs.html +"Error messages"_Errors_messages.html +"Warning messages"_Errors_warnings.html :all(b) + + diff --git a/doc/src/Errors_bugs.txt b/doc/src/Errors_bugs.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0a94c7a44b124bc6d987b40d9f0b25ca9b520b5 --- /dev/null +++ b/doc/src/Errors_bugs.txt @@ -0,0 +1,35 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Reporting bugs :h3 + +If you are confident that you have found a bug in LAMMPS, follow these +steps. + +Check the "New features and bug +fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW +site"_lws to see if the bug has already been reported or fixed or the +"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is +pending. + +Check the "mailing list"_http://lammps.sandia.gov/mail.html to see if +it has been discussed before. + +If not, send an email to the mailing list describing the problem with +any ideas you have as to what is causing it or where in the code the +problem might be. The developers will ask for more info if needed, +such as an input script or data files. + +The most useful thing you can do to help us fix the bug is to isolate +the problem. Run it on the smallest number of atoms and fewest number +of processors and with the simplest input script that reproduces the +bug and try to identify what command or combination of commands is +causing the problem. + +NOTE: this page needs to have GitHub issues info added diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt new file mode 100644 index 0000000000000000000000000000000000000000..86a25f7e7d4b262fc4e730b42a5584ce76133d12 --- /dev/null +++ b/doc/src/Errors_common.txt @@ -0,0 +1,123 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Common problems :h3 + +If two LAMMPS runs do not produce the exact same answer on different +machines or different numbers of processors, this is typically not a +bug. In theory you should get identical answers on any number of +processors and on any machine. In practice, numerical round-off can +cause slight differences and eventual divergence of molecular dynamics +phase space trajectories within a few 100s or few 1000s of timesteps. +However, the statistical properties of the two runs (e.g. average +energy or temperature) should still be the same. + +If the "velocity"_velocity.html command is used to set initial atom +velocities, a particular atom can be assigned a different velocity +when the problem is run on a different number of processors or on +different machines. If this happens, the phase space trajectories of +the two simulations will rapidly diverge. See the discussion of the +{loop} option in the "velocity"_velocity.html command for details and +options that avoid this issue. + +Similarly, the "create_atoms"_create_atoms.html command generates a +lattice of atoms. For the same physical system, the ordering and +numbering of atoms by atom ID may be different depending on the number +of processors. + +Some commands use random number generators which may be setup to +produce different random number streams on each processor and hence +will produce different effects when run on different numbers of +processors. A commonly-used example is the "fix +langevin"_fix_langevin.html command for thermostatting. + +A LAMMPS simulation typically has two stages, setup and run. Most +LAMMPS errors are detected at setup time; others like a bond +stretching too far may not occur until the middle of a run. + +LAMMPS tries to flag errors and print informative error messages so +you can fix the problem. For most errors it will also print the last +input script command that it was processing. Of course, LAMMPS cannot +figure out your physics or numerical mistakes, like choosing too big a +timestep, specifying erroneous force field coefficients, or putting 2 +atoms on top of each other! If you run into errors that LAMMPS +doesn't catch that you think it should flag, please send an email to +the "developers"_http://lammps.sandia.gov/authors.html. + +If you get an error message about an invalid command in your input +script, you can determine what command is causing the problem by +looking in the log.lammps file or using the "echo command"_echo.html +to see it on the screen. If you get an error like "Invalid ... +style", with ... being fix, compute, pair, etc, it means that you +mistyped the style name or that the command is part of an optional +package which was not compiled into your executable. The list of +available styles in your executable can be listed by using "the -h +command-line argument"_Section_start.html#start_6. The installation +and compilation of optional packages is explained in the "installation +instructions"_Section_start.html#start_3. + +For a given command, LAMMPS expects certain arguments in a specified +order. If you mess this up, LAMMPS will often flag the error, but it +may also simply read a bogus argument and assign a value that is +valid, but not what you wanted. E.g. trying to read the string "abc" +as an integer value of 0. Careful reading of the associated doc page +for the command should allow you to fix these problems. In most cases, +where LAMMPS expects to read a number, either integer or floating point, +it performs a stringent test on whether the provided input actually +is an integer or floating-point number, respectively, and reject the +input with an error message (for instance, when an integer is required, +but a floating-point number 1.0 is provided): + +ERROR: Expected integer parameter in input script or data file :pre + +Some commands allow for using variable references in place of numeric +constants so that the value can be evaluated and may change over the +course of a run. This is typically done with the syntax {v_name} for a +parameter, where name is the name of the variable. On the other hand, +immediate variable expansion with the syntax ${name} is performed while +reading the input and before parsing commands, + +NOTE: Using a variable reference (i.e. {v_name}) is only allowed if +the documentation of the corresponding command explicitly says it is. + +Generally, LAMMPS will print a message to the screen and logfile and +exit gracefully when it encounters a fatal error. Sometimes it will +print a WARNING to the screen and logfile and continue on; you can +decide if the WARNING is important or not. A WARNING message that is +generated in the middle of a run is only printed to the screen, not to +the logfile, to avoid cluttering up thermodynamic output. If LAMMPS +crashes or hangs without spitting out an error message first then it +could be a bug (see "this section"_#err_2) or one of the following +cases: + +LAMMPS runs in the available memory a processor allows to be +allocated. Most reasonable MD runs are compute limited, not memory +limited, so this shouldn't be a bottleneck on most platforms. Almost +all large memory allocations in the code are done via C-style malloc's +which will generate an error message if you run out of memory. +Smaller chunks of memory are allocated via C++ "new" statements. If +you are unlucky you could run out of memory just when one of these +small requests is made, in which case the code will crash or hang (in +parallel), since LAMMPS doesn't trap on those errors. + +Illegal arithmetic can cause LAMMPS to run slow or crash. This is +typically due to invalid physics and numerics that your simulation is +computing. If you see wild thermodynamic values or NaN values in your +LAMMPS output, something is wrong with your simulation. If you +suspect this is happening, it is a good idea to print out +thermodynamic info frequently (e.g. every timestep) via the +"thermo"_thermo.html so you can monitor what is happening. +Visualizing the atom movement is also a good idea to insure your model +is behaving as you expect. + +In parallel, one way LAMMPS can hang is due to how different MPI +implementations handle buffering of messages. If the code hangs +without an error message, it may be that you need to specify an MPI +setting or two (usually via an environment variable) to enable +buffering or boost the sizes of messages that can be buffered. diff --git a/doc/src/Section_errors.txt b/doc/src/Errors_messages.txt similarity index 87% rename from doc/src/Section_errors.txt rename to doc/src/Errors_messages.txt index 1cc72b2a9f6d3edeef43814f770e9c205b109461..39eabbd232dcaf447eed51a8ff9a682c08d6106d 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Errors_messages.txt @@ -1,6 +1,5 @@ -"Previous Section"_Section_python.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_history.html :c +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -8,185 +7,27 @@ Section"_Section_history.html :c :line -12. Errors :h2 +Error messages :h3 -This section describes the errors you can encounter when using LAMMPS, -either conceptually, or as printed out by the program. +This is an alphabetic list of the ERROR messages LAMMPS prints out and +the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. Error messages also +list the source file and line number where the error was generated. +For example, a message like this: -12.1 "Common problems"_#err_1 -12.2 "Reporting bugs"_#err_2 -12.3 "Error & warning messages"_#err_3 :all(b) - -:line -:line - -12.1 Common problems :link(err_1),h4 - -If two LAMMPS runs do not produce the exact same answer on different -machines or different numbers of processors, this is typically not a -bug. In theory you should get identical answers on any number of -processors and on any machine. In practice, numerical round-off can -cause slight differences and eventual divergence of molecular dynamics -phase space trajectories within a few 100s or few 1000s of timesteps. -However, the statistical properties of the two runs (e.g. average -energy or temperature) should still be the same. - -If the "velocity"_velocity.html command is used to set initial atom -velocities, a particular atom can be assigned a different velocity -when the problem is run on a different number of processors or on -different machines. If this happens, the phase space trajectories of -the two simulations will rapidly diverge. See the discussion of the -{loop} option in the "velocity"_velocity.html command for details and -options that avoid this issue. - -Similarly, the "create_atoms"_create_atoms.html command generates a -lattice of atoms. For the same physical system, the ordering and -numbering of atoms by atom ID may be different depending on the number -of processors. - -Some commands use random number generators which may be setup to -produce different random number streams on each processor and hence -will produce different effects when run on different numbers of -processors. A commonly-used example is the "fix -langevin"_fix_langevin.html command for thermostatting. - -A LAMMPS simulation typically has two stages, setup and run. Most -LAMMPS errors are detected at setup time; others like a bond -stretching too far may not occur until the middle of a run. - -LAMMPS tries to flag errors and print informative error messages so -you can fix the problem. For most errors it will also print the last -input script command that it was processing. Of course, LAMMPS cannot -figure out your physics or numerical mistakes, like choosing too big a -timestep, specifying erroneous force field coefficients, or putting 2 -atoms on top of each other! If you run into errors that LAMMPS -doesn't catch that you think it should flag, please send an email to -the "developers"_http://lammps.sandia.gov/authors.html. - -If you get an error message about an invalid command in your input -script, you can determine what command is causing the problem by -looking in the log.lammps file or using the "echo command"_echo.html -to see it on the screen. If you get an error like "Invalid ... -style", with ... being fix, compute, pair, etc, it means that you -mistyped the style name or that the command is part of an optional -package which was not compiled into your executable. The list of -available styles in your executable can be listed by using "the -h -command-line argument"_Section_start.html#start_6. The installation -and compilation of optional packages is explained in the "installation -instructions"_Section_start.html#start_3. - -For a given command, LAMMPS expects certain arguments in a specified -order. If you mess this up, LAMMPS will often flag the error, but it -may also simply read a bogus argument and assign a value that is -valid, but not what you wanted. E.g. trying to read the string "abc" -as an integer value of 0. Careful reading of the associated doc page -for the command should allow you to fix these problems. In most cases, -where LAMMPS expects to read a number, either integer or floating point, -it performs a stringent test on whether the provided input actually -is an integer or floating-point number, respectively, and reject the -input with an error message (for instance, when an integer is required, -but a floating-point number 1.0 is provided): - -ERROR: Expected integer parameter in input script or data file :pre - -Some commands allow for using variable references in place of numeric -constants so that the value can be evaluated and may change over the -course of a run. This is typically done with the syntax {v_name} for a -parameter, where name is the name of the variable. On the other hand, -immediate variable expansion with the syntax ${name} is performed while -reading the input and before parsing commands, - -NOTE: Using a variable reference (i.e. {v_name}) is only allowed if -the documentation of the corresponding command explicitly says it is. - -Generally, LAMMPS will print a message to the screen and logfile and -exit gracefully when it encounters a fatal error. Sometimes it will -print a WARNING to the screen and logfile and continue on; you can -decide if the WARNING is important or not. A WARNING message that is -generated in the middle of a run is only printed to the screen, not to -the logfile, to avoid cluttering up thermodynamic output. If LAMMPS -crashes or hangs without spitting out an error message first then it -could be a bug (see "this section"_#err_2) or one of the following -cases: - -LAMMPS runs in the available memory a processor allows to be -allocated. Most reasonable MD runs are compute limited, not memory -limited, so this shouldn't be a bottleneck on most platforms. Almost -all large memory allocations in the code are done via C-style malloc's -which will generate an error message if you run out of memory. -Smaller chunks of memory are allocated via C++ "new" statements. If -you are unlucky you could run out of memory just when one of these -small requests is made, in which case the code will crash or hang (in -parallel), since LAMMPS doesn't trap on those errors. - -Illegal arithmetic can cause LAMMPS to run slow or crash. This is -typically due to invalid physics and numerics that your simulation is -computing. If you see wild thermodynamic values or NaN values in your -LAMMPS output, something is wrong with your simulation. If you -suspect this is happening, it is a good idea to print out -thermodynamic info frequently (e.g. every timestep) via the -"thermo"_thermo.html so you can monitor what is happening. -Visualizing the atom movement is also a good idea to insure your model -is behaving as you expect. - -In parallel, one way LAMMPS can hang is due to how different MPI -implementations handle buffering of messages. If the code hangs -without an error message, it may be that you need to specify an MPI -setting or two (usually via an environment variable) to enable -buffering or boost the sizes of messages that can be buffered. - -:line - -12.2 Reporting bugs :link(err_2),h4 - -If you are confident that you have found a bug in LAMMPS, follow these -steps. - -Check the "New features and bug -fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW -site"_lws to see if the bug has already been reported or fixed or the -"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is -pending. - -Check the "mailing list"_http://lammps.sandia.gov/mail.html -to see if it has been discussed before. - -If not, send an email to the mailing list describing the problem with -any ideas you have as to what is causing it or where in the code the -problem might be. The developers will ask for more info if needed, -such as an input script or data files. - -The most useful thing you can do to help us fix the bug is to isolate -the problem. Run it on the smallest number of atoms and fewest number -of processors and with the simplest input script that reproduces the -bug and try to identify what command or combination of commands is -causing the problem. - -As a last resort, you can send an email directly to the -"developers"_http://lammps.sandia.gov/authors.html. - -:line - -12.3 Error & warning messages :h3,link(err_3) - -These are two alphabetic lists of the "ERROR"_#error and -"WARNING"_#warn messages LAMMPS prints out and the reason why. If the -explanation here is not sufficient, the documentation for the -offending command may help. -Error and warning messages also list the source file and line number -where the error was generated. For example, this message - -ERROR: Illegal velocity command (velocity.cpp:78) +ERROR: Illegal velocity command (velocity.cpp:78) :pre means that line #78 in the file src/velocity.cpp generated the error. Looking in the source code may help you figure out what went wrong. Note that error messages from "user-contributed -packages"_Section_start.html#start_3 are not listed here. If such an -error occurs and is not self-explanatory, you'll need to look in the -source code or contact the author of the package. +packages"_Packages_user.html are not listed here. If such an error +occurs and is not self-explanatory, you'll need to look in the source +code or contact the author of the package. -Errors: :h3,link(error) +Doc page with "WARNING messages"_Errors_warnings.html + +:line :dlb @@ -1565,15 +1406,6 @@ This operation is not allowed. :dd This operation is not allowed. :dd -{Cannot use -cuda on and -kokkos on together} :dt - -This is not allowed since both packages can use GPUs. :dd - -{Cannot use -cuda on without USER-CUDA installed} :dt - -The USER-CUDA package must be installed via "make yes-user-cuda" -before LAMMPS is built. :dd - {Cannot use -kokkos on without KOKKOS installed} :dt Self-explanatory. :dd @@ -1597,11 +1429,6 @@ solver/pair style. :dd This is a current restriction of this command. :dd -{Cannot use GPU package with USER-CUDA package enabled} :dt - -You cannot use both the GPU and USER-CUDA packages -together. Use one or the other. :dd - {Cannot use Kokkos pair style with rRESPA inner/middle} :dt Self-explanatory. :dd @@ -8252,12 +8079,6 @@ Self-explanatory. :dd The package command cannot be used afer a read_data, read_restart, or create_box command. :dd -{Package cuda command without USER-CUDA package enabled} :dt - -The USER-CUDA package must be installed via "make yes-user-cuda" -before LAMMPS is built, and the "-c on" must be used to enable the -package. :dd - {Package gpu command without GPU package installed} :dt The GPU package must be installed via "make yes-gpu" before LAMMPS is @@ -10230,22 +10051,6 @@ it in different ways. :dd Self-explanatory. :dd -{USER-CUDA mode requires CUDA variant of min style} :dt - -CUDA mode is enabled, so the min style must include a cuda suffix. :dd - -{USER-CUDA mode requires CUDA variant of run style} :dt - -CUDA mode is enabled, so the run style must include a cuda suffix. :dd - -{USER-CUDA package does not yet support comm_style tiled} :dt - -Self-explanatory. :dd - -{USER-CUDA package requires a cuda enabled atom_style} :dt - -Self-explanatory. :dd - {Unable to initialize accelerator for use} :dt There was a problem initializing an accelerator for the gpu package :dd @@ -10494,10 +10299,6 @@ Must use remap v option with fix deform with this pair style. :dd If fix deform is used, the remap v option is required. :dd -{Using suffix cuda without USER-CUDA package enabled} :dt - -Self-explanatory. :dd - {Using suffix gpu without GPU package installed} :dt Self-explanatory. :dd @@ -11036,904 +10837,3 @@ Self-explanatory. :dd Self-explanatory. :dd :dle - -Warnings: :h3,link(warn) - -:dlb - -{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt - -The adjust/cutoff command is turned on and the Coulombic cutoff has been -adjusted to match the user-specified accuracy. :dd - -{Angle atoms missing at step %ld} :dt - -One or more of 3 atoms needed to compute a particular angle are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the angle has blown apart and an atom is -too far away. :dd - -{Angle style in data file differs from currently defined angle style} :dt - -Self-explanatory. :dd - -{Atom style in data file differs from currently defined atom style} :dt - -Self-explanatory. :dd - -{Bond atom missing in box size check} :dt - -The 2nd atoms needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. :dd - -{Bond atom missing in image check} :dt - -The 2nd atom in a particular bond is missing on this processor. -Typically this is because the pairwise cutoff is set too short or the -bond has blown apart and an atom is too far away. :dd - -{Bond atoms missing at step %ld} :dt - -The 2nd atom needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. :dd - -{Bond style in data file differs from currently defined bond style} :dt - -Self-explanatory. :dd - -{Bond/angle/dihedral extent > half of periodic box length} :dt - -This is a restriction because LAMMPS can be confused about which image -of an atom in the bonded interaction is the correct one to use. -"Extent" in this context means the maximum end-to-end length of the -bond/angle/dihedral. LAMMPS computes this by taking the maximum bond -length, multiplying by the number of bonds in the interaction (e.g. 3 -for a dihedral) and adding a small amount of stretch. :dd - -{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt - -Self-explanatory. :dd - -{Calling write_dump before a full system init.} :dt - -The write_dump command is used before the system has been fully -initialized as part of a 'run' or 'minimize' command. Not all dump -styles and features are fully supported at this point and thus the -command may fail or produce incomplete or incorrect output. Insert -a "run 0" command, if a full system init is required. :dd - -{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt - -This means the temperature associated with the rigid bodies may be -incorrect on this timestep. :dd - -{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt - -This means the temperature associated with the rigid bodies may be -incorrect on this timestep. :dd - -{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt - -Self-explanatory. :dd - -{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt - -Self-explanatory. :dd - -{Charges are set, but coulombic solver is not used} :dt - -Self-explanatory. :dd - -{Charges did not converge at step %ld: %lg} :dt - -Self-explanatory. :dd - -{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt - -Self-explanatory. :dd - -{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt - -The neighbor cutoff used may not encompass enough ghost atoms -to perform this operation correctly. :dd - -{Computing temperature of portions of rigid bodies} :dt - -The group defined by the temperature compute does not encompass all -the atoms in one or more rigid bodies, so the change in -degrees-of-freedom for the atoms in those partial rigid bodies will -not be accounted for. :dd - -{Create_bonds max distance > minimum neighbor cutoff} :dt - -This means atom pairs for some atom types may not be in the neighbor -list and thus no bond can be created between them. :dd - -{Delete_atoms cutoff > minimum neighbor cutoff} :dt - -This means atom pairs for some atom types may not be in the neighbor -list and thus an atom in that pair cannot be deleted. :dd - -{Dihedral atoms missing at step %ld} :dt - -One or more of 4 atoms needed to compute a particular dihedral are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the dihedral has blown apart and an atom is -too far away. :dd - -{Dihedral problem} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Dihedral problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Dihedral style in data file differs from currently defined dihedral style} :dt - -Self-explanatory. :dd - -{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt - -If the fix changes the timestep, the dump dcd file will not -reflect the change. :dd - -{Energy due to X extra global DOFs will be included in minimizer energies} :dt - -When using fixes like box/relax, the potential energy used by the minimizer -is augmented by an additional energy provided by the fix. Thus the printed -converged energy may be different from the total potential energy. :dd - -{Energy tally does not account for 'zero yes'} :dt - -The energy removed by using the 'zero yes' flag is not accounted -for in the energy tally and thus energy conservation cannot be -monitored in this case. :dd - -{Estimated error in splitting of dispersion coeffs is %g} :dt - -Error is greater than 0.0001 percent. :dd - -{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt - -Self-explanatory. Choosing a different cutoff value may help. :dd - -{FENE bond too long} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{FENE bond too long: %ld %d %d %g} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{FENE bond too long: %ld %g} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{Fix SRD walls overlap but fix srd overlap not set} :dt - -You likely want to set this in your input script. :dd - -{Fix bond/swap will ignore defined angles} :dt - -See the doc page for fix bond/swap for more info on this -restriction. :dd - -{Fix deposit near setting < possible overlap separation %g} :dt - -This test is performed for finite size particles with a diameter, not -for point particles. The near setting is smaller than the particle -diameter which can lead to overlaps. :dd - -{Fix evaporate may delete atom with non-zero molecule ID} :dt - -This is probably an error, since you should not delete only one atom -of a molecule. :dd - -{Fix gcmc using full_energy option} :dt - -Fix gcmc has automatically turned on the full_energy option since it -is required for systems like the one specified by the user. User input -included one or more of the following: kspace, triclinic, a hybrid -pair style, an eam pair style, or no "single" function for the pair -style. :dd - -{Fix property/atom mol or charge w/out ghost communication} :dt - -A model typically needs these properties defined for ghost atoms. :dd - -{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt - -Self-explanatory. :dd - -{Fix qeq has non-zero lower Taper radius cutoff} :dt - -Absolute value must be <= 0.01. :dd - -{Fix qeq has very low Taper radius cutoff} :dt - -Value should typically be >= 5.0. :dd - -{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt - -Self-explanatory. :dd - -{Fix qeq/fire tolerance may be too small for damped fires} :dt - -Self-explanatory. :dd - -{Fix rattle should come after all other integration fixes} :dt - -This fix is designed to work after all other integration fixes change -atom positions. Thus it should be the last integration fix specified. -If not, it will not satisfy the desired constraints as well as it -otherwise would. :dd - -{Fix recenter should come after all other integration fixes} :dt - -Other fixes may change the position of the center-of-mass, so -fix recenter should come last. :dd - -{Fix srd SRD moves may trigger frequent reneighboring} :dt - -This is because the SRD particles may move long distances. :dd - -{Fix srd grid size > 1/4 of big particle diameter} :dt - -This may cause accuracy problems. :dd - -{Fix srd particle moved outside valid domain} :dt - -This may indicate a problem with your simulation parameters. :dd - -{Fix srd particles may move > big particle diameter} :dt - -This may cause accuracy problems. :dd - -{Fix srd viscosity < 0.0 due to low SRD density} :dt - -This may cause accuracy problems. :dd - -{Fix thermal/conductivity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that fix -thermal/conductivity comes first. If you are using fix ave/spatial to -measure the temperature profile induced by fix viscosity, then this -may cause a glitch in the profile since you are averaging immediately -after swaps have occurred. Flipping the order of the 2 fixes -typically helps. :dd - -{Fix viscosity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that -fix viscosity comes first. If you are using fix ave/spatial -to measure the velocity profile induced by fix viscosity, then -this may cause a glitch in the profile since you are averaging -immediately after swaps have occurred. Flipping the order -of the 2 fixes typically helps. :dd - -{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt - -This is current restriction with Kokkos. :dd - -{For better accuracy use 'pair_modify table 0'} :dt - -The user-specified force accuracy cannot be achieved unless the table -feature is disabled by using 'pair_modify table 0'. :dd - -{Geometric mixing assumed for 1/r^6 coefficients} :dt - -Self-explanatory. :dd - -{Group for fix_modify temp != fix group} :dt - -The fix_modify command is specifying a temperature computation that -computes a temperature on a different group of atoms than the fix -itself operates on. This is probably not what you want to do. :dd - -{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt - -This is the size of the matrix. :dd - -{Ignoring unknown or incorrect info command flag} :dt - -Self-explanatory. An unknown argument was given to the info command. -Compare your input with the documentation. :dd - -{Improper atoms missing at step %ld} :dt - -One or more of 4 atoms needed to compute a particular improper are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the improper has blown apart and an atom is -too far away. :dd - -{Improper problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed improper atoms is extreme; you may want -to check your simulation geometry. :dd - -{Improper style in data file differs from currently defined improper style} :dt - -Self-explanatory. :dd - -{Inconsistent image flags} :dt - -The image flags for a pair on bonded atoms appear to be inconsistent. -Inconsistent means that when the coordinates of the two atoms are -unwrapped using the image flags, the two atoms are far apart. -Specifically they are further apart than half a periodic box length. -Or they are more than a box length apart in a non-periodic dimension. -This is usually due to the initial data file not having correct image -flags for the 2 atoms in a bond that straddles a periodic boundary. -They should be different by 1 in that case. This is a warning because -inconsistent image flags will not cause problems for dynamics or most -LAMMPS simulations. However they can cause problems when such atoms -are used with the fix rigid or replicate commands. Note that if you -have an infinite periodic crystal with bonds then it is impossible to -have fully consistent image flags, since some bonds will cross -periodic boundaries and connect two atoms with the same image -flag. :dd - -{KIM Model does not provide 'energy'; Potential energy will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'forces'; Forces will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt - -Self-explanatory. :dd - -{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt - -The kspace_modify slab parameter should be larger to insure periodic -grids padded with empty space do not overlap. :dd - -{Less insertions than requested} :dt - -The fix pour command was unsuccessful at finding open space -for as many particles as it tried to insert. :dd - -{Library error in lammps_gather_atoms} :dt - -This library function cannot be used if atom IDs are not defined -or are not consecutively numbered. :dd - -{Library error in lammps_scatter_atoms} :dt - -This library function cannot be used if atom IDs are not defined or -are not consecutively numbered, or if no atom map is defined. See the -atom_modify command for details about atom maps. :dd - -{Lost atoms via change_box: original %ld current %ld} :dt - -The command options you have used caused atoms to be lost. :dd - -{Lost atoms via displace_atoms: original %ld current %ld} :dt - -The command options you have used caused atoms to be lost. :dd - -{Lost atoms: original %ld current %ld} :dt - -Lost atoms are checked for each time thermo output is done. See the -thermo_modify lost command for options. Lost atoms usually indicate -bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved further than one processor's sub-domain away before -reneighboring. :dd - -{MSM mesh too small, increasing to 2 points in each direction} :dt - -Self-explanatory. :dd - -{Mismatch between velocity and compute groups} :dt - -The temperature computation used by the velocity command will not be -on the same group of atoms that velocities are being set for. :dd - -{Mixing forced for lj coefficients} :dt - -Self-explanatory. :dd - -{Molecule attributes do not match system attributes} :dt - -An attribute is specified (e.g. diameter, charge) that is -not defined for the specified atom style. :dd - -{Molecule has bond topology but no special bond settings} :dt - -This means the bonded atoms will not be excluded in pair-wise -interactions. :dd - -{Molecule template for create_atoms has multiple molecules} :dt - -The create_atoms command will only create molecules of a single type, -i.e. the first molecule in the template. :dd - -{Molecule template for fix gcmc has multiple molecules} :dt - -The fix gcmc command will only create molecules of a single type, -i.e. the first molecule in the template. :dd - -{Molecule template for fix shake has multiple molecules} :dt - -The fix shake command will only recognize molecules of a single -type, i.e. the first molecule in the template. :dd - -{More than one compute centro/atom} :dt - -It is not efficient to use compute centro/atom more than once. :dd - -{More than one compute cluster/atom} :dt - -It is not efficient to use compute cluster/atom more than once. :dd - -{More than one compute cna/atom defined} :dt - -It is not efficient to use compute cna/atom more than once. :dd - -{More than one compute contact/atom} :dt - -It is not efficient to use compute contact/atom more than once. :dd - -{More than one compute coord/atom} :dt - -It is not efficient to use compute coord/atom more than once. :dd - -{More than one compute damage/atom} :dt - -It is not efficient to use compute ke/atom more than once. :dd - -{More than one compute dilatation/atom} :dt - -Self-explanatory. :dd - -{More than one compute erotate/sphere/atom} :dt - -It is not efficient to use compute erorate/sphere/atom more than once. :dd - -{More than one compute hexorder/atom} :dt - -It is not efficient to use compute hexorder/atom more than once. :dd - -{More than one compute ke/atom} :dt - -It is not efficient to use compute ke/atom more than once. :dd - -{More than one compute orientorder/atom} :dt - -It is not efficient to use compute orientorder/atom more than once. :dd - -{More than one compute plasticity/atom} :dt - -Self-explanatory. :dd - -{More than one compute sna/atom} :dt - -Self-explanatory. :dd - -{More than one compute snad/atom} :dt - -Self-explanatory. :dd - -{More than one compute snav/atom} :dt - -Self-explanatory. :dd - -{More than one fix poems} :dt - -It is not efficient to use fix poems more than once. :dd - -{More than one fix rigid} :dt - -It is not efficient to use fix rigid more than once. :dd - -{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt - -This is because excluding specific pair interactions also excludes -them from long-range interactions which may not be the desired effect. -The special_bonds command handles this consistently by insuring -excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated -consistently by both the short-range pair style and the long-range -solver. This is not done for exclusions of charged atom pairs via the -neigh_modify exclude command. :dd - -{New thermo_style command, previous thermo_modify settings will be lost} :dt - -If a thermo_style command is used after a thermo_modify command, the -settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify command acts on -the currently defined thermo style, and a thermo_style command creates -a new style. :dd - -{No Kspace calculation with verlet/split} :dt - -The 2nd partition performs a kspace calculation so the kspace_style -command must be used. :dd - -{No automatic unit conversion to XTC file format conventions possible for units lj} :dt - -This means no scaling will be performed. :dd - -{No fixes defined, atoms won't move} :dt - -If you are not using a fix like nve, nvt, npt then atom velocities and -coordinates will not be updated during timestepping. :dd - -{No joints between rigid bodies, use fix rigid instead} :dt - -The bodies defined by fix poems are not connected by joints. POEMS -will integrate the body motion, but it would be more efficient to use -fix rigid. :dd - -{Not using real units with pair reax} :dt - -This is most likely an error, unless you have created your own ReaxFF -parameter file in a different set of units. :dd - -{Number of MSM mesh points changed to be a multiple of 2} :dt - -MSM requires that the number of grid points in each direction be a multiple -of two and the number of grid points in one or more directions have been -adjusted to meet this requirement. :dd - -{OMP_NUM_THREADS environment is not set.} :dt - -This environment variable must be set appropriately to use the -USER-OMP package. :dd - -{One or more atoms are time integrated more than once} :dt - -This is probably an error since you typically do not want to -advance the positions or velocities of an atom more than once -per timestep. :dd - -{One or more chunks do not contain all atoms in molecule} :dt - -This may not be what you intended. :dd - -{One or more dynamic groups may not be updated at correct point in timestep} :dt - -If there are other fixes that act immediately after the initial stage -of time integration within a timestep (i.e. after atoms move), then -the command that sets up the dynamic group should appear after those -fixes. This will insure that dynamic group assignments are made -after all atoms have moved. :dd - -{One or more respa levels compute no forces} :dt - -This is computationally inefficient. :dd - -{Pair COMB charge %.10f with force %.10f hit max barrier} :dt - -Something is possibly wrong with your model. :dd - -{Pair COMB charge %.10f with force %.10f hit min barrier} :dt - -Something is possibly wrong with your model. :dd - -{Pair brownian needs newton pair on for momentum conservation} :dt - -Self-explanatory. :dd - -{Pair dpd needs newton pair on for momentum conservation} :dt - -Self-explanatory. :dd - -{Pair dsmc: num_of_collisions > number_of_A} :dt - -Collision model in DSMC is breaking down. :dd - -{Pair dsmc: num_of_collisions > number_of_B} :dt - -Collision model in DSMC is breaking down. :dd - -{Pair style in data file differs from currently defined pair style} :dt - -Self-explanatory. :dd - -{Particle deposition was unsuccessful} :dt - -The fix deposit command was not able to insert as many atoms as -needed. The requested volume fraction may be too high, or other atoms -may be in the insertion region. :dd - -{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt - -The decomposition of the physical domain (likely due to load -balancing) has led to a processor's sub-domain being smaller than the -neighbor skin in one or more dimensions. Since reneighboring is -triggered by atoms moving the skin distance, this may lead to lost -atoms, if an atom moves all the way across a neighboring processor's -sub-domain before reneighboring is triggered. :dd - -{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Replacing a fix, but new group != old group} :dt - -The ID and style of a fix match for a fix you are changing with a fix -command, but the new group you are specifying does not match the old -group. :dd - -{Replicating in a non-periodic dimension} :dt - -The parameters for a replicate command will cause a non-periodic -dimension to be replicated; this may cause unwanted behavior. :dd - -{Resetting reneighboring criteria during PRD} :dt - -A PRD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. :dd - -{Resetting reneighboring criteria during TAD} :dt - -A TAD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. :dd - -{Resetting reneighboring criteria during minimization} :dt - -Minimization requires that neigh_modify settings be delay = 0, every = -1, check = yes. Since these settings were not in place, LAMMPS -changed them and will restore them to their original values after the -minimization. :dd - -{Restart file used different # of processors} :dt - -The restart file was written out by a LAMMPS simulation running on a -different number of processors. Due to round-off, the trajectories of -your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. :dd - -{Restart file used different 3d processor grid} :dt - -The restart file was written out by a LAMMPS simulation running on a -different 3d grid of processors. Due to round-off, the trajectories -of your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. :dd - -{Restart file used different boundary settings, using restart file values} :dt - -Your input script cannot change these restart file settings. :dd - -{Restart file used different newton bond setting, using restart file value} :dt - -The restart file value will override the setting in the input script. :dd - -{Restart file used different newton pair setting, using input script value} :dt - -The input script value will override the setting in the restart file. :dd - -{Restrain problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Running PRD with only one replica} :dt - -This is allowed, but you will get no parallel speed-up. :dd - -{SRD bin shifting turned on due to small lamda} :dt - -This is done to try to preserve accuracy. :dd - -{SRD bin size for fix srd differs from user request} :dt - -Fix SRD had to adjust the bin size to fit the simulation box. See the -cubic keyword if you want this message to be an error vs warning. :dd - -{SRD bins for fix srd are not cubic enough} :dt - -The bin shape is not within tolerance of cubic. See the cubic -keyword if you want this message to be an error vs warning. :dd - -{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt - -See the inside keyword if you want this message to be an error vs -warning. :dd - -{SRD particle %d started inside wall %d on step %ld bounce %d} :dt - -See the inside keyword if you want this message to be an error vs -warning. :dd - -{Shake determinant < 0.0} :dt - -The determinant of the quadratic equation being solved for a single -cluster specified by the fix shake command is numerically suspect. LAMMPS -will set it to 0.0 and continue. :dd - -{Shell command '%s' failed with error '%s'} :dt - -Self-explanatory. :dd - -{Shell command returned with non-zero status} :dt - -This may indicate the shell command did not operate as expected. :dd - -{Should not allow rigid bodies to bounce off relecting walls} :dt - -LAMMPS allows this, but their dynamics are not computed correctly. :dd - -{Should not use fix nve/limit with fix shake or fix rattle} :dt - -This will lead to invalid constraint forces in the SHAKE/RATTLE -computation. :dd - -{Simulations might be very slow because of large number of structure factors} :dt - -Self-explanatory. :dd - -{Slab correction not needed for MSM} :dt - -Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd - -{System is not charge neutral, net charge = %g} :dt - -The total charge on all atoms on the system is not 0.0. -For some KSpace solvers this is only a warning. :dd - -{Table inner cutoff >= outer cutoff} :dt - -You specified an inner cutoff for a Coulombic table that is longer -than the global cutoff. Probably not what you wanted. :dd - -{Temperature for MSST is not for group all} :dt - -User-assigned temperature to MSST fix does not compute temperature for -all atoms. Since MSST computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by MSST could be inaccurate. :dd - -{Temperature for NPT is not for group all} :dt - -User-assigned temperature to NPT fix does not compute temperature for -all atoms. Since NPT computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by NPT could be inaccurate. :dd - -{Temperature for fix modify is not for group all} :dt - -The temperature compute is being used with a pressure calculation -which does operate on group all, so this may be inconsistent. :dd - -{Temperature for thermo pressure is not for group all} :dt - -User-assigned temperature to thermo via the thermo_modify command does -not compute temperature for all atoms. Since thermo computes a global -pressure, the kinetic energy contribution from the temperature is -assumed to also be for all atoms. Thus the pressure printed by thermo -could be inaccurate. :dd - -{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt - -Self-explanatory. :dd - -{The minimizer does not re-orient dipoles when using fix efield} :dt - -This means that only the atom coordinates will be minimized, -not the orientation of the dipoles. :dd - -{Too many common neighbors in CNA %d times} :dt - -More than the maximum # of neighbors was found multiple times. This -was unexpected. :dd - -{Too many inner timesteps in fix ttm} :dt - -Self-explanatory. :dd - -{Too many neighbors in CNA for %d atoms} :dt - -More than the maximum # of neighbors was found multiple times. This -was unexpected. :dd - -{Triclinic box skew is large} :dt - -The displacement in a skewed direction is normally required to be less -than half the box length in that dimension. E.g. the xy tilt must be -between -half and +half of the x box length. You have relaxed the -constraint using the box tilt command, but the warning means that a -LAMMPS simulation may be inefficient as a result. :dd - -{Use special bonds = 0,1,1 with bond style fene} :dt - -Most FENE models need this setting for the special_bonds command. :dd - -{Use special bonds = 0,1,1 with bond style fene/expand} :dt - -Most FENE models need this setting for the special_bonds command. :dd - -{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt - -This is likely not what you want to do. The exclusion settings will -eliminate neighbors in the neighbor list, which the manybody potential -needs to calculated its terms correctly. :dd - -{Using compute temp/deform with inconsistent fix deform remap option} :dt - -Fix nvt/sllod assumes deforming atoms have a velocity profile provided -by "remap v" or "remap none" as a fix deform option. :dd - -{Using compute temp/deform with no fix deform defined} :dt - -This is probably an error, since it makes little sense to use -compute temp/deform in this case. :dd - -{Using fix srd with box deformation but no SRD thermostat} :dt - -The deformation will heat the SRD particles so this can -be dangerous. :dd - -{Using kspace solver on system with no charge} :dt - -Self-explanatory. :dd - -{Using largest cut-off for lj/long/dipole/long long long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for buck/long/coul/long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for lj/long/coul/long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for pair_style lj/long/tip4p/long} :dt - -Self-explanatory. :dd - -{Using package gpu without any pair style defined} :dt - -Self-explanatory. :dd - -{Using pair potential shift with pair_modify compute no} :dt - -The shift effects will thus not be computed. :dd - -{Using pair tail corrections with nonperiodic system} :dt - -This is probably a bogus thing to do, since tail corrections are -computed by integrating the density of a periodic system out to -infinity. :dd - -{Using pair tail corrections with pair_modify compute no} :dt - -The tail corrections will thus not be computed. :dd - -{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt - -Self-explanatory. :dd - -:dle - diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt new file mode 100644 index 0000000000000000000000000000000000000000..1da777043c975de136d486fac100485d51e25367 --- /dev/null +++ b/doc/src/Errors_warnings.txt @@ -0,0 +1,934 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Warning messages :h3 + +This is an alphabetic list of the WARNING messages LAMMPS prints out +and the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. Warning messages +also list the source file and line number where the warning was +generated. For example, a message lile this: + +WARNING: Bond atom missing in box size check (domain.cpp:187) :pre + +means that line #187 in the file src/domain.cpp generated the error. +Looking in the source code may help you figure out what went wrong. + +Note that warning messages from "user-contributed +packages"_Packages_user.html are not listed here. If such a warning +occurs and is not self-explanatory, you'll need to look in the source +code or contact the author of the package. + +Doc page with "ERROR messages"_Errors_messages.html + +:line + +:dlb + +{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt + +The adjust/cutoff command is turned on and the Coulombic cutoff has been +adjusted to match the user-specified accuracy. :dd + +{Angle atoms missing at step %ld} :dt + +One or more of 3 atoms needed to compute a particular angle are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the angle has blown apart and an atom is +too far away. :dd + +{Angle style in data file differs from currently defined angle style} :dt + +Self-explanatory. :dd + +{Atom style in data file differs from currently defined atom style} :dt + +Self-explanatory. :dd + +{Bond atom missing in box size check} :dt + +The 2nd atoms needed to compute a particular bond is missing on this +processor. Typically this is because the pairwise cutoff is set too +short or the bond has blown apart and an atom is too far away. :dd + +{Bond atom missing in image check} :dt + +The 2nd atom in a particular bond is missing on this processor. +Typically this is because the pairwise cutoff is set too short or the +bond has blown apart and an atom is too far away. :dd + +{Bond atoms missing at step %ld} :dt + +The 2nd atom needed to compute a particular bond is missing on this +processor. Typically this is because the pairwise cutoff is set too +short or the bond has blown apart and an atom is too far away. :dd + +{Bond style in data file differs from currently defined bond style} :dt + +Self-explanatory. :dd + +{Bond/angle/dihedral extent > half of periodic box length} :dt + +This is a restriction because LAMMPS can be confused about which image +of an atom in the bonded interaction is the correct one to use. +"Extent" in this context means the maximum end-to-end length of the +bond/angle/dihedral. LAMMPS computes this by taking the maximum bond +length, multiplying by the number of bonds in the interaction (e.g. 3 +for a dihedral) and adding a small amount of stretch. :dd + +{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt + +Self-explanatory. :dd + +{Calling write_dump before a full system init.} :dt + +The write_dump command is used before the system has been fully +initialized as part of a 'run' or 'minimize' command. Not all dump +styles and features are fully supported at this point and thus the +command may fail or produce incomplete or incorrect output. Insert +a "run 0" command, if a full system init is required. :dd + +{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt + +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. :dd + +{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt + +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. :dd + +{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt + +Self-explanatory. :dd + +{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt + +Self-explanatory. :dd + +{Charges are set, but coulombic solver is not used} :dt + +Self-explanatory. :dd + +{Charges did not converge at step %ld: %lg} :dt + +Self-explanatory. :dd + +{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt + +Self-explanatory. :dd + +{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt + +The neighbor cutoff used may not encompass enough ghost atoms +to perform this operation correctly. :dd + +{Computing temperature of portions of rigid bodies} :dt + +The group defined by the temperature compute does not encompass all +the atoms in one or more rigid bodies, so the change in +degrees-of-freedom for the atoms in those partial rigid bodies will +not be accounted for. :dd + +{Create_bonds max distance > minimum neighbor cutoff} :dt + +This means atom pairs for some atom types may not be in the neighbor +list and thus no bond can be created between them. :dd + +{Delete_atoms cutoff > minimum neighbor cutoff} :dt + +This means atom pairs for some atom types may not be in the neighbor +list and thus an atom in that pair cannot be deleted. :dd + +{Dihedral atoms missing at step %ld} :dt + +One or more of 4 atoms needed to compute a particular dihedral are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the dihedral has blown apart and an atom is +too far away. :dd + +{Dihedral problem} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Dihedral problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Dihedral style in data file differs from currently defined dihedral style} :dt + +Self-explanatory. :dd + +{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt + +If the fix changes the timestep, the dump dcd file will not +reflect the change. :dd + +{Energy due to X extra global DOFs will be included in minimizer energies} :dt + +When using fixes like box/relax, the potential energy used by the minimizer +is augmented by an additional energy provided by the fix. Thus the printed +converged energy may be different from the total potential energy. :dd + +{Energy tally does not account for 'zero yes'} :dt + +The energy removed by using the 'zero yes' flag is not accounted +for in the energy tally and thus energy conservation cannot be +monitored in this case. :dd + +{Estimated error in splitting of dispersion coeffs is %g} :dt + +Error is greater than 0.0001 percent. :dd + +{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt + +Self-explanatory. Choosing a different cutoff value may help. :dd + +{FENE bond too long} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{FENE bond too long: %ld %d %d %g} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{FENE bond too long: %ld %g} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{Fix SRD walls overlap but fix srd overlap not set} :dt + +You likely want to set this in your input script. :dd + +{Fix bond/swap will ignore defined angles} :dt + +See the doc page for fix bond/swap for more info on this +restriction. :dd + +{Fix deposit near setting < possible overlap separation %g} :dt + +This test is performed for finite size particles with a diameter, not +for point particles. The near setting is smaller than the particle +diameter which can lead to overlaps. :dd + +{Fix evaporate may delete atom with non-zero molecule ID} :dt + +This is probably an error, since you should not delete only one atom +of a molecule. :dd + +{Fix gcmc using full_energy option} :dt + +Fix gcmc has automatically turned on the full_energy option since it +is required for systems like the one specified by the user. User input +included one or more of the following: kspace, triclinic, a hybrid +pair style, an eam pair style, or no "single" function for the pair +style. :dd + +{Fix property/atom mol or charge w/out ghost communication} :dt + +A model typically needs these properties defined for ghost atoms. :dd + +{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt + +Self-explanatory. :dd + +{Fix qeq has non-zero lower Taper radius cutoff} :dt + +Absolute value must be <= 0.01. :dd + +{Fix qeq has very low Taper radius cutoff} :dt + +Value should typically be >= 5.0. :dd + +{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt + +Self-explanatory. :dd + +{Fix qeq/fire tolerance may be too small for damped fires} :dt + +Self-explanatory. :dd + +{Fix rattle should come after all other integration fixes} :dt + +This fix is designed to work after all other integration fixes change +atom positions. Thus it should be the last integration fix specified. +If not, it will not satisfy the desired constraints as well as it +otherwise would. :dd + +{Fix recenter should come after all other integration fixes} :dt + +Other fixes may change the position of the center-of-mass, so +fix recenter should come last. :dd + +{Fix srd SRD moves may trigger frequent reneighboring} :dt + +This is because the SRD particles may move long distances. :dd + +{Fix srd grid size > 1/4 of big particle diameter} :dt + +This may cause accuracy problems. :dd + +{Fix srd particle moved outside valid domain} :dt + +This may indicate a problem with your simulation parameters. :dd + +{Fix srd particles may move > big particle diameter} :dt + +This may cause accuracy problems. :dd + +{Fix srd viscosity < 0.0 due to low SRD density} :dt + +This may cause accuracy problems. :dd + +{Fix thermal/conductivity comes before fix ave/spatial} :dt + +The order of these 2 fixes in your input script is such that fix +thermal/conductivity comes first. If you are using fix ave/spatial to +measure the temperature profile induced by fix viscosity, then this +may cause a glitch in the profile since you are averaging immediately +after swaps have occurred. Flipping the order of the 2 fixes +typically helps. :dd + +{Fix viscosity comes before fix ave/spatial} :dt + +The order of these 2 fixes in your input script is such that +fix viscosity comes first. If you are using fix ave/spatial +to measure the velocity profile induced by fix viscosity, then +this may cause a glitch in the profile since you are averaging +immediately after swaps have occurred. Flipping the order +of the 2 fixes typically helps. :dd + +{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt + +This is current restriction with Kokkos. :dd + +{For better accuracy use 'pair_modify table 0'} :dt + +The user-specified force accuracy cannot be achieved unless the table +feature is disabled by using 'pair_modify table 0'. :dd + +{Geometric mixing assumed for 1/r^6 coefficients} :dt + +Self-explanatory. :dd + +{Group for fix_modify temp != fix group} :dt + +The fix_modify command is specifying a temperature computation that +computes a temperature on a different group of atoms than the fix +itself operates on. This is probably not what you want to do. :dd + +{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt + +This is the size of the matrix. :dd + +{Ignoring unknown or incorrect info command flag} :dt + +Self-explanatory. An unknown argument was given to the info command. +Compare your input with the documentation. :dd + +{Improper atoms missing at step %ld} :dt + +One or more of 4 atoms needed to compute a particular improper are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the improper has blown apart and an atom is +too far away. :dd + +{Improper problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed improper atoms is extreme; you may want +to check your simulation geometry. :dd + +{Improper style in data file differs from currently defined improper style} :dt + +Self-explanatory. :dd + +{Inconsistent image flags} :dt + +The image flags for a pair on bonded atoms appear to be inconsistent. +Inconsistent means that when the coordinates of the two atoms are +unwrapped using the image flags, the two atoms are far apart. +Specifically they are further apart than half a periodic box length. +Or they are more than a box length apart in a non-periodic dimension. +This is usually due to the initial data file not having correct image +flags for the 2 atoms in a bond that straddles a periodic boundary. +They should be different by 1 in that case. This is a warning because +inconsistent image flags will not cause problems for dynamics or most +LAMMPS simulations. However they can cause problems when such atoms +are used with the fix rigid or replicate commands. Note that if you +have an infinite periodic crystal with bonds then it is impossible to +have fully consistent image flags, since some bonds will cross +periodic boundaries and connect two atoms with the same image +flag. :dd + +{KIM Model does not provide 'energy'; Potential energy will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'forces'; Forces will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt + +Self-explanatory. :dd + +{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt + +The kspace_modify slab parameter should be larger to insure periodic +grids padded with empty space do not overlap. :dd + +{Less insertions than requested} :dt + +The fix pour command was unsuccessful at finding open space +for as many particles as it tried to insert. :dd + +{Library error in lammps_gather_atoms} :dt + +This library function cannot be used if atom IDs are not defined +or are not consecutively numbered. :dd + +{Library error in lammps_scatter_atoms} :dt + +This library function cannot be used if atom IDs are not defined or +are not consecutively numbered, or if no atom map is defined. See the +atom_modify command for details about atom maps. :dd + +{Lost atoms via change_box: original %ld current %ld} :dt + +The command options you have used caused atoms to be lost. :dd + +{Lost atoms via displace_atoms: original %ld current %ld} :dt + +The command options you have used caused atoms to be lost. :dd + +{Lost atoms: original %ld current %ld} :dt + +Lost atoms are checked for each time thermo output is done. See the +thermo_modify lost command for options. Lost atoms usually indicate +bad dynamics, e.g. atoms have been blown far out of the simulation +box, or moved further than one processor's sub-domain away before +reneighboring. :dd + +{MSM mesh too small, increasing to 2 points in each direction} :dt + +Self-explanatory. :dd + +{Mismatch between velocity and compute groups} :dt + +The temperature computation used by the velocity command will not be +on the same group of atoms that velocities are being set for. :dd + +{Mixing forced for lj coefficients} :dt + +Self-explanatory. :dd + +{Molecule attributes do not match system attributes} :dt + +An attribute is specified (e.g. diameter, charge) that is +not defined for the specified atom style. :dd + +{Molecule has bond topology but no special bond settings} :dt + +This means the bonded atoms will not be excluded in pair-wise +interactions. :dd + +{Molecule template for create_atoms has multiple molecules} :dt + +The create_atoms command will only create molecules of a single type, +i.e. the first molecule in the template. :dd + +{Molecule template for fix gcmc has multiple molecules} :dt + +The fix gcmc command will only create molecules of a single type, +i.e. the first molecule in the template. :dd + +{Molecule template for fix shake has multiple molecules} :dt + +The fix shake command will only recognize molecules of a single +type, i.e. the first molecule in the template. :dd + +{More than one compute centro/atom} :dt + +It is not efficient to use compute centro/atom more than once. :dd + +{More than one compute cluster/atom} :dt + +It is not efficient to use compute cluster/atom more than once. :dd + +{More than one compute cna/atom defined} :dt + +It is not efficient to use compute cna/atom more than once. :dd + +{More than one compute contact/atom} :dt + +It is not efficient to use compute contact/atom more than once. :dd + +{More than one compute coord/atom} :dt + +It is not efficient to use compute coord/atom more than once. :dd + +{More than one compute damage/atom} :dt + +It is not efficient to use compute ke/atom more than once. :dd + +{More than one compute dilatation/atom} :dt + +Self-explanatory. :dd + +{More than one compute erotate/sphere/atom} :dt + +It is not efficient to use compute erorate/sphere/atom more than once. :dd + +{More than one compute hexorder/atom} :dt + +It is not efficient to use compute hexorder/atom more than once. :dd + +{More than one compute ke/atom} :dt + +It is not efficient to use compute ke/atom more than once. :dd + +{More than one compute orientorder/atom} :dt + +It is not efficient to use compute orientorder/atom more than once. :dd + +{More than one compute plasticity/atom} :dt + +Self-explanatory. :dd + +{More than one compute sna/atom} :dt + +Self-explanatory. :dd + +{More than one compute snad/atom} :dt + +Self-explanatory. :dd + +{More than one compute snav/atom} :dt + +Self-explanatory. :dd + +{More than one fix poems} :dt + +It is not efficient to use fix poems more than once. :dd + +{More than one fix rigid} :dt + +It is not efficient to use fix rigid more than once. :dd + +{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt + +This is because excluding specific pair interactions also excludes +them from long-range interactions which may not be the desired effect. +The special_bonds command handles this consistently by insuring +excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated +consistently by both the short-range pair style and the long-range +solver. This is not done for exclusions of charged atom pairs via the +neigh_modify exclude command. :dd + +{New thermo_style command, previous thermo_modify settings will be lost} :dt + +If a thermo_style command is used after a thermo_modify command, the +settings changed by the thermo_modify command will be reset to their +default values. This is because the thermo_modify command acts on +the currently defined thermo style, and a thermo_style command creates +a new style. :dd + +{No Kspace calculation with verlet/split} :dt + +The 2nd partition performs a kspace calculation so the kspace_style +command must be used. :dd + +{No automatic unit conversion to XTC file format conventions possible for units lj} :dt + +This means no scaling will be performed. :dd + +{No fixes defined, atoms won't move} :dt + +If you are not using a fix like nve, nvt, npt then atom velocities and +coordinates will not be updated during timestepping. :dd + +{No joints between rigid bodies, use fix rigid instead} :dt + +The bodies defined by fix poems are not connected by joints. POEMS +will integrate the body motion, but it would be more efficient to use +fix rigid. :dd + +{Not using real units with pair reax} :dt + +This is most likely an error, unless you have created your own ReaxFF +parameter file in a different set of units. :dd + +{Number of MSM mesh points changed to be a multiple of 2} :dt + +MSM requires that the number of grid points in each direction be a multiple +of two and the number of grid points in one or more directions have been +adjusted to meet this requirement. :dd + +{OMP_NUM_THREADS environment is not set.} :dt + +This environment variable must be set appropriately to use the +USER-OMP package. :dd + +{One or more atoms are time integrated more than once} :dt + +This is probably an error since you typically do not want to +advance the positions or velocities of an atom more than once +per timestep. :dd + +{One or more chunks do not contain all atoms in molecule} :dt + +This may not be what you intended. :dd + +{One or more dynamic groups may not be updated at correct point in timestep} :dt + +If there are other fixes that act immediately after the initial stage +of time integration within a timestep (i.e. after atoms move), then +the command that sets up the dynamic group should appear after those +fixes. This will insure that dynamic group assignments are made +after all atoms have moved. :dd + +{One or more respa levels compute no forces} :dt + +This is computationally inefficient. :dd + +{Pair COMB charge %.10f with force %.10f hit max barrier} :dt + +Something is possibly wrong with your model. :dd + +{Pair COMB charge %.10f with force %.10f hit min barrier} :dt + +Something is possibly wrong with your model. :dd + +{Pair brownian needs newton pair on for momentum conservation} :dt + +Self-explanatory. :dd + +{Pair dpd needs newton pair on for momentum conservation} :dt + +Self-explanatory. :dd + +{Pair dsmc: num_of_collisions > number_of_A} :dt + +Collision model in DSMC is breaking down. :dd + +{Pair dsmc: num_of_collisions > number_of_B} :dt + +Collision model in DSMC is breaking down. :dd + +{Pair style in data file differs from currently defined pair style} :dt + +Self-explanatory. :dd + +{Pair style restartinfo set but has no restart support} :dt + +This pair style has a bug, where it does not support reading and +writing information to a restart file, but does not set the member +variable "restartinfo" to 0 as required in that case. :dd + +{Particle deposition was unsuccessful} :dt + +The fix deposit command was not able to insert as many atoms as +needed. The requested volume fraction may be too high, or other atoms +may be in the insertion region. :dd + +{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt + +The decomposition of the physical domain (likely due to load +balancing) has led to a processor's sub-domain being smaller than the +neighbor skin in one or more dimensions. Since reneighboring is +triggered by atoms moving the skin distance, this may lead to lost +atoms, if an atom moves all the way across a neighboring processor's +sub-domain before reneighboring is triggered. :dd + +{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Replacing a fix, but new group != old group} :dt + +The ID and style of a fix match for a fix you are changing with a fix +command, but the new group you are specifying does not match the old +group. :dd + +{Replicating in a non-periodic dimension} :dt + +The parameters for a replicate command will cause a non-periodic +dimension to be replicated; this may cause unwanted behavior. :dd + +{Resetting reneighboring criteria during PRD} :dt + +A PRD simulation requires that neigh_modify settings be delay = 0, +every = 1, check = yes. Since these settings were not in place, +LAMMPS changed them and will restore them to their original values +after the PRD simulation. :dd + +{Resetting reneighboring criteria during TAD} :dt + +A TAD simulation requires that neigh_modify settings be delay = 0, +every = 1, check = yes. Since these settings were not in place, +LAMMPS changed them and will restore them to their original values +after the PRD simulation. :dd + +{Resetting reneighboring criteria during minimization} :dt + +Minimization requires that neigh_modify settings be delay = 0, every = +1, check = yes. Since these settings were not in place, LAMMPS +changed them and will restore them to their original values after the +minimization. :dd + +{Restart file used different # of processors} :dt + +The restart file was written out by a LAMMPS simulation running on a +different number of processors. Due to round-off, the trajectories of +your restarted simulation may diverge a little more quickly than if +you ran on the same # of processors. :dd + +{Restart file used different 3d processor grid} :dt + +The restart file was written out by a LAMMPS simulation running on a +different 3d grid of processors. Due to round-off, the trajectories +of your restarted simulation may diverge a little more quickly than if +you ran on the same # of processors. :dd + +{Restart file used different boundary settings, using restart file values} :dt + +Your input script cannot change these restart file settings. :dd + +{Restart file used different newton bond setting, using restart file value} :dt + +The restart file value will override the setting in the input script. :dd + +{Restart file used different newton pair setting, using input script value} :dt + +The input script value will override the setting in the restart file. :dd + +{Restrain problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Running PRD with only one replica} :dt + +This is allowed, but you will get no parallel speed-up. :dd + +{SRD bin shifting turned on due to small lamda} :dt + +This is done to try to preserve accuracy. :dd + +{SRD bin size for fix srd differs from user request} :dt + +Fix SRD had to adjust the bin size to fit the simulation box. See the +cubic keyword if you want this message to be an error vs warning. :dd + +{SRD bins for fix srd are not cubic enough} :dt + +The bin shape is not within tolerance of cubic. See the cubic +keyword if you want this message to be an error vs warning. :dd + +{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt + +See the inside keyword if you want this message to be an error vs +warning. :dd + +{SRD particle %d started inside wall %d on step %ld bounce %d} :dt + +See the inside keyword if you want this message to be an error vs +warning. :dd + +{Shake determinant < 0.0} :dt + +The determinant of the quadratic equation being solved for a single +cluster specified by the fix shake command is numerically suspect. LAMMPS +will set it to 0.0 and continue. :dd + +{Shell command '%s' failed with error '%s'} :dt + +Self-explanatory. :dd + +{Shell command returned with non-zero status} :dt + +This may indicate the shell command did not operate as expected. :dd + +{Should not allow rigid bodies to bounce off relecting walls} :dt + +LAMMPS allows this, but their dynamics are not computed correctly. :dd + +{Should not use fix nve/limit with fix shake or fix rattle} :dt + +This will lead to invalid constraint forces in the SHAKE/RATTLE +computation. :dd + +{Simulations might be very slow because of large number of structure factors} :dt + +Self-explanatory. :dd + +{Slab correction not needed for MSM} :dt + +Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd + +{System is not charge neutral, net charge = %g} :dt + +The total charge on all atoms on the system is not 0.0. +For some KSpace solvers this is only a warning. :dd + +{Table inner cutoff >= outer cutoff} :dt + +You specified an inner cutoff for a Coulombic table that is longer +than the global cutoff. Probably not what you wanted. :dd + +{Temperature for MSST is not for group all} :dt + +User-assigned temperature to MSST fix does not compute temperature for +all atoms. Since MSST computes a global pressure, the kinetic energy +contribution from the temperature is assumed to also be for all atoms. +Thus the pressure used by MSST could be inaccurate. :dd + +{Temperature for NPT is not for group all} :dt + +User-assigned temperature to NPT fix does not compute temperature for +all atoms. Since NPT computes a global pressure, the kinetic energy +contribution from the temperature is assumed to also be for all atoms. +Thus the pressure used by NPT could be inaccurate. :dd + +{Temperature for fix modify is not for group all} :dt + +The temperature compute is being used with a pressure calculation +which does operate on group all, so this may be inconsistent. :dd + +{Temperature for thermo pressure is not for group all} :dt + +User-assigned temperature to thermo via the thermo_modify command does +not compute temperature for all atoms. Since thermo computes a global +pressure, the kinetic energy contribution from the temperature is +assumed to also be for all atoms. Thus the pressure printed by thermo +could be inaccurate. :dd + +{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt + +Self-explanatory. :dd + +{The minimizer does not re-orient dipoles when using fix efield} :dt + +This means that only the atom coordinates will be minimized, +not the orientation of the dipoles. :dd + +{Too many common neighbors in CNA %d times} :dt + +More than the maximum # of neighbors was found multiple times. This +was unexpected. :dd + +{Too many inner timesteps in fix ttm} :dt + +Self-explanatory. :dd + +{Too many neighbors in CNA for %d atoms} :dt + +More than the maximum # of neighbors was found multiple times. This +was unexpected. :dd + +{Triclinic box skew is large} :dt + +The displacement in a skewed direction is normally required to be less +than half the box length in that dimension. E.g. the xy tilt must be +between -half and +half of the x box length. You have relaxed the +constraint using the box tilt command, but the warning means that a +LAMMPS simulation may be inefficient as a result. :dd + +{Use special bonds = 0,1,1 with bond style fene} :dt + +Most FENE models need this setting for the special_bonds command. :dd + +{Use special bonds = 0,1,1 with bond style fene/expand} :dt + +Most FENE models need this setting for the special_bonds command. :dd + +{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt + +This is likely not what you want to do. The exclusion settings will +eliminate neighbors in the neighbor list, which the manybody potential +needs to calculated its terms correctly. :dd + +{Using compute temp/deform with inconsistent fix deform remap option} :dt + +Fix nvt/sllod assumes deforming atoms have a velocity profile provided +by "remap v" or "remap none" as a fix deform option. :dd + +{Using compute temp/deform with no fix deform defined} :dt + +This is probably an error, since it makes little sense to use +compute temp/deform in this case. :dd + +{Using fix srd with box deformation but no SRD thermostat} :dt + +The deformation will heat the SRD particles so this can +be dangerous. :dd + +{Using kspace solver on system with no charge} :dt + +Self-explanatory. :dd + +{Using largest cut-off for lj/long/dipole/long long long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for buck/long/coul/long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for lj/long/coul/long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for pair_style lj/long/tip4p/long} :dt + +Self-explanatory. :dd + +{Using package gpu without any pair style defined} :dt + +Self-explanatory. :dd + +{Using pair potential shift with pair_modify compute no} :dt + +The shift effects will thus not be computed. :dd + +{Using pair tail corrections with nonperiodic system} :dt + +This is probably a bogus thing to do, since tail corrections are +computed by integrating the density of a periodic system out to +infinity. :dd + +{Using pair tail corrections with pair_modify compute no} :dt + +The tail corrections will thus not be computed. :dd + +{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt + +Self-explanatory. :dd + +:dle diff --git a/doc/src/Section_example.txt b/doc/src/Examples.txt similarity index 95% rename from doc/src/Section_example.txt rename to doc/src/Examples.txt index a2a9940f4845f10c2df5fe3333c8de30cba1ea7d..467ddcc959ddd2656a2173ce9abea8a1f57162a7 100644 --- a/doc/src/Section_example.txt +++ b/doc/src/Examples.txt @@ -1,4 +1,6 @@ -"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c +"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Section_perf.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -6,7 +8,7 @@ :line -7. Example problems :h2 +Example scripts :h3 The LAMMPS distribution includes an examples sub-directory with many sample problems. Many are 2d models that run quickly are are @@ -46,7 +48,7 @@ Lists of both kinds of directories are given below. :line -Lowercase directories :h3 +Lowercase directories :h4 accelerate: run with various acceleration options (OpenMP, GPU, Phi) airebo: polyethylene with AIREBO potential @@ -122,7 +124,7 @@ browser. :line -Uppercase directories :h3 +Uppercase directories :h4 ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc COUPLE: examples of how to use LAMMPS as a library @@ -141,5 +143,5 @@ The USER directory has a large number of sub-directories which correspond by name to a USER package. They contain scripts that illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further -instructions. See the "Section 4"_Section_packages.html doc +instructions. See the "Packages_details"_Packages_details.html doc page for more info on specific USER packages. diff --git a/doc/src/JPG/pair_body_rounded.jpg b/doc/src/JPG/pair_body_rounded.jpg new file mode 100644 index 0000000000000000000000000000000000000000..cd745c44e27e96585be021b3dcca342f686e15e9 Binary files /dev/null and b/doc/src/JPG/pair_body_rounded.jpg differ diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index eb07bbe0a788f5637ea950a4b4d3f0db98181c32..fd31c83c017eb3ac8c4ba0c95e0dfff03f51b58f 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ - +< LAMMPS Users Manual - + @@ -19,7 +19,7 @@ :line LAMMPS Documentation :c,h1 -30 Mar 2018 version :c,h2 +2 Aug 2018 version :c,h2 Version info: :h3 @@ -111,15 +111,14 @@ it gives quick access to documentation for all LAMMPS commands. Section_intro Section_start Section_commands - Section_packages - Section_accelerate + Packages + Speed Section_howto - Section_example - Section_perf - Section_tools - Section_modify - Section_python - Section_errors + Examples + Tools + Modify + Python + Errors Section_history .. toctree:: @@ -167,19 +166,8 @@ END_RST --> 3.3 "Input script structure"_cmd_3 :b 3.4 "Commands listed by category"_cmd_4 :b 3.5 "Commands listed alphabetically"_cmd_5 :ule,b -"Packages"_Section_packages.html :l - 4.1 "Standard packages"_pkg_1 :ulb,b - 4.2 "User packages"_pkg_2 :ule,b -"Accelerating LAMMPS performance"_Section_accelerate.html :l - 5.1 "Measuring performance"_acc_1 :ulb,b - 5.2 "Algorithms and code options to boost performace"_acc_2 :b - 5.3 "Accelerator packages with optimized styles"_acc_3 :b - 5.3.1 "GPU package"_accelerate_gpu.html :b - 5.3.2 "USER-INTEL package"_accelerate_intel.html :b - 5.3.3 "KOKKOS package"_accelerate_kokkos.html :b - 5.3.4 "USER-OMP package"_accelerate_omp.html :b - 5.3.5 "OPT package"_accelerate_opt.html :b - 5.4 "Comparison of various accelerator packages"_acc_4 :ule,b +"Optional packages"_Packages.html :l +"Accelerate performance"_Speed.html :l "How-to discussions"_Section_howto.html :l 6.1 "Restarting a simulation"_howto_1 :ulb,b 6.2 "2d simulations"_howto_2 :b @@ -208,38 +196,11 @@ END_RST --> 6.25 "Polarizable models"_howto_25 :b 6.26 "Adiabatic core/shell model"_howto_26 :b 6.27 "Drude induced dipoles"_howto_27 :ule,b -"Example problems"_Section_example.html :l -"Performance & scalability"_Section_perf.html :l -"Additional tools"_Section_tools.html :l -"Modifying & extending LAMMPS"_Section_modify.html :l - 10.1 "Atom styles"_mod_1 :ulb,b - 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b - 10.3 "Compute styles"_mod_3 :b - 10.4 "Dump styles"_mod_4 :b - 10.5 "Dump custom output options"_mod_5 :b - 10.6 "Fix styles"_mod_6 :b - 10.7 "Input script commands"_mod_7 :b - 10.8 "Kspace computations"_mod_8 :b - 10.9 "Minimization styles"_mod_9 :b - 10.10 "Pairwise potentials"_mod_10 :b - 10.11 "Region styles"_mod_11 :b - 10.12 "Body styles"_mod_12 :b - 10.13 "Thermodynamic output options"_mod_13 :b - 10.14 "Variable options"_mod_14 :b - 10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b -"Python interface"_Section_python.html :l - 11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b - 11.2 "Overview of using Python from a LAMMPS script"_py_2 :b - 11.3 "Building LAMMPS as a shared library"_py_3 :b - 11.4 "Installing the Python wrapper into Python"_py_4 :b - 11.5 "Extending Python with MPI to run in parallel"_py_5 :b - 11.6 "Testing the Python-LAMMPS interface"_py_6 :b - 11.7 "Using LAMMPS from Python"_py_7 :b - 11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b -"Errors"_Section_errors.html :l - 12.1 "Common problems"_err_1 :ulb,b - 12.2 "Reporting bugs"_err_2 :b - 12.3 "Error & warning messages"_err_3 :ule,b +"Example scripts"_Examples.html :l +"Auxiliary tools"_Tools.html :l +"Modify & extend LAMMPS"_Modify.html :l +"Use Python with LAMMPS"_Python.html :l +"Errors"_Errors.html :l "Future and history"_Section_history.html :l 13.1 "Coming attractions"_hist_1 :ulb,b 13.2 "Past versions"_hist_2 :ule,b @@ -266,14 +227,6 @@ END_RST --> :link(cmd_4,Section_commands.html#cmd_4) :link(cmd_5,Section_commands.html#cmd_5) -:link(pkg_1,Section_packages.html#pkg_1) -:link(pkg_2,Section_packages.html#pkg_2) - -:link(acc_1,Section_accelerate.html#acc_1) -:link(acc_2,Section_accelerate.html#acc_2) -:link(acc_3,Section_accelerate.html#acc_3) -:link(acc_4,Section_accelerate.html#acc_4) - :link(howto_1,Section_howto.html#howto_1) :link(howto_2,Section_howto.html#howto_2) :link(howto_3,Section_howto.html#howto_3) @@ -302,33 +255,6 @@ END_RST --> :link(howto_26,Section_howto.html#howto_26) :link(howto_27,Section_howto.html#howto_27) -:link(mod_1,Section_modify.html#mod_1) -:link(mod_2,Section_modify.html#mod_2) -:link(mod_3,Section_modify.html#mod_3) -:link(mod_4,Section_modify.html#mod_4) -:link(mod_5,Section_modify.html#mod_5) -:link(mod_6,Section_modify.html#mod_6) -:link(mod_7,Section_modify.html#mod_7) -:link(mod_8,Section_modify.html#mod_8) -:link(mod_9,Section_modify.html#mod_9) -:link(mod_10,Section_modify.html#mod_10) -:link(mod_11,Section_modify.html#mod_11) -:link(mod_12,Section_modify.html#mod_12) -:link(mod_13,Section_modify.html#mod_13) -:link(mod_14,Section_modify.html#mod_14) -:link(mod_15,Section_modify.html#mod_15) - -:link(py_1,Section_python.html#py_1) -:link(py_2,Section_python.html#py_2) -:link(py_3,Section_python.html#py_3) -:link(py_4,Section_python.html#py_4) -:link(py_5,Section_python.html#py_5) -:link(py_6,Section_python.html#py_6) - -:link(err_1,Section_errors.html#err_1) -:link(err_2,Section_errors.html#err_2) -:link(err_3,Section_errors.html#err_3) - :link(hist_1,Section_history.html#hist_1) :link(hist_2,Section_history.html#hist_2) diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae0b0dc6bdf2371f9a205c39fbc267b91ecd11b3 --- /dev/null +++ b/doc/src/Modify.txt @@ -0,0 +1,76 @@ +"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Python.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Modify & extend LAMMPS :h2 + +LAMMPS is designed in a modular fashion so as to be easy to modify and +extend with new functionality. In fact, about 95% of its source code +is add-on files. These doc pages give basic instructions on how to do +this. + +If you add a new feature to LAMMPS and think it will be of interest to +general users, we encourage you to submit it for inclusion in LAMMPS +as a pull request on our "GitHub +site"_https://github.com/lammps/lammps, after reading the "Modify +contribute"_Modify_contribute.html doc page. + + + + + +"Overview"_Modify_overview.html +"Submitting new features for inclusion in LAMMPS"_Modify_contribute.html :all(b) + +"Atom styles"_Modify_atom.html +"Pair styles"_Modify_pair.html +"Bond, angle, dihedral, improper styles"_Modify_bond.html +"Compute styles"_Modify_compute.html +"Fix styles"_Modify_fix.html +"Input script command styles"_Modify_command.html :all(b) + +"Dump styles"_Modify_dump.html +"Kspace styles"_Modify_kspace.html +"Minimization styles"_Modify_min.html +"Region styles"_Modify_region.html +"Body styles"_Modify_body.html :all(b) + +"Thermodynamic output options"_Modify_thermo.html +"Variable options"_Modify_variable.html :all(b) + + diff --git a/doc/src/Modify_atom.txt b/doc/src/Modify_atom.txt new file mode 100644 index 0000000000000000000000000000000000000000..afa1c319d25539594bb65f9dcb1f146023623ff8 --- /dev/null +++ b/doc/src/Modify_atom.txt @@ -0,0 +1,90 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Atom styles :h3 + +Classes that define an "atom style"_atom_style.html are derived from +the AtomVec class and managed by the Atom class. The atom style +determines what attributes are associated with an atom. A new atom +style can be created if one of the existing atom styles does not +define all the attributes you need to store and communicate with +atoms. + +Atom_vec_atomic.cpp is a simple example of an atom style. + +Here is a brief description of methods you define in your new derived +class. See atom_vec.h for details. + +init: one time setup (optional) +grow: re-allocate atom arrays to longer lengths (required) +grow_reset: make array pointers in Atom and AtomVec classes consistent (required) +copy: copy info for one atom to another atom's array locations (required) +pack_comm: store an atom's info in a buffer communicated every timestep (required) +pack_comm_vel: add velocity info to communication buffer (required) +pack_comm_hybrid: store extra info unique to this atom style (optional) +unpack_comm: retrieve an atom's info from the buffer (required) +unpack_comm_vel: also retrieve velocity info (required) +unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) +pack_reverse: store an atom's info in a buffer communicating partial forces (required) +pack_reverse_hybrid: store extra info unique to this atom style (optional) +unpack_reverse: retrieve an atom's info from the buffer (required) +unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) +pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) +pack_border_vel: add velocity info to buffer (required) +pack_border_hybrid: store extra info unique to this atom style (optional) +unpack_border: retrieve an atom's info from the buffer (required) +unpack_border_vel: also retrieve velocity info (required) +unpack_border_hybrid: retrieve extra info unique to this atom style (optional) +pack_exchange: store all an atom's info to migrate to another processor (required) +unpack_exchange: retrieve an atom's info from the buffer (required) +size_restart: number of restart quantities associated with proc's atoms (required) +pack_restart: pack atom quantities into a buffer (required) +unpack_restart: unpack atom quantities from a buffer (required) +create_atom: create an individual atom of this style (required) +data_atom: parse an atom line from the data file (required) +data_atom_hybrid: parse additional atom info unique to this atom style (optional) +data_vel: parse one line of velocity information from data file (optional) +data_vel_hybrid: parse additional velocity data unique to this atom style (optional) +memory_usage: tally memory allocated by atom arrays (required) :tb(s=:) + +The constructor of the derived class sets values for several variables +that you must set when defining a new atom style, which are documented +in atom_vec.h. New atom arrays are defined in atom.cpp. Search for +the word "customize" and you will find locations you will need to +modify. + +NOTE: It is possible to add some attributes, such as a molecule ID, to +atom styles that do not have them via the "fix +property/atom"_fix_property_atom.html command. This command also +allows new custom attributes consisting of extra integer or +floating-point values to be added to atoms. See the "fix +property/atom"_fix_property_atom.html doc page for examples of cases +where this is useful and details on how to initialize, access, and +output the custom values. + +New "pair styles"_pair_style.html, "fixes"_fix.html, or +"computes"_compute.html can be added to LAMMPS, as discussed below. +The code for these classes can use the per-atom properties defined by +fix property/atom. The Atom class has a find_custom() method that is +useful in this context: + +int index = atom->find_custom(char *name, int &flag); :pre + +The "name" of a custom attribute, as specified in the "fix +property/atom"_fix_property_atom.html command, is checked to verify +that it exists and its index is returned. The method also sets flag = +0/1 depending on whether it is an integer or floating-point attribute. +The vector of values associated with the attribute can then be +accessed using the returned index as + +int *ivector = atom->ivector\[index\]; +double *dvector = atom->dvector\[index\]; :pre + +Ivector or dvector are vectors of length Nlocal = # of owned atoms, +which store the attributes of individual atoms. diff --git a/doc/src/Modify_body.txt b/doc/src/Modify_body.txt new file mode 100644 index 0000000000000000000000000000000000000000..b1dc8130cd6ad46318fe7a9c336b7e8978cbdbe5 --- /dev/null +++ b/doc/src/Modify_body.txt @@ -0,0 +1,35 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Body styles :h3 + +Classes that define body particles are derived from the Body class. +Body particles can represent complex entities, such as surface meshes +of discrete points, collections of sub-particles, deformable objects, +etc. + +See "Section 6.14"_Section_howto.html#howto_14 of the manual for +an overview of using body particles and the "body"_body.html doc page +for details on the various body styles LAMMPS supports. New styles +can be created to add new kinds of body particles to LAMMPS. + +Body_nparticle.cpp is an example of a body particle that is treated as +a rigid body containing N sub-particles. + +Here is a brief description of methods you define in your new derived +class. See body.h for details. + +data_body: process a line from the Bodies section of a data file +noutrow: number of sub-particles output is generated for +noutcol: number of values per-sub-particle output is generated for +output: output values for the Mth sub-particle +pack_comm_body: body attributes to communicate every timestep +unpack_comm_body: unpacking of those attributes +pack_border_body: body attributes to communicate when reneighboring is done +unpack_border_body: unpacking of those attributes :tb(s=:) diff --git a/doc/src/Modify_bond.txt b/doc/src/Modify_bond.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0828a0c3b8544c84fa8539c7eb9f30e63489cfb --- /dev/null +++ b/doc/src/Modify_bond.txt @@ -0,0 +1,33 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Bond, angle, dihedral, improper styles :h3 + +Classes that compute molecular interactions are derived from the Bond, +Angle, Dihedral, and Improper classes. New styles can be created to +add new potentials to LAMMPS. + +Bond_harmonic.cpp is the simplest example of a bond style. Ditto for +the harmonic forms of the angle, dihedral, and improper style +commands. + +Here is a brief description of common methods you define in your +new derived class. See bond.h, angle.h, dihedral.h, and improper.h +for details and specific additional methods. + +init: check if all coefficients are set, calls {init_style} (optional) +init_style: check if style specific conditions are met (optional) +compute: compute the molecular interactions (required) +settings: apply global settings for all types (optional) +coeff: set coefficients for one type (required) +equilibrium_distance: length of bond, used by SHAKE (required, bond only) +equilibrium_angle: opening of angle, used by SHAKE (required, angle only) +write & read_restart: writes/reads coeffs to restart files (required) +single: force and energy of a single bond or angle (required, bond or angle only) +memory_usage: tally memory allocated by the style (optional) :tb(s=:) diff --git a/doc/src/Modify_command.txt b/doc/src/Modify_command.txt new file mode 100644 index 0000000000000000000000000000000000000000..6fc9aad1fc55174fa3be29eda559966b34db2259 --- /dev/null +++ b/doc/src/Modify_command.txt @@ -0,0 +1,27 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Input script command style :h3 + +New commands can be added to LAMMPS input scripts by adding new +classes that have a "command" method. For example, the create_atoms, +read_data, velocity, and run commands are all implemented in this +fashion. When such a command is encountered in the LAMMPS input +script, LAMMPS simply creates a class with the corresponding name, +invokes the "command" method of the class, and passes it the arguments +from the input script. The command method can perform whatever +operations it wishes on LAMMPS data structures. + +The single method your new class must define is as follows: + +command: operations performed by the new command :tb(s=:) + +Of course, the new class can define other methods and variables as +needed. + diff --git a/doc/src/Modify_compute.txt b/doc/src/Modify_compute.txt new file mode 100644 index 0000000000000000000000000000000000000000..b02b8a983ec4c32f0935c7b00b1c3c3dd59e7f5d --- /dev/null +++ b/doc/src/Modify_compute.txt @@ -0,0 +1,49 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Compute styles :h3 + +Classes that compute scalar and vector quantities like temperature +and the pressure tensor, as well as classes that compute per-atom +quantities like kinetic energy and the centro-symmetry parameter +are derived from the Compute class. New styles can be created +to add new calculations to LAMMPS. + +Compute_temp.cpp is a simple example of computing a scalar +temperature. Compute_ke_atom.cpp is a simple example of computing +per-atom kinetic energy. + +Here is a brief description of methods you define in your new derived +class. See compute.h for details. + +init: perform one time setup (required) +init_list: neighbor list setup, if needed (optional) +compute_scalar: compute a scalar quantity (optional) +compute_vector: compute a vector of quantities (optional) +compute_peratom: compute one or more quantities per atom (optional) +compute_local: compute one or more quantities per processor (optional) +pack_comm: pack a buffer with items to communicate (optional) +unpack_comm: unpack the buffer (optional) +pack_reverse: pack a buffer with items to reverse communicate (optional) +unpack_reverse: unpack the buffer (optional) +remove_bias: remove velocity bias from one atom (optional) +remove_bias_all: remove velocity bias from all atoms in group (optional) +restore_bias: restore velocity bias for one atom after remove_bias (optional) +restore_bias_all: same as before, but for all atoms in group (optional) +pair_tally_callback: callback function for {tally}-style computes (optional). +memory_usage: tally memory usage (optional) :tb(s=:) + +Tally-style computes are a special case, as their computation is done +in two stages: the callback function is registered with the pair style +and then called from the Pair::ev_tally() function, which is called for +each pair after force and energy has been computed for this pair. Then +the tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The USER-TALLY package +provides {examples}_compute_tally.html for utilizing this mechanism. + diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt new file mode 100644 index 0000000000000000000000000000000000000000..80795b5e205332fdfac501c74bee8153706ad33e --- /dev/null +++ b/doc/src/Modify_contribute.txt @@ -0,0 +1,210 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Submitting new features for inclusion in LAMMPS :h3 + +We encourage users to submit new features or modifications for LAMMPS +to "the core developers"_http://lammps.sandia.gov/authors.html so they +can be added to the LAMMPS distribution. The preferred way to manage +and coordinate this is as of Fall 2016 via the LAMMPS project on +"GitHub"_https://github.com/lammps/lammps. An alternative is to +contact the LAMMPS developers or the indicated developer of a package +or feature directly and send in your contribution via e-mail. + +For any larger modifications or programming project, you are +encouraged to contact the LAMMPS developers ahead of time, in order to +discuss implementation strategies and coding guidelines, that will +make it easier to integrate your contribution and result in less work +for everybody involved. You are also encouraged to search through the +list of "open issues on +GitHub"_https://github.com/lammps/lammps/issues and submit a new issue +for a planned feature, so you would not duplicate the work of others +(and possibly get scooped by them) or have your work duplicated by +others. + +How quickly your contribution will be integrated depends largely on +how much effort it will cause to integrate and test it, how much it +requires changes to the core codebase, and of how much interest it is +to the larger LAMMPS community. Please see below for a checklist of +typical requirements. Once you have prepared everything, see "this +tutorial"_tutorial_github.html for instructions on how to submit your +changes or new files through a GitHub pull request. If you prefer to +submit patches or full files, you should first make certain, that your +code works correctly with the latest patch-level version of LAMMPS and +contains all bugfixes from it. Then create a gzipped tar file of all +changed or added files or a corresponding patch file using 'diff -u' +or 'diff -c' and compress it with gzip. Please only use gzip +compression, as this works well on all platforms. + +If the new features/files are broadly useful we may add them as core +files to LAMMPS or as part of a "standard +package"_Section_start.html#start_3. Else we will add them as a +user-contributed file or package. Examples of user packages are in +src sub-directories that start with USER. The USER-MISC package is +simply a collection of (mostly) unrelated single files, which is the +simplest way to have your contribution quickly added to the LAMMPS +distribution. You can see a list of the both standard and user +packages by typing "make package" in the LAMMPS src directory. + +Note that by providing us files to release, you are agreeing to make +them open-source, i.e. we can release them under the terms of the GPL, +used as a license for the rest of LAMMPS. See "Section +1.4"_Section_intro.html#intro_4 for details. + +With user packages and files, all we are really providing (aside from +the fame and fortune that accompanies having your name in the source +code and on the "Authors page"_http://lammps.sandia.gov/authors.html +of the "LAMMPS WWW site"_lws), is a means for you to distribute your +work to the LAMMPS user community, and a mechanism for others to +easily try out your new feature. This may help you find bugs or make +contact with new collaborators. Note that you're also implicitly +agreeing to support your code which means answer questions, fix bugs, +and maintain it if LAMMPS changes in some way that breaks it (an +unusual event). + +NOTE: If you prefer to actively develop and support your add-on +feature yourself, then you may wish to make it available for download +from your own website, as a user package that LAMMPS users can add to +their copy of LAMMPS. See the "Offsite LAMMPS packages and +tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web +site for examples of groups that do this. We are happy to advertise +your package and web site from that page. Simply email the +"developers"_http://lammps.sandia.gov/authors.html with info about +your package and we will post it there. + +The previous sections of this doc page describe how to add new "style" +files of various kinds to LAMMPS. Packages are simply collections of +one or more new class files which are invoked as a new style within a +LAMMPS input script. If designed correctly, these additions typically +do not require changes to the main core of LAMMPS; they are simply +add-on files. If you think your new feature requires non-trivial +changes in core LAMMPS files, you'll need to "communicate with the +developers"_http://lammps.sandia.gov/authors.html, since we may or may +not want to make those changes. An example of a trivial change is +making a parent-class method "virtual" when you derive a new child +class from it. + +Here is a checklist of steps you need to follow to submit a single file +or user package for our consideration. Following these steps will save +both you and us time. See existing files in packages in the src dir for +examples. If you are uncertain, please ask. + +All source files you provide must compile with the most current +version of LAMMPS with multiple configurations. In particular you +need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG +set in addition to the default -DLAMMPS_SMALLBIG setting. Your code +will need to work correctly in serial and in parallel using MPI. :ulb,l + +For consistency with the rest of LAMMPS and especially, if you want +your contribution(s) to be added to main LAMMPS code or one of its +standard packages, it needs to be written in a style compatible with +other LAMMPS source files. This means: 2-character indentation per +level, [no tabs], no lines over 80 characters. I/O is done via +the C-style stdio library, class header files should not import any +system headers outside , STL containers should be avoided +in headers, and forward declarations used where possible or needed. +All added code should be placed into the LAMMPS_NS namespace or a +sub-namespace; global or static variables should be avoided, as they +conflict with the modular nature of LAMMPS and the C++ class structure. +Header files must [not] import namespaces with {using}. +This all is so the developers can more easily understand, integrate, +and maintain your contribution and reduce conflicts with other parts +of LAMMPS. This basically means that the code accesses data +structures, performs its operations, and is formatted similar to other +LAMMPS source files, including the use of the error class for error +and warning messages. :l + +If you want your contribution to be added as a user-contributed +feature, and it's a single file (actually a *.cpp and *.h file) it can +rapidly be added to the USER-MISC directory. Send us the one-line +entry to add to the USER-MISC/README file in that dir, along with the +2 source files. You can do this multiple times if you wish to +contribute several individual features. :l + +If you want your contribution to be added as a user-contribution and +it is several related features, it is probably best to make it a user +package directory with a name like USER-FOO. In addition to your new +files, the directory should contain a README text file. The README +should contain your name and contact information and a brief +description of what your new package does. If your files depend on +other LAMMPS style files also being installed (e.g. because your file +is a derived class from the other LAMMPS class), then an Install.sh +file is also needed to check for those dependencies. See other README +and Install.sh files in other USER directories as examples. Send us a +tarball of this USER-FOO directory. :l + +Your new source files need to have the LAMMPS copyright, GPL notice, +and your name and email address at the top, like other +user-contributed LAMMPS source files. They need to create a class +that is inside the LAMMPS namespace. If the file is for one of the + +USER packages, including USER-MISC, then we are not as picky about the +coding style (see above). I.e. the files do not need to be in the +same stylistic format and syntax as other LAMMPS files, though that +would be nice for developers as well as users who try to read your +code. :l + +You [must] also create a [documentation] file for each new command or +style you are adding to LAMMPS. For simplicity and convenience, the +documentation of groups of closely related commands or styles may be +combined into a single file. This will be one file for a single-file +feature. For a package, it might be several files. These are simple +text files with a specific markup language, that are then auto-converted +to HTML and PDF. The tools for this conversion are included in the +source distribution, and the translation can be as simple as doing +"make html pdf" in the doc folder. +Thus the documentation source files must be in the same format and +style as other *.txt files in the lammps/doc/src directory for similar +commands and styles; use one or more of them as a starting point. +A description of the markup can also be found in +lammps/doc/utils/txt2html/README.html +As appropriate, the text files can include links to equations +(see doc/Eqs/*.tex for examples, we auto-create the associated JPG +files), or figures (see doc/JPG for examples), or even additional PDF +files with further details (see doc/PDF for examples). The doc page +should also include literature citations as appropriate; see the +bottom of doc/fix_nh.txt for examples and the earlier part of the same +file for how to format the cite itself. The "Restrictions" section of +the doc page should indicate that your command is only available if +LAMMPS is built with the appropriate USER-MISC or USER-FOO package. +See other user package doc files for examples of how to do this. The +prerequisite for building the HTML format files are Python 3.x and +virtualenv, the requirement for generating the PDF format manual +is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least +"make html" and carefully inspect and proofread the resulting HTML format +doc page before submitting your code. :l + +For a new package (or even a single command) you should include one or +more example scripts demonstrating its use. These should run in no +more than a couple minutes, even on a single processor, and not require +large data files as input. See directories under examples/USER for +examples of input scripts other users provided for their packages. +These example inputs are also required for validating memory accesses +and testing for memory leaks with valgrind :l + +If there is a paper of yours describing your feature (either the +algorithm/science behind the feature itself, or its initial usage, or +its implementation in LAMMPS), you can add the citation to the *.cpp +source file. See src/USER-EFF/atom_vec_electron.cpp for an example. +A LaTeX citation is stored in a variable at the top of the file and a +single line of code that references the variable is added to the +constructor of the class. Whenever a user invokes your feature from +their input script, this will cause LAMMPS to output the citation to a +log.cite file and prompt the user to examine the file. Note that you +should only use this for a paper you or your group authored. +E.g. adding a cite in the code for a paper by Nose and Hoover if you +write a fix that implements their integrator is not the intended +usage. That kind of citation should just be in the doc page you +provide. :l +:ule + +Finally, as a general rule-of-thumb, the more clear and +self-explanatory you make your documentation and README files, and the +easier you make it for people to get started, e.g. by providing example +scripts, the more likely it is that users will try out your new feature. diff --git a/doc/src/Modify_dump.txt b/doc/src/Modify_dump.txt new file mode 100644 index 0000000000000000000000000000000000000000..81af54e0039a3ad9f95f34f7f0498457914a6f6d --- /dev/null +++ b/doc/src/Modify_dump.txt @@ -0,0 +1,35 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Dump styles :h3 + +Classes that dump per-atom info to files are derived from the Dump +class. To dump new quantities or in a new format, a new derived dump +class can be added, but it is typically simpler to modify the +DumpCustom class contained in the dump_custom.cpp file. + +Dump_atom.cpp is a simple example of a derived dump class. + +Here is a brief description of methods you define in your new derived +class. See dump.h for details. + +write_header: write the header section of a snapshot of atoms +count: count the number of lines a processor will output +pack: pack a proc's output data into a buffer +write_data: write a proc's data to a file :tb(s=:) + +See the "dump"_dump.html command and its {custom} style for a list of +keywords for atom information that can already be dumped by +DumpCustom. It includes options to dump per-atom info from Compute +classes, so adding a new derived Compute class is one way to calculate +new quantities to dump. + +Note that new keywords for atom properties are not typically +added to the "dump custom"_dump.html command. Instead they are added +to the "compute property/atom"_compute_property_atom.html command. diff --git a/doc/src/Modify_fix.txt b/doc/src/Modify_fix.txt new file mode 100644 index 0000000000000000000000000000000000000000..ba985475cc9e72721b7dd50bf3bc9268f97f60c0 --- /dev/null +++ b/doc/src/Modify_fix.txt @@ -0,0 +1,107 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Fix styles :h3 + +In LAMMPS, a "fix" is any operation that is computed during +timestepping that alters some property of the system. Essentially +everything that happens during a simulation besides force computation, +neighbor list construction, and output, is a "fix". This includes +time integration (update of coordinates and velocities), force +constraints or boundary conditions (SHAKE or walls), and diagnostics +(compute a diffusion coefficient). New styles can be created to add +new options to LAMMPS. + +Fix_setforce.cpp is a simple example of setting forces on atoms to +prescribed values. There are dozens of fix options already in LAMMPS; +choose one as a template that is similar to what you want to +implement. + +Here is a brief description of methods you can define in your new +derived class. See fix.h for details. + +setmask: determines when the fix is called during the timestep (required) +init: initialization before a run (optional) +setup_pre_exchange: called before atom exchange in setup (optional) +setup_pre_force: called before force computation in setup (optional) +setup: called immediately before the 1st timestep and after forces are computed (optional) +min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional) +min_setup: like setup, but for minimizations instead of MD runs (optional) +initial_integrate: called at very beginning of each timestep (optional) +pre_exchange: called before atom exchange on re-neighboring steps (optional) +pre_neighbor: called before neighbor list build (optional) +pre_force: called before pair & molecular forces are computed (optional) +post_force: called after pair & molecular forces are computed and communicated (optional) +final_integrate: called at end of each timestep (optional) +end_of_step: called at very end of timestep (optional) +write_restart: dumps fix info to restart file (optional) +restart: uses info from restart file to re-initialize the fix (optional) +grow_arrays: allocate memory for atom-based arrays used by fix (optional) +copy_arrays: copy atom info when an atom migrates to a new processor (optional) +pack_exchange: store atom's data in a buffer (optional) +unpack_exchange: retrieve atom's data from a buffer (optional) +pack_restart: store atom's data for writing to restart file (optional) +unpack_restart: retrieve atom's data from a restart file buffer (optional) +size_restart: size of atom's data (optional) +maxsize_restart: max size of atom's data (optional) +setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional) +initial_integrate_respa: same as initial_integrate, but for rRESPA (optional) +post_integrate_respa: called after the first half integration step is done in rRESPA (optional) +pre_force_respa: same as pre_force, but for rRESPA (optional) +post_force_respa: same as post_force, but for rRESPA (optional) +final_integrate_respa: same as final_integrate, but for rRESPA (optional) +min_pre_force: called after pair & molecular forces are computed in minimizer (optional) +min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) +min_store: store extra data for linesearch based minimization on a LIFO stack (optional) +min_pushstore: push the minimization LIFO stack one element down (optional) +min_popstore: pop the minimization LIFO stack one element up (optional) +min_clearstore: clear minimization LIFO stack (optional) +min_step: reset or move forward on line search minimization (optional) +min_dof: report number of degrees of freedom {added} by this fix in minimization (optional) +max_alpha: report maximum allowed step size during linesearch minimization (optional) +pack_comm: pack a buffer to communicate a per-atom quantity (optional) +unpack_comm: unpack a buffer to communicate a per-atom quantity (optional) +pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional) +unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional) +dof: report number of degrees of freedom {removed} by this fix during MD (optional) +compute_scalar: return a global scalar property that the fix computes (optional) +compute_vector: return a component of a vector property that the fix computes (optional) +compute_array: return a component of an array property that the fix computes (optional) +deform: called when the box size is changed (optional) +reset_target: called when a change of the target temperature is requested during a run (optional) +reset_dt: is called when a change of the time step is requested during a run (optional) +modify_param: called when a fix_modify request is executed (optional) +memory_usage: report memory used by fix (optional) +thermo: compute quantities for thermodynamic output (optional) :tb(s=:) + +Typically, only a small fraction of these methods are defined for a +particular fix. Setmask is mandatory, as it determines when the fix +will be invoked during the timestep. Fixes that perform time +integration ({nve}, {nvt}, {npt}) implement initial_integrate() and +final_integrate() to perform velocity Verlet updates. Fixes that +constrain forces implement post_force(). + +Fixes that perform diagnostics typically implement end_of_step(). For +an end_of_step fix, one of your fix arguments must be the variable +"nevery" which is used to determine when to call the fix and you must +set this variable in the constructor of your fix. By convention, this +is the first argument the fix defines (after the ID, group-ID, style). + +If the fix needs to store information for each atom that persists from +timestep to timestep, it can manage that memory and migrate the info +with the atoms as they move from processors to processor by +implementing the grow_arrays, copy_arrays, pack_exchange, and +unpack_exchange methods. Similarly, the pack_restart and +unpack_restart methods can be implemented to store information about +the fix in restart files. If you wish an integrator or force +constraint fix to work with rRESPA (see the "run_style"_run_style.html +command), the initial_integrate, post_force_integrate, and +final_integrate_respa methods can be implemented. The thermo method +enables a fix to contribute values to thermodynamic output, as printed +quantities and/or to be summed to the potential energy of the system. diff --git a/doc/src/Modify_kspace.txt b/doc/src/Modify_kspace.txt new file mode 100644 index 0000000000000000000000000000000000000000..21407bf2e9af32f5aa836889ca40824845eb5b98 --- /dev/null +++ b/doc/src/Modify_kspace.txt @@ -0,0 +1,25 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Kspace styles :h3 + +Classes that compute long-range Coulombic interactions via K-space +representations (Ewald, PPPM) are derived from the KSpace class. New +styles can be created to add new K-space options to LAMMPS. + +Ewald.cpp is an example of computing K-space interactions. + +Here is a brief description of methods you define in your new derived +class. See kspace.h for details. + +init: initialize the calculation before a run +setup: computation before the 1st timestep of a run +compute: every-timestep computation +memory_usage: tally of memory usage :tb(s=:) + diff --git a/doc/src/Modify_min.txt b/doc/src/Modify_min.txt new file mode 100644 index 0000000000000000000000000000000000000000..5dcf0f1e6751899be88458220e188dde5e6f716a --- /dev/null +++ b/doc/src/Modify_min.txt @@ -0,0 +1,23 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Minimization styles :h3 + +Classes that perform energy minimization derived from the Min class. +New styles can be created to add new minimization algorithms to +LAMMPS. + +Min_cg.cpp is an example of conjugate gradient minimization. + +Here is a brief description of methods you define in your new derived +class. See min.h for details. + +init: initialize the minimization before a run +run: perform the minimization +memory_usage: tally of memory usage :tb(s=:) diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt new file mode 100644 index 0000000000000000000000000000000000000000..f9964d964b14d0ae81d219aab6891278e37a3f36 --- /dev/null +++ b/doc/src/Modify_overview.txt @@ -0,0 +1,101 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Overview :h3 + +The best way to add a new feature to LAMMPS is to find a similar +featureand look at the corresponding source and header files to figure +out what it does. You will need some knowledge of C++ to be able to +understand the hi-level structure of LAMMPS and its class +organization, but functions (class methods) that do actual +computations are written in vanilla C-style code and operate on simple +C-style data structures (vectors and arrays). + +Most of the new features described on the "Modify"_Modify.html doc +page require you to write a new C++ derived class (except for +exceptions described below, where you can make small edits to existing +files). Creating a new class requires 2 files, a source code file +(*.cpp) and a header file (*.h). The derived class must provide +certain methods to work as a new option. Depending on how different +your new feature is compared to existing features, you can either +derive from the base class itself, or from a derived class that +already exists. Enabling LAMMPS to invoke the new class is as simple +as putting the two source files in the src dir and re-building LAMMPS. + +The advantage of C++ and its object-orientation is that all the code +and variables needed to define the new feature are in the 2 files you +write, and thus shouldn't make the rest of LAMMPS more complex or +cause side-effect bugs. + +Here is a concrete example. Suppose you write 2 files pair_foo.cpp +and pair_foo.h that define a new class PairFoo that computes pairwise +potentials described in the classic 1997 "paper"_#Foo by Foo, et al. +If you wish to invoke those potentials in a LAMMPS input script with a +command like + +pair_style foo 0.1 3.5 :pre + +then your pair_foo.h file should be structured as follows: + +#ifdef PAIR_CLASS +PairStyle(foo,PairFoo) +#else +... +(class definition for PairFoo) +... +#endif :pre + +where "foo" is the style keyword in the pair_style command, and +PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h +files. + +When you re-build LAMMPS, your new pairwise potential becomes part of +the executable and can be invoked with a pair_style command like the +example above. Arguments like 0.1 and 3.5 can be defined and +processed by your new class. + +As illustrated by this pairwise example, many kinds of options are +referred to in the LAMMPS documentation as the "style" of a particular +command. + +The "Modify page"_Modify.html lists all the common styles in LAMMPS, +and discusses the header file for the base class that these styles are +derived from. Public variables in that file are ones used and set by +the derived classes which are also used by the base class. Sometimes +they are also used by the rest of LAMMPS. Virtual functions in the +base class header file which are set = 0 are ones you must define in +your new derived class to give it the functionality LAMMPS expects. +Virtual functions that are not set to 0 are functions you can +optionally define. + +Additionally, new output options can be added directly to the +thermo.cpp, dump_custom.cpp, and variable.cpp files. These are also +listed on the "Modify page"_Modify.html. + +Here are additional guidelines for modifying LAMMPS and adding new +functionality: + +Think about whether what you want to do would be better as a pre- or +post-processing step. Many computations are more easily and more +quickly done that way. :ulb,l + +Don't do anything within the timestepping of a run that isn't +parallel. E.g. don't accumulate a bunch of data on a single processor +and analyze it. You run the risk of seriously degrading the parallel +efficiency. :l + +If your new feature reads arguments or writes output, make sure you +follow the unit conventions discussed by the "units"_units.html +command. :l +:ule + +:line + +:link(Foo) +[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt new file mode 100644 index 0000000000000000000000000000000000000000..8c234dc62135f635bccc3e96ce93179cb901c569 --- /dev/null +++ b/doc/src/Modify_pair.txt @@ -0,0 +1,33 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Pair styles :h3 + +Classes that compute pairwise interactions are derived from the Pair +class. In LAMMPS, pairwise calculation include manybody potentials +such as EAM or Tersoff where particles interact without a static bond +topology. New styles can be created to add new pair potentials to +LAMMPS. + +Pair_lj_cut.cpp is a simple example of a Pair class, though it +includes some optional methods to enable its use with rRESPA. + +Here is a brief description of the class methods in pair.h: + +compute: workhorse routine that computes pairwise interactions +settings: reads the input script line with arguments you define +coeff: set coefficients for one i,j type pair +init_one: perform initialization for one i,j type pair +init_style: initialization specific to this pair style +write & read_restart: write/read i,j pair coeffs to restart files +write & read_restart_settings: write/read global settings to restart files +single: force and energy of a single pairwise interaction between 2 atoms +compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:) + +The inner/middle/outer routines are optional. diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt new file mode 100644 index 0000000000000000000000000000000000000000..9fbf359292b3e2edd95a3e1b6bd616c4336831a2 --- /dev/null +++ b/doc/src/Modify_region.txt @@ -0,0 +1,25 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Region styles :h3 + +Classes that define geometric regions are derived from the Region +class. Regions are used elsewhere in LAMMPS to group atoms, delete +atoms to create a void, insert atoms in a specified region, etc. New +styles can be created to add new region shapes to LAMMPS. + +Region_sphere.cpp is an example of a spherical region. + +Here is a brief description of methods you define in your new derived +class. See region.h for details. + +inside: determine whether a point is in the region +surface_interior: determine if a point is within a cutoff distance inside of surc +surface_exterior: determine if a point is within a cutoff distance outside of surf +shape_update : change region shape if set by time-dependent variable :tb(s=:) diff --git a/doc/src/Modify_thermo.txt b/doc/src/Modify_thermo.txt new file mode 100644 index 0000000000000000000000000000000000000000..001a9f99e108e2fb26285ee8a672f0a54d9f0097 --- /dev/null +++ b/doc/src/Modify_thermo.txt @@ -0,0 +1,35 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Thermodynamic output options :h3 + +There is one class that computes and prints thermodynamic information +to the screen and log file; see the file thermo.cpp. + +There are two styles defined in thermo.cpp: "one" and "multi". There +is also a flexible "custom" style which allows the user to explicitly +list keywords for quantities to print when thermodynamic info is +output. See the "thermo_style"_thermo_style.html command for a list +of defined quantities. + +The thermo styles (one, multi, etc) are simply lists of keywords. +Adding a new style thus only requires defining a new list of keywords. +Search for the word "customize" with references to "thermo style" in +thermo.cpp to see the two locations where code will need to be added. + +New keywords can also be added to thermo.cpp to compute new quantities +for output. Search for the word "customize" with references to +"keyword" in thermo.cpp to see the several locations where code will +need to be added. + +Note that the "thermo_style custom"_thermo.html command already allows +for thermo output of quantities calculated by "fixes"_fix.html, +"computes"_compute.html, and "variables"_variable.html. Thus, it may +be simpler to compute what you wish via one of those constructs, than +by adding a new keyword to the thermo command. diff --git a/doc/src/Modify_variable.txt b/doc/src/Modify_variable.txt new file mode 100644 index 0000000000000000000000000000000000000000..3c5b29cd1af5d234dd76b2d573bcc07d2eb8087f --- /dev/null +++ b/doc/src/Modify_variable.txt @@ -0,0 +1,46 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Variable options :h3 + +There is one class that computes and stores "variable"_variable.html +information in LAMMPS; see the file variable.cpp. The value +associated with a variable can be periodically printed to the screen +via the "print"_print.html, "fix print"_fix_print.html, or +"thermo_style custom"_thermo_style.html commands. Variables of style +"equal" can compute complex equations that involve the following types +of arguments: + +thermo keywords = ke, vol, atoms, ... +other variables = v_a, v_myvar, ... +math functions = div(x,y), mult(x,y), add(x,y), ... +group functions = mass(group), xcm(group,x), ... +atom values = x\[123\], y\[3\], vx\[34\], ... +compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre + +Adding keywords for the "thermo_style custom"_thermo_style.html +command (which can then be accessed by variables) is discussed on the +"Modify thermo"_Modify_thermo.html doc page. + +Adding a new math function of one or two arguments can be done by +editing one section of the Variable::evaluate() method. Search for +the word "customize" to find the appropriate location. + +Adding a new group function can be done by editing one section of the +Variable::evaluate() method. Search for the word "customize" to find +the appropriate location. You may need to add a new method to the +Group class as well (see the group.cpp file). + +Accessing a new atom-based vector can be done by editing one section +of the Variable::evaluate() method. Search for the word "customize" +to find the appropriate location. + +Adding new "compute styles"_compute.html (whose calculated values can +then be accessed by variables) is discussed on the "Modify +compute"_Modify_compute.html doc page. diff --git a/doc/src/PDF/USER-CGDNA-overview.pdf b/doc/src/PDF/USER-CGDNA-overview.pdf deleted file mode 100644 index e329877bc2cc5953574ea8fbd65789158a050879..0000000000000000000000000000000000000000 Binary files a/doc/src/PDF/USER-CGDNA-overview.pdf and /dev/null differ diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/USER-CGDNA.pdf new file mode 100644 index 0000000000000000000000000000000000000000..843bba00d5c5a707577d07dda1929ba4c8a07987 Binary files /dev/null and b/doc/src/PDF/USER-CGDNA.pdf differ diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 2d28758819a9a7a0dac700cd4a8239f51257b8e1..7f52367c82eec09a0465b356b326e996482a9bc3 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt new file mode 100644 index 0000000000000000000000000000000000000000..6498d030634a184f04d2a8a489a81949740789f2 --- /dev/null +++ b/doc/src/Packages.txt @@ -0,0 +1,39 @@ +"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Speed.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Optional packages :h2 + +This section gives an overview of the optional packages that extend +LAMMPS functionality. Packages are groups of files that enable a +specific set of features. For example, force fields for molecular +systems or rigid-body constraint are in packages. You can see the +list of all packages and "make" commands to manage them by typing +"make package" from within the src directory of the LAMMPS +distribution. "Section 2.3"_Section_start.html#start_3 gives general +info on how to install and un-install packages as part of the LAMMPS +build process. + + + + + +"Standard packages"_Packages_standard.html +"User packages"_Packages_user.html +"Details on each package"_Packages_details.html :ul + + diff --git a/doc/src/Section_packages.txt b/doc/src/Packages_details.txt similarity index 87% rename from doc/src/Section_packages.txt rename to doc/src/Packages_details.txt index ade75c588f071fc75fb85e35b9e28e304f693070..af18d097d9041654b2cc3b6c457bd4e487a82605 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Packages_details.txt @@ -1,6 +1,5 @@ -"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_accelerate.html :c +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -8,151 +7,89 @@ Section"_Section_accelerate.html :c :line -4. Packages :h2 - -This section gives an overview of the optional packages that extend -LAMMPS functionality with instructions on how to build LAMMPS with -each of them. Packages are groups of files that enable a specific set -of features. For example, force fields for molecular systems or -granular systems are in packages. You can see the list of all -packages and "make" commands to manage them by typing "make package" -from within the src directory of the LAMMPS distribution. "Section -2.3"_Section_start.html#start_3 gives general info on how to install -and un-install packages as part of the LAMMPS build process. - -There are two kinds of packages in LAMMPS, standard and user packages: - -"Table of standard packages"_#table_standard -"Table of user packages"_#table_user :ul - -Either of these kinds of packages may work as is, may require some -additional code compiled located in the lib folder, or may require -an external library to be downloaded, compiled, installed, and LAMMPS -configured to know about its location and additional compiler flags. -You can often do the build of the internal or external libraries -in one step by typing "make lib-name args='...'" from the src dir, -with appropriate arguments included in args='...'. If you just type -"make lib-name" you should see a help message about supported flags -and some examples. For more details about this, please study the -tables below and the sections about the individual packages. - -Standard packages are supported by the LAMMPS developers and are -written in a syntax and style consistent with the rest of LAMMPS. -This means the developers will answer questions about them, debug and -fix them if necessary, and keep them compatible with future changes to -LAMMPS. - -User packages have been contributed by users, and begin with the -"user" prefix. If they are a single command (single file), they are -typically in the user-misc package. User packages don't necessarily -meet the requirements of the standard packages. This means the -developers will try to keep things working and usually can answer -technical questions about compiling the package. If you have problems -using a feature provided in a user package, you may need to contact -the contributor directly to get help. Information on how to submit -additions you make to LAMMPS as single files or as a standard or user -package are given in "this section"_Section_modify.html#mod_15 of the -manual. - -Following the next two tables is a sub-section for each package. It -lists authors (if applicable) and summarizes the package contents. It -has specific instructions on how to install the package, including (if -necessary) downloading or building any extra library it requires. It -also gives links to documentation, example scripts, and -pictures/movies (if available) that illustrate use of the package. +Package details :h3 + +Here is a brief description of all the standard and user packages in +LAMMPS. It lists authors (if applicable) and summarizes the package +contents. It has specific instructions on how to install the package, +including, if necessary, info on how to download or build any extra +library it requires. It also gives links to documentation, example +scripts, and pictures/movies (if available) that illustrate use of the +package. NOTE: To see the complete list of commands a package adds to LAMMPS, -just look at the files in its src directory, e.g. "ls src/GRANULAR". -Files with names that start with fix, compute, atom, pair, bond, -angle, etc correspond to commands with the same style names. - -In these two tables, the "Example" column is a sub-directory in the -examples directory of the distribution which has an input script that -uses the package. E.g. "peptide" refers to the examples/peptide -directory; USER/atc refers to the examples/USER/atc directory. The -"Library" column indicates whether an extra library is needed to build -and use the package: - -dash = no library -sys = system library: you likely have it on your machine -int = internal library: provided with LAMMPS, but you may need to build it -ext = external library: you will need to download and install it on your machine :ul - -:line -:line - -[Standard packages] :link(table_standard),p - -Package, Description, Doc page, Example, Library -"ASPHERE"_#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, - -"BODY"_#BODY, body-style particles, "body"_body.html, body, - -"CLASS2"_#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, - -"COLLOID"_#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, - -"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys -"CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - -"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, - -"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int -"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, - -"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext -"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - -"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext -"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - -"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - -"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int -"MISC"_#MISC, miscellanous single-file commands, -, -, - -"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - -"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, - -"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext -"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, - -"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int -"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys -"QEQ"_#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, - -"REAX"_#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int -"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, - -"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, - -"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - -"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, - -"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - -"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) - -[USER packages] :link(table_user),p - -Package, Description, Doc page, Example, Library -"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int -"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int -"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, - -"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, - -"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int -"USER-DIFFRACTION"_#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, - -"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, - -"USER-DRUDE"_#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, - -"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, - -"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, - -"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext -"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - -"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - -"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - -"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, - -"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - -"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - -"USER-MOFFF"_#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, - -"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext -"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext -"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, - -"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext -"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, - -"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext -"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, - -"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext -"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - -"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - -"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - -"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - -"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) +you can examine the files in its src directory, e.g. "ls +src/GRANULAR". Files with names that start with fix, compute, atom, +pair, bond, angle, etc correspond to commands with the same style name +as contained in the file name. + +"ASPHERE"_#ASPHERE, +"BODY"_#BODY, +"CLASS2"_#CLASS2, +"COLLOID"_#COLLOID, +"COMPRESS"_#COMPRESS, +"CORESHELL"_#CORESHELL, +"DIPOLE"_#DIPOLE, +"GPU"_#GPU, +"GRANULAR"_#GRANULAR, +"KIM"_#KIM, +"KOKKOS"_#KOKKOS, +"KSPACE"_#KSPACE, +"LATTE"_#LATTE, +"MANYBODY"_#MANYBODY, +"MC"_#MC, +"MEAM"_#MEAM, +"MISC"_#MISC, +"MOLECULE"_#MOLECULE, +"MPIIO"_#MPIIO, +"MSCG"_#MSCG, +"OPT"_#OPT, +"PERI"_#PERI, +"POEMS"_#POEMS, +"PYTHON"_#PYTHON, +"QEQ"_#QEQ, +"REAX"_#REAX, +"REPLICA"_#REPLICA, +"RIGID"_#RIGID, +"SHOCK"_#SHOCK, +"SNAP"_#SNAP, +"SRD"_#SRD, +"VORONOI"_#VORONOI :tb(c=6,ea=c) + +"USER-ATC"_#USER-ATC, +"USER-AWPMD"_#USER-AWPMD, +"USER-BOCS"_#USER-BOCS, +"USER-CGDNA"_#USER-CGDNA, +"USER-CGSDK"_#USER-CGSDK, +"USER-COLVARS"_#USER-COLVARS, +"USER-DIFFRACTION"_#USER-DIFFRACTION, +"USER-DPD"_#USER-DPD, +"USER-DRUDE"_#USER-DRUDE, +"USER-EFF"_#USER-EFF, +"USER-FEP"_#USER-FEP, +"USER-H5MD"_#USER-H5MD, +"USER-INTEL"_#USER-INTEL, +"USER-LB"_#USER-LB, +"USER-MANIFOLD"_#USER-MANIFOLD, +"USER-MEAMC"_#USER-MEAMC, +"USER-MESO"_#USER-MESO, +"USER-MGPT"_#USER-MGPT, +"USER-MISC"_#USER-MISC, +"USER-MOFFF"_#USER-MOFFF, +"USER-MOLFILE"_#USER-MOLFILE, +"USER-NETCDF"_#USER-NETCDF, +"USER-OMP"_#USER-OMP, +"USER-PHONON"_#USER-PHONON, +"USER-QMMM"_#USER-QMMM, +"USER-QTB"_#USER-QTB, +"USER-QUIP"_#USER-QUIP, +"USER-REAXC"_#USER-REAXC, +"USER-SMD"_#USER-SMD, +"USER-SMTBQ"_#USER-SMTBQ, +"USER-SPH"_#USER-SPH, +"USER-TALLY"_#USER-TALLY, +"USER-UEF"_#USER-UEF, +"USER-VTK"_#USER-VTK :tb(c=6,ea=c) :line :line @@ -379,14 +316,14 @@ GPU package :link(GPU),h4 [Contents:] Dozens of pair styles and a version of the PPPM long-range Coulombic -solver optimized for GPUs. All such styles have a "gpu" as a -suffix in their style name. The GPU code can be compiled with either -CUDA or OpenCL, however the OpenCL variants are no longer actively -maintained and only the CUDA versions are regularly tested. -"Section 5.3.1"_accelerate_gpu.html gives details of what -hardware and GPU software is required on your system, -and details on how to build and use this package. Its styles can be -invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line +solver optimized for GPUs. All such styles have a "gpu" as a suffix +in their style name. The GPU code can be compiled with either CUDA or +OpenCL, however the OpenCL variants are no longer actively maintained +and only the CUDA versions are regularly tested. The "Speed +gpu"_Speed_gpu.html doc page gives details of what hardware and GPU +software is required on your system, and details on how to build and +use this package. Its styles can be invoked at run time via the "-sf +gpu" or "-suffix gpu" "command-line switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS package, which has GPU-enabled styles. @@ -452,8 +389,8 @@ GPU library. src/GPU: filenames -> commands src/GPU/README lib/gpu/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.1"_accelerate_gpu.html +"Speed packages"_Speed_packages.html +"Speed gpu"_Speed_gpu.html.html "Section 2.6 -sf gpu"_Section_start.html#start_6 "Section 2.6 -pk gpu"_Section_start.html#start_6 "package gpu"_package.html @@ -578,10 +515,10 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their -style name. "Section 5.3.3"_accelerate_kokkos.html gives details of -what hardware and software is required on your system, and how to -build and use this package. Its styles can be invoked at run time via -the "-sf kk" or "-suffix kk" "command-line +style name. The "Speed kokkos"_Speed_kokkos.html doc page gives +details of what hardware and software is required on your system, and +how to build and use this package. Its styles can be invoked at run +time via the "-sf kk" or "-suffix kk" "command-line switches"_Section_start.html#start_6. Also see the "GPU"_#GPU, "OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which have styles optimized for CPUs, KNLs, and GPUs. @@ -648,8 +585,8 @@ make machine :pre src/KOKKOS: filenames -> commands src/KOKKOS/README lib/kokkos/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.3"_accelerate_kokkos.html +"Speed packages"_Speed_packages.html +"Speed kokkos"_Speed_kokkos.html "Section 2.6 -k on ..."_Section_start.html#start_6 "Section 2.6 -sf kk"_Section_start.html#start_6 "Section 2.6 -pk kokkos"_Section_start.html#start_6 @@ -1047,9 +984,9 @@ OPT package :link(OPT),h4 A handful of pair styles which are optimized for improved CPU performance on single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials. The styles have an "opt" suffix in -their style name. "Section 5.3.5"_accelerate_opt.html gives details -of how to build and use this package. Its styles can be invoked at -run time via the "-sf opt" or "-suffix opt" "command-line +their style name. The "Speed opt"_Speed_opt.html doc page gives +details of how to build and use this package. Its styles can be +invoked at run time via the "-sf opt" or "-suffix opt" "command-line switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which have styles optimized for CPU performance. @@ -1075,8 +1012,8 @@ CCFLAGS: add -restrict for Intel compilers :ul [Supporting info:] src/OPT: filenames -> commands -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.5"_accelerate_opt.html +"Speed packages"_Speed_packages.html +"Speed opt"_Speed_opt.html "Section 2.6 -sf opt"_Section_start.html#start_6 Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul @@ -1625,6 +1562,43 @@ examples/USER/awpmd :ul :line +USER-BOCS package :link(USER-BOCS),h4 + +[Contents:] + +This package provides "fix bocs"_fix_bocs.html, a modified version +of "fix npt"_fix_nh.html which includes the pressure correction to +the barostat as outlined in: + +N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that +accurately describe the structure, pressure, and compressibility of +molecular liquids," J. Chem. Phys. 143, 243148 (2015). + +[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University) + +[Install or un-install:] + +make yes-user-bocs +make machine :pre + +make no-user-bocs +make machine :pre + +[Supporting info:] + +The USER-BOCS user package for LAMMPS is part of the BOCS software package: +"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS + +See the following reference for information about the entire package: + +Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG. +"BOCS: Bottom-Up Open-Source Coarse-Graining Software." +J. Phys. Chem. B. 122, 13, 3363-3377 (2018). + +Example inputs are in the examples/USER/bocs folder. + +:line + USER-CGDNA package :link(USER-CGDNA),h4 [Contents:] @@ -1995,8 +1969,8 @@ USER-INTEL package :link(USER-INTEL),h4 Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. "Section -5.3.2"_accelerate_intel.html gives details of what hardware and +All of them have an "intel" in their style name. The "Speed +intel"_Speed_intel.html doc page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf intel" or "-suffix intel" "command-line switches"_Section_start.html#start_6. @@ -2046,7 +2020,7 @@ hardware target, to produce a separate executable. You should also typically install the USER-OMP package, as it can be used in tandem with the USER-INTEL package to good effect, as -explained in "Section 5.3.2"_accelerate_intel.html. +explained on the "Speed intel"_Speed_intel.html doc page. make yes-user-intel yes-user-omp make machine :pre @@ -2058,8 +2032,8 @@ make machine :pre src/USER-INTEL: filenames -> commands src/USER-INTEL/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.2"_accelerate_gpu.html +"Speed packages"_Speed_packages.html +"Speed intel"_Speed_intel.html "Section 2.6 -sf intel"_Section_start.html#start_6 "Section 2.6 -pk intel"_Section_start.html#start_6 "package intel"_package.html @@ -2405,10 +2379,10 @@ USER-OMP package :link(USER-OMP),h4 Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace styles which are altered to enable threading on many-core CPUs via OpenMP directives. All of them have an "omp" in their style name. -"Section 5.3.4"_accelerate_omp.html gives details of what hardware and -compilers are required on your system, and how to build and use this -package. Its styles can be invoked at run time via the "-sf omp" or -"-suffix omp" "command-line switches"_Section_start.html#start_6. +The "Speed omp"_Speed_omp.html doc page gives details of what hardware +and compilers are required on your system, and how to build and use +this package. Its styles can be invoked at run time via the "-sf omp" +or "-suffix omp" "command-line switches"_Section_start.html#start_6. Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-INTEL"_#USER-INTEL packages, which have styles optimized for CPUs. @@ -2443,8 +2417,8 @@ LINKFLAGS: add -fopenmp :ul src/USER-OMP: filenames -> commands src/USER-OMP/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.4"_accelerate_omp.html +"Speed packages"_Speed_packages.html +"Speed omp"_Speed_omp.html "Section 2.6 -sf omp"_Section_start.html#start_6 "Section 2.6 -pk omp"_Section_start.html#start_6 "package omp"_package.html diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt new file mode 100644 index 0000000000000000000000000000000000000000..095bf699a62b0dd3eca98952bcff2e7230ae498c --- /dev/null +++ b/doc/src/Packages_standard.txt @@ -0,0 +1,65 @@ +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Standard packages :h3 + +This is the list of standard packages in LAMMPS. The link for each +package name gives more details. + +Standard packages are supported by the LAMMPS developers and are +written in a syntax and style consistent with the rest of LAMMPS. +This means the developers will answer questions about them, debug and +fix them if necessary, and keep them compatible with future changes to +LAMMPS. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; USER/atc +refers to the examples/USER/atc directory. The "Library" column +indicates whether an extra library is needed to build and use the +package: + +dash = no library +sys = system library: you likely have it on your machine +int = internal library: provided with LAMMPS, but you may need to build it +ext = external library: you will need to download and install it on your machine :ul + +Package, Description, Doc page, Example, Library +"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, - +"BODY"_Packages_details.html#BODY, body-style particles, "body"_body.html, body, - +"CLASS2"_Packages_details.html#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, - +"COLLOID"_Packages_details.html#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, - +"COMPRESS"_Packages_details.html#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys +"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - +"DIPOLE"_Packages_details.html#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, - +"GPU"_Packages_details.html#GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int +"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, - +"KIM"_Packages_details.html#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext +"KOKKOS"_Packages_details.html#KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"KSPACE"_Packages_details.html#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - +"LATTE"_Packages_details.html#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext +"MANYBODY"_Packages_details.html#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - +"MC"_Packages_details.html#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - +"MEAM"_Packages_details.html#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int +"MISC"_Packages_details.html#MISC, miscellanous single-file commands, -, -, - +"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - +"MPIIO"_Packages_details.html#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, - +"MSCG"_Packages_details.html#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext +"OPT"_Packages_details.html#OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"PERI"_Packages_details.html#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, - +"POEMS"_Packages_details.html#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int +"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys +"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, - +"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int +"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, - +"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, - +"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - +"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, - +"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - +"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt new file mode 100644 index 0000000000000000000000000000000000000000..73c7fdb65d95e084f5e4fdcf1df0458f1687ecc8 --- /dev/null +++ b/doc/src/Packages_user.txt @@ -0,0 +1,74 @@ +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +User packages :h3 + +This is a list of user packages in LAMMPS. The link for each package +name gives more details. + +User packages have been contributed by users, and begin with the +"user" prefix. If a contribution is a single command (single file), +it is typically in the user-misc package. User packages don't +necessarily meet the requirements of the "standard +packages"_Packages_standard.html. This means the developers will try +to keep things working and usually can answer technical questions +about compiling the package. If you have problems using a specific +feature provided in a user package, you may need to contact the +contributor directly to get help. Information on how to submit +additions you make to LAMMPS as single files or as a standard or user +package is explained on the "Modify contribute"_Modify_contribute.html +doc page. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; USER/atc +refers to the examples/USER/atc directory. The "Library" column +indicates whether an extra library is needed to build and use the +package: + +dash = no library +sys = system library: you likely have it on your machine +int = internal library: provided with LAMMPS, but you may need to build it +ext = external library: you will need to download and install it on your machine :ul + +Package, Description, Doc page, Example, Library +"USER-ATC"_Packages_details.html#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int +"USER-AWPMD"_Packages_details.html#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int +"USER-BOCS"_Packages_details.html#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, - +"USER-CGDNA"_Packages_details.html#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, - +"USER-CGSDK"_Packages_details.html#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, - +"USER-COLVARS"_Packages_details.html#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int +"USER-DIFFRACTION"_Packages_details.html#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, - +"USER-DPD"_Packages_details.html#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, - +"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, - +"USER-EFF"_Packages_details.html#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, - +"USER-FEP"_Packages_details.html#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, - +"USER-H5MD"_Packages_details.html#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext +"USER-INTEL"_Packages_details.html#USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"USER-LB"_Packages_details.html#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - +"USER-MANIFOLD"_Packages_details.html#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - +"USER-MEAMC"_Packages_details.html#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - +"USER-MESO"_Packages_details.html#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, - +"USER-MGPT"_Packages_details.html#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - +"USER-MISC"_Packages_details.html#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - +"USER-MOFFF"_Packages_details.html#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, - +"USER-MOLFILE"_Packages_details.html#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext +"USER-NETCDF"_Packages_details.html#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext +"USER-OMP"_Packages_details.html#USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"USER-PHONON"_Packages_details.html#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, - +"USER-QMMM"_Packages_details.html#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext +"USER-QTB"_Packages_details.html#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, - +"USER-QUIP"_Packages_details.html#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext +"USER-REAXC"_Packages_details.html#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, - +"USER-SMD"_Packages_details.html#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext +"USER-SMTBQ"_Packages_details.html#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - +"USER-SPH"_Packages_details.html#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - +"USER-TALLY"_Packages_details.html#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - +"USER-UEF"_Packages_details.html#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - +"USER-VTK"_Packages_details.html#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) diff --git a/doc/src/Python.txt b/doc/src/Python.txt new file mode 100644 index 0000000000000000000000000000000000000000..169670d669da6bbfcbdcb9adb491276819685f9f --- /dev/null +++ b/doc/src/Python.txt @@ -0,0 +1,79 @@ +"Previous Section"_Modify.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Errors.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Use Python with LAMMPS :h2 + +These doc pages describe various ways that LAMMPS and Python can be +used together. + + + + + +"Overview of Python and LAMMPS"_Python_overview.html :all(b) + +"Run LAMMPS from Python"_Python_run.html +"Build LAMMPS as a shared library"_Python_shlib.html +"Install LAMMPS in Python"_Python_install.html +"Extend Python to run in parallel"_Python_mpi.html +"Test the Python/LAMMPS interface"_Python_test.html +"Python library interface"_Python_library.html +"PyLammps interface"_Python_pylammps.html +"Example Python scripts that use LAMMPS"_Python_examples.html :all(b) + +"Call Python from a LAMMPS input script"_Python_call.html :all(b) + + + +If you're not familiar with "Python"_http://www.python.org, it's a +powerful scripting and programming language which can do most +everything that lower-level languages like C or C++ can do in fewer +lines of code. The only drawback is slower execution speed. Python +is also easy to use as a "glue" language to drive a program through +its library interface, or to hook multiple pieces of software +together, such as a simulation code plus a visualization tool, or to +run a coupled multiscale or multiphysics model. + +See the "Howto_couple"_Howto_couple.html doc page for more ideas about +coupling LAMMPS to other codes. See the "Howto +library"_Howto_library.html doc page for a description of the LAMMPS +library interface provided in src/library.h and src/library.h. That +interface is exposed to Python either when calling LAMMPS from Python +or when calling Python from a LAMMPS input script and then calling +back to LAMMPS from Python code. The library interface is designed to +be easy to add funcionality to. Thus the Python interface to LAMMPS +is also easy to extend as well. + +If you create interesting Python scripts that run LAMMPS or +interesting Python functions that can be called from a LAMMPS input +script, that you think would be genearlly useful, please post them as +a pull request to our "GitHub site"_https://github.com/lammps/lammps, +and they can be added to the LAMMPS distribution or webpage. diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e30a5a7c7e7d831413c1e532de421d40555fdd0 --- /dev/null +++ b/doc/src/Python_call.txt @@ -0,0 +1,85 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Call Python from a LAMMPS input script :h3 + +LAMMPS has several commands which can be used to invoke Python +code directly from an input script: + +"python"_python.html +"variable python"_variable.html +"fix python/invoke"_fix_python_invoke.html +"pair_style python"_pair_python.html :ul + +The "python"_python.html command which can be used to define and +execute a Python function that you write the code for. The Python +function can also be assigned to a LAMMPS python-style variable via +the "variable"_variable.html command. Each time the variable is +evaluated, either in the LAMMPS input script itself, or by another +LAMMPS command that uses the variable, this will trigger the Python +function to be invoked. + +The Python code for the function can be included directly in the input +script or in an auxiliary file. The function can have arguments which +are mapped to LAMMPS variables (also defined in the input script) and +it can return a value to a LAMMPS variable. This is thus a mechanism +for your input script to pass information to a piece of Python code, +ask Python to execute the code, and return information to your input +script. + +Note that a Python function can be arbitrarily complex. It can import +other Python modules, instantiate Python classes, call other Python +functions, etc. The Python code that you provide can contain more +code than the single function. It can contain other functions or +Python classes, as well as global variables or other mechanisms for +storing state between calls from LAMMPS to the function. + +The Python function you provide can consist of "pure" Python code that +only performs operations provided by standard Python. However, the +Python function can also "call back" to LAMMPS through its +Python-wrapped library interface, in the manner described in the +"Python run"_Python_run.html doc page. This means it can issue LAMMPS +input script commands or query and set internal LAMMPS state. As an +example, this can be useful in an input script to create a more +complex loop with branching logic, than can be created using the +simple looping and branching logic enabled by the "next"_next.html and +"if"_if.html commands. + +See the "python"_python.html doc page and the "variable"_variable.html +doc page for its python-style variables for more info, including +examples of Python code you can write for both pure Python operations +and callbacks to LAMMPS. + +The "fix python/invoke"_fix_python_invoke.html command can execute +Python code at selected timesteps during a simulation run. + +The "pair_style python"_pair_python command allows you to define +pairwise potentials as python code which encodes a single pairwise +interaction. This is useful for rapid-developement and debugging of a +new potential. + +To use any of these commands, you only need to build LAMMPS with the +PYTHON package installed: + +make yes-python +make machine :pre + +Note that this will link LAMMPS with the Python library on your +system, which typically requires several auxiliary system libraries to +also be linked. The list of these libraries and the paths to find +them are specified in the lib/python/Makefile.lammps file. You need +to insure that file contains the correct information for your version +of Python and your machine to successfully build LAMMPS. See the +lib/python/README file for more info. + +If you want to write Python code with callbacks to LAMMPS, then you +must also follow the steps overviewed in the "Python +run"_Python_run.html doc page. I.e. you must build LAMMPS as a shared +library and insure that Python can find the python/lammps.py file and +the shared library. diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt new file mode 100644 index 0000000000000000000000000000000000000000..fbca381e8b0f1cc4084e491162f2dad6dd7ddb36 --- /dev/null +++ b/doc/src/Python_examples.txt @@ -0,0 +1,81 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Example Python scripts that use LAMMPS :h3 + +These are the Python scripts included as demos in the python/examples +directory of the LAMMPS distribution, to illustrate the kinds of +things that are possible when Python wraps LAMMPS. If you create your +own scripts, send them to us and we can include them in the LAMMPS +distribution. + +trivial.py, read/run a LAMMPS input script thru Python, +demo.py, invoke various LAMMPS library interface routines, +simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, +split.py, same as simple.py but running in parallel on a subset of procs, +gui.py, GUI go/stop/temperature-slider to control LAMMPS, +plot.py, real-time temperature plot with GnuPlot via Pizza.py, +viz_tool.py, real-time viz via some viz package, +vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) + +:line + +For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" +with "gl" or "atomeye" or "pymol" or "vmd", depending on what +visualization package you have installed. + +Note that for GL, you need to be able to run the Pizza.py GL tool, +which is included in the pizza sub-directory. See the "Pizza.py doc +pages"_pizza for more info: + +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) + +Note that for AtomEye, you need version 3, and there is a line in the +scripts that specifies the path and name of the executable. See the +AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details: + +http://mt.seas.upenn.edu/Archive/Graphics/A +http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre + +:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) +:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) + +The latter link is to AtomEye 3 which has the scriping +capability needed by these Python scripts. + +Note that for PyMol, you need to have built and installed the +open-source version of PyMol in your Python, so that you can import it +from a Python script. See the PyMol WWW pages "here"_pymolhome or +"here"_pymolopen for more details: + +http://www.pymol.org +http://sourceforge.net/scm/?type=svn&group_id=4546 :pre + +:link(pymolhome,http://www.pymol.org) +:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) + +The latter link is to the open-source version. + +Note that for VMD, you need a fairly current version (1.8.7 works for +me) and there are some lines in the pizza/vmd.py script for 4 PIZZA +variables that have to match the VMD installation on your system. + +:line + +See the python/README file for instructions on how to run them and the +source code for individual scripts for comments about what they do. + +Here are screenshots of the vizplotgui_tool.py script in action for +different visualization package options. Click to see larger images: + +:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg) +:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg) +:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg) +:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg) + diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt new file mode 100644 index 0000000000000000000000000000000000000000..631f6c4a7f1a3a40245e3d7ab98b7b195bb4fefc --- /dev/null +++ b/doc/src/Python_install.txt @@ -0,0 +1,74 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Installing LAMMPS in Python :h3 + +For Python to invoke LAMMPS, there are 2 files it needs to know about: + +python/lammps.py +src/liblammps.so :ul + +Lammps.py is the Python wrapper on the LAMMPS library interface. +Liblammps.so is the shared LAMMPS library that Python loads, as +described above. + +You can insure Python can find these files in one of two ways: + +set two environment variables +run the python/install.py script :ul + +If you set the paths to these files as environment variables, you only +have to do it once. For the csh or tcsh shells, add something like +this to your ~/.cshrc file, one line for each of the two files: + +setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python +setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre + +If you use the python/install.py script, you need to invoke it every +time you rebuild LAMMPS (as a shared library) or make changes to the +python/lammps.py file. + +You can invoke install.py from the python directory as + +% python install.py \[libdir\] \[pydir\] :pre + +The optional libdir is where to copy the LAMMPS shared library to; the +default is /usr/local/lib. The optional pydir is where to copy the +lammps.py file to; the default is the site-packages directory of the +version of Python that is running the install script. + +Note that libdir must be a location that is in your default +LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a +location that Python looks in by default for imported modules, like +its site-packages dir. If you want to copy these files to +non-standard locations, such as within your own user space, you will +need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables +accordingly, as above. + +If the install.py script does not allow you to copy files into system +directories, prefix the python command with "sudo". If you do this, +make sure that the Python that root runs is the same as the Python you +run. E.g. you may need to do something like + +% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre + +You can also invoke install.py from the make command in the src +directory as + +% make install-python :pre + +In this mode you cannot append optional arguments. Again, you may +need to prefix this with "sudo". In this mode you cannot control +which Python is invoked by root. + +Note that if you want Python to be able to load different versions of +the LAMMPS shared library (see "this section"_#py_5 below), you will +need to manually copy files like liblammps_g++.so into the appropriate +system directory. This is not needed if you set the LD_LIBRARY_PATH +environment variable as described above. diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt new file mode 100644 index 0000000000000000000000000000000000000000..4babbb746cc3c1753f85ef6f5146dfdc51e8ee9a --- /dev/null +++ b/doc/src/Python_library.txt @@ -0,0 +1,256 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Python library interface :h3 + +As described previously, the Python interface to LAMMPS consists of a +Python "lammps" module, the source code for which is in +python/lammps.py, which creates a "lammps" object, with a set of +methods that can be invoked on that object. The sample Python code +below assumes you have first imported the "lammps" module in your +Python script, as follows: + +from lammps import lammps :pre + +These are the methods defined by the lammps module. If you look at +the files src/library.cpp and src/library.h you will see they +correspond one-to-one with calls you can make to the LAMMPS library +from a C++ or C or Fortran program, and which are described in +"Section 6.19"_Section_howto.html#howto_19 of the manual. + +The python/examples directory has Python scripts which show how Python +can run LAMMPS, grab data, change it, and put it back into LAMMPS. + +lmp = lammps() # create a LAMMPS object using the default liblammps.so library + # 4 optional args are allowed: name, cmdargs, ptr, comm +lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object +lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later +lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library +lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre + +lmp.close() # destroy a LAMMPS object :pre + +version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre + +lmp.file(file) # run an entire input script, file = "in.lj" +lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" +lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"] +lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre + +size = lmp.extract_setting(name) # return data type info :pre + +xlo = lmp.extract_global(name,type) # extract a global quantity + # name = "boxxlo", "nlocal", etc + # type = 0 = int + # 1 = double :pre + +boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre + +coords = lmp.extract_atom(name,type) # extract a per-atom quantity + # name = "x", "type", etc + # type = 0 = vector of ints + # 1 = array of ints + # 2 = vector of doubles + # 3 = array of doubles :pre + +eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute +v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix + # id = ID of compute or fix + # style = 0 = global data + # 1 = per-atom data + # 2 = local data + # type = 0 = scalar + # 1 = vector + # 2 = array + # i,j = indices of value in global vector or array :pre + +var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable + # name = name of variable + # group = group ID (ignored for equal-style variables) + # flag = 0 = equal-style variable + # 1 = atom-style variable :pre + +value = lmp.get_thermo(name) # return current value of a thermo keyword +natoms = lmp.get_natoms() # total # of atoms as int :pre + +flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful +lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre + +data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID + # name = "x", "charge", "type", etc +data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered) +data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre + +lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID + # name = "x", "charge", "type", etc + # count = # of per-atom values, 1 or 3, etc :pre +lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre + +lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre + +:line + +The lines + +from lammps import lammps +lmp = lammps() :pre + +create an instance of LAMMPS, wrapped in a Python class by the lammps +Python module, and return an instance of the Python class as lmp. It +is used to make all subsequent calls to the LAMMPS library. + +Additional arguments to lammps() can be used to tell Python the name +of the shared library to load or to pass arguments to the LAMMPS +instance, the same as if LAMMPS were launched from a command-line +prompt. + +If the ptr argument is set like this: + +lmp = lammps(ptr=lmpptr) :pre + +then lmpptr must be an argument passed to Python via the LAMMPS +"python"_python.html command, when it is used to define a Python +function that is invoked by the LAMMPS input script. This mode of +calling Python from LAMMPS is described in the "Python +call"_Python_call.html doc page. The variable lmpptr refers to the +instance of LAMMPS that called the embedded Python interpreter. Using +it as an argument to lammps() allows the returned Python class +instance "lmp" to make calls to that instance of LAMMPS. See the +"python"_python.html command doc page for examples using this syntax. + +Note that you can create multiple LAMMPS objects in your Python +script, and coordinate and run multiple simulations, e.g. + +from lammps import lammps +lmp1 = lammps() +lmp2 = lammps() +lmp1.file("in.file1") +lmp2.file("in.file2") :pre + +The file(), command(), commands_list(), commands_string() methods +allow an input script, a single command, or multiple commands to be +invoked. + +The extract_setting(), extract_global(), extract_box(), +extract_atom(), extract_compute(), extract_fix(), and +extract_variable() methods return values or pointers to data +structures internal to LAMMPS. + +For extract_global() see the src/library.cpp file for the list of +valid names. New names could easily be added. A double or integer is +returned. You need to specify the appropriate data type via the type +argument. + +For extract_atom(), a pointer to internal LAMMPS atom-based data is +returned, which you can use via normal Python subscripting. See the +extract() method in the src/atom.cpp file for a list of valid names. +Again, new names could easily be added if the property you want is not +listed. A pointer to a vector of doubles or integers, or a pointer to +an array of doubles (double **) or integers (int **) is returned. You +need to specify the appropriate data type via the type argument. + +For extract_compute() and extract_fix(), the global, per-atom, or +local data calculated by the compute or fix can be accessed. What is +returned depends on whether the compute or fix calculates a scalar or +vector or array. For a scalar, a single double value is returned. If +the compute or fix calculates a vector or array, a pointer to the +internal LAMMPS data is returned, which you can use via normal Python +subscripting. The one exception is that for a fix that calculates a +global vector or array, a single double value from the vector or array +is returned, indexed by I (vector) or I and J (array). I,J are +zero-based indices. The I,J arguments can be left out if not needed. +See "Section 6.15"_Section_howto.html#howto_15 of the manual for a +discussion of global, per-atom, and local data, and of scalar, vector, +and array data types. See the doc pages for individual +"computes"_compute.html and "fixes"_fix.html for a description of what +they calculate and store. + +For extract_variable(), an "equal-style or atom-style +variable"_variable.html is evaluated and its result returned. + +For equal-style variables a single double value is returned and the +group argument is ignored. For atom-style variables, a vector of +doubles is returned, one value per atom, which you can use via normal +Python subscripting. The values will be zero for atoms not in the +specified group. + +The get_thermo() method returns returns the current value of a thermo +keyword as a float. + +The get_natoms() method returns the total number of atoms in the +simulation, as an int. + +The set_variable() methosd sets an existing string-style variable to a +new string value, so that subsequent LAMMPS commands can access the +variable. + +The reset_box() emthods resets the size and shape of the simulation +box, e.g. as part of restoring a previously extracted and saved state +of a simulation. + +The gather methods collect peratom info of the requested type (atom +coords, atom types, forces, etc) from all processors, and returns the +same vector of values to each callling processor. The scatter +functions do the inverse. They distribute a vector of peratom values, +passed by all calling processors, to invididual atoms, which may be +owned by different processos. + +Note that the data returned by the gather methods, +e.g. gather_atoms("x"), is different from the data structure returned +by extract_atom("x") in four ways. (1) Gather_atoms() returns a +vector which you index as x\[i\]; extract_atom() returns an array +which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms +by atom ID while extract_atom() does not. (3) Gather_atoms() returns +a list of all atoms in the simulation; extract_atoms() returns just +the atoms local to each processor. (4) Finally, the gather_atoms() +data structure is a copy of the atom coords stored internally in +LAMMPS, whereas extract_atom() returns an array that effectively +points directly to the internal data. This means you can change +values inside LAMMPS from Python by assigning a new values to the +extract_atom() array. To do this with the gather_atoms() vector, you +need to change values in the vector, then invoke the scatter_atoms() +method. + +For the scatter methods, the array of coordinates passed to must be a +ctypes vector of ints or doubles, allocated and initialized something +like this: + +from ctypes import * +natoms = lmp.get_natoms() +n3 = 3*natoms +x = (n3*c_double)() +x\[0\] = x coord of atom with ID 1 +x\[1\] = y coord of atom with ID 1 +x\[2\] = z coord of atom with ID 1 +x\[3\] = x coord of atom with ID 2 +... +x\[n3-1\] = z coord of atom with ID natoms +lmp.scatter_atoms("x",1,3,x) :pre + +Alternatively, you can just change values in the vector returned by +the gather methods, since they are also ctypes vectors. + +:line + +As noted above, these Python class methods correspond one-to-one with +the functions in the LAMMPS library interface in src/library.cpp and +library.h. This means you can extend the Python wrapper via the +following steps: + +Add a new interface function to src/library.cpp and +src/library.h. :ulb,l + +Rebuild LAMMPS as a shared library. :l + +Add a wrapper method to python/lammps.py for this interface +function. :l + +You should now be able to invoke the new interface function from a +Python script. :l +:ule diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt new file mode 100644 index 0000000000000000000000000000000000000000..8377bbb3d0a0ac058c1f97274ba7fe7ba054b648 --- /dev/null +++ b/doc/src/Python_mpi.txt @@ -0,0 +1,67 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Extending Python to run in parallel :h3 + +If you wish to run LAMMPS in parallel from Python, you need to extend +your Python with an interface to MPI. This also allows you to +make MPI calls directly from Python in your script, if you desire. + +We recommend use of mpi4py: + +"PyPar"_https://github.com/daleroberts/pypar :ul + +As of version 2.0.0 it allows passing a custom MPI communicator to +the LAMMPS constructor, which means one can easily run one or more +LAMMPS instances on subsets of the total MPI ranks. + +To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it +and from its main directory, type + +python setup.py build +sudo python setup.py install :pre + +Again, the "sudo" is only needed if required to copy mpi4py files into +your Python distribution's site-packages directory. To install with +user privilege into the user local directory type + +python setup.py install --user :pre + +If you have successfully installed mpi4py, you should be able to run +Python and type + +from mpi4py import MPI :pre + +without error. You should also be able to run python in parallel +on a simple test script + +% mpirun -np 4 python test.py :pre + +where test.py contains the lines + +from mpi4py import MPI +comm = MPI.COMM_WORLD +print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre + +and see one line of output for each processor you run on. + +NOTE: To use mpi4py and LAMMPS in parallel from Python, you must +insure both are using the same version of MPI. If you only have one +MPI installed on your system, this is not an issue, but it can be if +you have multiple MPIs. Your LAMMPS build is explicit about which MPI +it is using, since you specify the details in your lo-level +src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find +information about the MPI it uses to build against. And it tries to +load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find +the MPI library that LAMMPS is using. If you have problems running +both mpi4py and LAMMPS together, this is an issue you may need to +address, e.g. by moving other MPI installations so that mpi4py finds +the right one. + + diff --git a/doc/src/Python_overview.txt b/doc/src/Python_overview.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5d6a469ffdaffddfe5347e1c5ecaec0be5257cb --- /dev/null +++ b/doc/src/Python_overview.txt @@ -0,0 +1,35 @@ +"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Tools.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +Overview of Python and LAMMPS :h3 + +LAMMPS can work together with Python in three ways. First, Python can +wrap LAMMPS through the its "library interface"_Howto_library.html, so +that a Python script can create one or more instances of LAMMPS and +launch one or more simulations. In Python lingo, this is "extending" +Python with LAMMPS. + +Second, a lower-level Python interface can be used indirectly through +provided PyLammps and IPyLammps wrapper classes, written in Python. +These wrappers try to simplify the usage of LAMMPS in Python by +providing an object-based interface to common LAMMPS functionality. +They also reduces the amount of code necessary to parameterize LAMMPS +scripts through Python and make variables and computes directly +accessible. + +Third, LAMMPS can use the Python interpreter, so that a LAMMPS +input script can invoke Python code directly, and pass information +back-and-forth between the input script and Python functions you +write. This Python code can also callback to LAMMPS to query or change +its attributes. In Python lingo, this is "embedding" Python in +LAMMPS. When used in this mode, Python can perform operations that +the simple LAMMPS input script syntax cannot. + + diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt new file mode 100644 index 0000000000000000000000000000000000000000..ad5ed192ee669f0b14fcaa10ccd9097391e74f54 --- /dev/null +++ b/doc/src/Python_pylammps.txt @@ -0,0 +1,14 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +PyLammps interface :h3 + +PyLammps is a Python wrapper class which can be created on its own or +use an existing lammps Python object. It has its own "PyLammps +Tutorial"_tutorial_pylammps.html doc page. diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt new file mode 100644 index 0000000000000000000000000000000000000000..03ab2ed3d7dc3e6b4703c78950978323835c394d --- /dev/null +++ b/doc/src/Python_run.txt @@ -0,0 +1,40 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Run LAMMPS from Python :h3 + +The LAMMPS distribution includes a python directory with all you need +to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS +library interface, with one wrapper function per LAMMPS library +function. This file makes it is possible to do the following either +from a Python script, or interactively from a Python prompt: create +one or more instances of LAMMPS, invoke LAMMPS commands or give it an +input script, run LAMMPS incrementally, extract LAMMPS results, an +modify internal LAMMPS variables. From a Python script you can do +this in serial or parallel. Running Python interactively in parallel +does not generally work, unless you have a version of Python that +extends Python to enable multiple instances of Python to read what you +type. + +To do all of this, you must first build LAMMPS as a shared library, +then insure that your Python can find the python/lammps.py file and +the shared library. + +Two advantages of using Python to run LAMMPS are how concise the +language is, and that it can be run interactively, enabling rapid +development and debugging. If you use it to mostly invoke costly +operations within LAMMPS, such as running a simulation for a +reasonable number of timesteps, then the overhead cost of invoking +LAMMPS thru Python will be negligible. + +The Python wrapper for LAMMPS uses the "ctypes" package in Python, +which auto-generates the interface code needed between Python and a +set of C-style library functions. Ctypes is part of standard Python +for versions 2.5 and later. You can check which version of Python you +have by simply typing "python" at a shell prompt. diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt new file mode 100644 index 0000000000000000000000000000000000000000..1aafbe2e847e3b486f10b7991b85bbea9009d45b --- /dev/null +++ b/doc/src/Python_shlib.txt @@ -0,0 +1,34 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Build LAMMPS as a shared library :h3 + +Instructions on how to build LAMMPS as a shared library are given in +"Section 2.4"_Section_start.html#start_4. A shared library is one +that is dynamically loadable, which is what Python requires to wrap +LAMMPS. On Linux this is a library file that ends in ".so", not ".a". + +From the src directory, type + +make foo mode=shlib :pre + +where foo is the machine target name, such as mpi or serial. +This should create the file liblammps_foo.so in the src directory, as +well as a soft link liblammps.so, which is what the Python wrapper will +load by default. Note that if you are building multiple machine +versions of the shared library, the soft link is always set to the +most recently built version. + +NOTE: If you are building LAMMPS with an MPI or FFT library or other +auxiliary libraries (used by various packages), then all of these +extra libraries must also be shared libraries. If the LAMMPS +shared-library build fails with an error complaining about this, see +"Section 2.4"_Section_start.html#start_4 for more details. + +Also include CMake info on this diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f361a500b6c8ba12748fed18b61af3c81d9028b --- /dev/null +++ b/doc/src/Python_test.txt @@ -0,0 +1,131 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Test the Python/LAMMPS interface :h3 + +To test if LAMMPS is callable from Python, launch Python interactively +and type: + +>>> from lammps import lammps +>>> lmp = lammps() :pre + +If you get no errors, you're ready to use LAMMPS from Python. If the +2nd command fails, the most common error to see is + +OSError: Could not load LAMMPS dynamic library :pre + +which means Python was unable to load the LAMMPS shared library. This +typically occurs if the system can't find the LAMMPS shared library or +one of the auxiliary shared libraries it depends on, or if something +about the library is incompatible with your Python. The error message +should give you an indication of what went wrong. + +You can also test the load directly in Python as follows, without +first importing from the lammps.py file: + +>>> from ctypes import CDLL +>>> CDLL("liblammps.so") :pre + +If an error occurs, carefully go thru the steps in "Section +2.4"_Section_start.html#start_4 and above about building a shared +library and about insuring Python can find the necessary two files +it needs. + +[Test LAMMPS and Python in serial:] :h4 + +To run a LAMMPS test in serial, type these lines into Python +interactively from the bench directory: + +>>> from lammps import lammps +>>> lmp = lammps() +>>> lmp.file("in.lj") :pre + +Or put the same lines in the file test.py and run it as + +% python test.py :pre + +Either way, you should see the results of running the in.lj benchmark +on a single processor appear on the screen, the same as if you had +typed something like: + +lmp_g++ -in in.lj :pre + +[Test LAMMPS and Python in parallel:] :h4 + +To run LAMMPS in parallel, assuming you have installed the +"PyPar"_https://github.com/daleroberts/pypar package as discussed +above, create a test.py file containing these lines: + +import pypar +from lammps import lammps +lmp = lammps() +lmp.file("in.lj") +print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp +pypar.finalize() :pre + +To run LAMMPS in parallel, assuming you have installed the +"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed +above, create a test.py file containing these lines: + +from mpi4py import MPI +from lammps import lammps +lmp = lammps() +lmp.file("in.lj") +me = MPI.COMM_WORLD.Get_rank() +nprocs = MPI.COMM_WORLD.Get_size() +print "Proc %d out of %d procs has" % (me,nprocs),lmp +MPI.Finalize() :pre + +You can either script in parallel as: + +% mpirun -np 4 python test.py :pre + +and you should see the same output as if you had typed + +% mpirun -np 4 lmp_g++ -in in.lj :pre + +Note that if you leave out the 3 lines from test.py that specify PyPar +commands you will instantiate and run LAMMPS independently on each of +the P processors specified in the mpirun command. In this case you +should get 4 sets of output, each showing that a LAMMPS run was made +on a single processor, instead of one set of output showing that +LAMMPS ran on 4 processors. If the 1-processor outputs occur, it +means that PyPar is not working correctly. + +Also note that once you import the PyPar module, PyPar initializes MPI +for you, and you can use MPI calls directly in your Python script, as +described in the PyPar documentation. The last line of your Python +script should be pypar.finalize(), to insure MPI is shut down +correctly. + +[Running Python scripts:] :h4 + +Note that any Python script (not just for LAMMPS) can be invoked in +one of several ways: + +% python foo.script +% python -i foo.script +% foo.script :pre + +The last command requires that the first line of the script be +something like this: + +#!/usr/local/bin/python +#!/usr/local/bin/python -i :pre + +where the path points to where you have Python installed, and that you +have made the script file executable: + +% chmod +x foo.script :pre + +Without the "-i" flag, Python will exit when the script finishes. +With the "-i" flag, you will be left in the Python interpreter when +the script finishes, so you can type subsequent commands. As +mentioned above, you can only run Python interactively when running +Python on a single processor, not in parallel. diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt deleted file mode 100644 index d5cbf77a84e2881a7cfd2f23d6cd94d98031cfec..0000000000000000000000000000000000000000 --- a/doc/src/Section_accelerate.txt +++ /dev/null @@ -1,391 +0,0 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_howto.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -5. Accelerating LAMMPS performance :h2 - -This section describes various methods for improving LAMMPS -performance for different classes of problems running on different -kinds of machines. - -There are two thrusts to the discussion that follows. The -first is using code options that implement alternate algorithms -that can speed-up a simulation. The second is to use one -of the several accelerator packages provided with LAMMPS that -contain code optimized for certain kinds of hardware, including -multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors. - -5.1 "Measuring performance"_#acc_1 :ulb,l -5.2 "Algorithms and code options to boost performace"_#acc_2 :l -5.3 "Accelerator packages with optimized styles"_#acc_3 :l - 5.3.1 "GPU package"_accelerate_gpu.html :l - 5.3.2 "USER-INTEL package"_accelerate_intel.html :l - 5.3.3 "KOKKOS package"_accelerate_kokkos.html :l - 5.3.4 "USER-OMP package"_accelerate_omp.html :l - 5.3.5 "OPT package"_accelerate_opt.html :l -5.4 "Comparison of various accelerator packages"_#acc_4 :l -:ule - -The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS -web site gives performance results for the various accelerator -packages discussed in Section 5.2, for several of the standard LAMMPS -benchmark problems, as a function of problem size and number of -compute nodes, on different hardware platforms. - -:line -:line - -5.1 Measuring performance :h3,link(acc_1) - -Before trying to make your simulation run faster, you should -understand how it currently performs and where the bottlenecks are. - -The best way to do this is run the your system (actual number of -atoms) for a modest number of timesteps (say 100 steps) on several -different processor counts, including a single processor if possible. -Do this for an equilibrium version of your system, so that the -100-step timings are representative of a much longer run. There is -typically no need to run for 1000s of timesteps to get accurate -timings; you can simply extrapolate from short runs. - -For the set of runs, look at the timing data printed to the screen and -log file at the end of each LAMMPS run. "This -section"_Section_start.html#start_7 of the manual has an overview. - -Running on one (or a few processors) should give a good estimate of -the serial performance and what portions of the timestep are taking -the most time. Running the same problem on a few different processor -counts should give an estimate of parallel scalability. I.e. if the -simulation runs 16x faster on 16 processors, its 100% parallel -efficient; if it runs 8x faster on 16 processors, it's 50% efficient. - -The most important data to look at in the timing info is the timing -breakdown and relative percentages. For example, trying different -options for speeding up the long-range solvers will have little impact -if they only consume 10% of the run time. If the pairwise time is -dominating, you may want to look at GPU or OMP versions of the pair -style, as discussed below. Comparing how the percentages change as -you increase the processor count gives you a sense of how different -operations within the timestep are scaling. Note that if you are -running with a Kspace solver, there is additional output on the -breakdown of the Kspace time. For PPPM, this includes the fraction -spent on FFTs, which can be communication intensive. - -Another important detail in the timing info are the histograms of -atoms counts and neighbor counts. If these vary widely across -processors, you have a load-imbalance issue. This often results in -inaccurate relative timing data, because processors have to wait when -communication occurs for other processors to catch up. Thus the -reported times for "Communication" or "Other" may be higher than they -really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile -LAMMPS, to obtain synchronized timings. - -:line - -5.2 General strategies :h3,link(acc_2) - -NOTE: this section 5.2 is still a work in progress - -Here is a list of general ideas for improving simulation performance. -Most of them are only applicable to certain models and certain -bottlenecks in the current performance, so let the timing data you -generate be your guide. It is hard, if not impossible, to predict how -much difference these options will make, since it is a function of -problem size, number of processors used, and your machine. There is -no substitute for identifying performance bottlenecks, and trying out -various options. - -rRESPA -2-FFT PPPM -Staggered PPPM -single vs double PPPM -partial charge PPPM -verlet/split run style -processor command for proc layout and numa layout -load-balancing: balance and fix balance :ul - -2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses -2 FFTs instead of the 4 FFTs used by the default {ik differentiation} -PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to -achieve the same accuracy as 4-FFT PPPM. For problems where the FFT -cost is the performance bottleneck (typically large problems running -on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. - -Staggered PPPM performs calculations using two different meshes, one -shifted slightly with respect to the other. This can reduce force -aliasing errors and increase the accuracy of the method, but also -doubles the amount of work required. For high relative accuracy, using -staggered PPPM allows one to half the mesh size in each dimension as -compared to regular PPPM, which can give around a 4x speedup in the -kspace time. However, for low relative accuracy, using staggered PPPM -gives little benefit and can be up to 2x slower in the kspace -time. For example, the rhodopsin benchmark was run on a single -processor, and results for kspace time vs. relative accuracy for the -different methods are shown in the figure below. For this system, -staggered PPPM (using ik differentiation) becomes useful when using a -relative accuracy of slightly greater than 1e-5 and above. - -:c,image(JPG/rhodo_staggered.jpg) - -NOTE: Using staggered PPPM may not give the same increase in accuracy -of energy and pressure as it does in forces, so some caution must be -used if energy and/or pressure are quantities of interest, such as -when using a barostat. - -:line - -5.3 Packages with optimized styles :h3,link(acc_3) - -Accelerated versions of various "pair_style"_pair_style.html, -"fixes"_fix.html, "computes"_compute.html, and other commands have -been added to LAMMPS, which will typically run faster than the -standard non-accelerated versions. Some require appropriate hardware -to be present on your system, e.g. GPUs or Intel Xeon Phi -coprocessors. - -All of these commands are in packages provided with LAMMPS. An -overview of packages is give in "Section -packages"_Section_packages.html. - -These are the accelerator packages -currently in LAMMPS, either as standard or user packages: - -"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support -"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi -"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading -"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations -"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:) - - - -Inverting this list, LAMMPS currently has acceleration support for -three kinds of hardware, via the listed packages: - -Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages -NVIDIA GPUs : "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages -Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:) - -Which package is fastest for your hardware may depend on the size -problem you are running and what commands (accelerated and -non-accelerated) are invoked by your input script. While these doc -pages include performance guidelines, there is no substitute for -trying out the different packages appropriate to your hardware. - -Any accelerated style has the same name as the corresponding standard -style, except that a suffix is appended. Otherwise, the syntax for -the command that uses the style is identical, their functionality is -the same, and the numerical results it produces should also be the -same, except for precision and round-off effects. - -For example, all of these styles are accelerated variants of the -Lennard-Jones "pair_style lj/cut"_pair_lj.html: - -"pair_style lj/cut/gpu"_pair_lj.html -"pair_style lj/cut/intel"_pair_lj.html -"pair_style lj/cut/kk"_pair_lj.html -"pair_style lj/cut/omp"_pair_lj.html -"pair_style lj/cut/opt"_pair_lj.html :ul - -To see what accelerate styles are currently available, see -"Section 3.5"_Section_commands.html#cmd_5 of the manual. The -doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or -"fix nve"_fix_nve.html) also list any accelerated variants available -for that style. - -To use an accelerator package in LAMMPS, and one or more of the styles -it provides, follow these general steps. Details vary from package to -package and are explained in the individual accelerator doc pages, -listed above: - -build the accelerator library | - only for GPU package | -install the accelerator package | - make yes-opt, make yes-user-intel, etc | -add compile/link flags to Makefile.machine in src/MAKE | - only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | -re-build LAMMPS | - make machine | -prepare and test a regular LAMMPS simulation | - lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | -enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, | - only needed for KOKKOS package | -set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, | - only if defaults need to be changed | -use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu -:tb(c=2,s=|) - -Note that the first 4 steps can be done as a single command with -suitable make command invocations. This is discussed in "Section -4"_Section_packages.html of the manual, and its use is -illustrated in the individual accelerator sections. Typically these -steps only need to be done once, to create an executable that uses one -or more accelerator packages. - -The last 4 steps can all be done from the command-line when LAMMPS is -launched, without changing your input script, as illustrated in the -individual accelerator sections. Or you can add -"package"_package.html and "suffix"_suffix.html commands to your input -script. - -NOTE: With a few exceptions, you can build a single LAMMPS executable -with all its accelerator packages installed. Note however that the -USER-INTEL and KOKKOS packages require you to choose one of their -hardware options when building for a specific platform. I.e. CPU or -Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi -option for the KOKKOS package. - -These are the exceptions. You cannot build a single executable with: - -both the USER-INTEL Phi and KOKKOS Phi options -the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul - -See the examples/accelerate/README and make.list files for sample -Make.py commands that build LAMMPS with any or all of the accelerator -packages. As an example, here is a command that builds with all the -GPU related packages installed (GPU, KOKKOS with Cuda), including -settings to build the needed auxiliary GPU libraries for Kepler GPUs: - -Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \ - -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre - -The examples/accelerate directory also has input scripts that can be -used with all of the accelerator packages. See its README file for -details. - -Likewise, the bench directory has FERMI and KEPLER and PHI -sub-directories with Make.py commands and input scripts for using all -the accelerator packages on various machines. See the README files in -those dirs. - -As mentioned above, the "Benchmark -page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives -performance results for the various accelerator packages for several -of the standard LAMMPS benchmark problems, as a function of problem -size and number of compute nodes, on different hardware platforms. - -Here is a brief summary of what the various packages provide. Details -are in the individual accelerator sections. - -Styles with a "gpu" suffix are part of the GPU package, and can be run -on NVIDIA GPUs. The speed-up on a GPU depends on a variety of -factors, discussed in the accelerator sections. :ulb,l - -Styles with an "intel" suffix are part of the USER-INTEL -package. These styles support vectorized single and mixed precision -calculations, in addition to full double precision. In extreme cases, -this can provide speedups over 3.5x on CPUs. The package also -supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) -coprocessors. This can result in additional speedup over 2x depending -on the hardware configuration. :l - -Styles with a "kk" suffix are part of the KOKKOS package, and can be -run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel -Xeon Phi in "native" mode. The speed-up depends on a variety of -factors, as discussed on the KOKKOS accelerator page. :l - -Styles with an "omp" suffix are part of the USER-OMP package and allow -a pair-style to be run in multi-threaded mode using OpenMP. This can -be useful on nodes with high-core counts when using less MPI processes -than cores is advantageous, e.g. when running with PPPM so that FFTs -are run on fewer MPI processors or when the many MPI tasks would -overload the available bandwidth for communication. :l - -Styles with an "opt" suffix are part of the OPT package and typically -speed-up the pairwise calculations of your simulation by 5-25% on a -CPU. :l -:ule - -The individual accelerator package doc pages explain: - -what hardware and software the accelerated package requires -how to build LAMMPS with the accelerated package -how to run with the accelerated package either via command-line switches or modifying the input script -speed-ups to expect -guidelines for best performance -restrictions :ul - -:line - -5.4 Comparison of various accelerator packages :h3,link(acc_4) - -NOTE: this section still needs to be re-worked with additional KOKKOS -and USER-INTEL information. - -The next section compares and contrasts the various accelerator -options, since there are multiple ways to perform OpenMP threading, -run on GPUs, and run on Intel Xeon Phi coprocessors. - -All 3 of these packages accelerate a LAMMPS calculation using NVIDIA -hardware, but they do it in different ways. - -As a consequence, for a particular simulation on specific hardware, -one package may be faster than the other. We give guidelines below, -but the best way to determine which package is faster for your input -script is to try both of them on your machine. See the benchmarking -section below for examples where this has been done. - -[Guidelines for using each package optimally:] - -The GPU package allows you to assign multiple CPUs (cores) to a single -GPU (a common configuration for "hybrid" nodes that contain multicore -CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l - -The GPU package moves per-atom data (coordinates, forces) -back-and-forth between the CPU and GPU every timestep. The -KOKKOS/CUDA package only does this on timesteps when a CPU calculation -is required (e.g. to invoke a fix or compute that is non-GPU-ized). -Hence, if you can formulate your input script to only use GPU-ized -fixes and computes, and avoid doing I/O too often (thermo output, dump -file snapshots, restart files), then the data transfer cost of the -KOKKOS/CUDA package can be very low, causing it to run faster than the -GPU package. :l - -The GPU package is often faster than the KOKKOS/CUDA package, if the -number of atoms per GPU is smaller. The crossover point, in terms of -atoms/GPU at which the KOKKOS/CUDA package becomes faster depends -strongly on the pair style. For example, for a simple Lennard Jones -system the crossover (in single precision) is often about 50K-100K -atoms per GPU. When performing double precision calculations the -crossover point can be significantly smaller. :l - -Both packages compute bonded interactions (bonds, angles, etc) on the -CPU. If the GPU package is running with several MPI processes -assigned to one GPU, the cost of computing the bonded interactions is -spread across more CPUs and hence the GPU package can run faster. :l - -When using the GPU package with multiple CPUs assigned to one GPU, its -performance depends to some extent on high bandwidth between the CPUs -and the GPU. Hence its performance is affected if full 16 PCIe lanes -are not available for each GPU. In HPC environments this can be the -case if S2050/70 servers are used, where two devices generally share -one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide -full 16 lanes to each of the PCIe 2.0 16x slots. :l -:ule - -[Differences between the two packages:] - -The GPU package accelerates only pair force, neighbor list, and PPPM -calculations. :ulb,l - -The GPU package requires neighbor lists to be built on the CPU when using -exclusion lists, hybrid pair styles, or a triclinic simulation box. :l -:ule diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 76051490e401b9ff5b9ac3c4aeb292a1b86b66b3..daedb00a0a6f6b431356d04fece2dfaeddbb9f23 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -1,4 +1,4 @@ -"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c +"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Packages.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -67,7 +67,7 @@ values are not desired, the "processors"_processors.html and tell LAMMPS how to map processors to the simulation box. Many input script errors are detected by LAMMPS and an ERROR or -WARNING message is printed. "This section"_Section_errors.html gives +WARNING message is printed. The "Errors"_Errors.html doc page gives more information on what errors mean. The documentation for each command lists restrictions on how the command can be used. @@ -129,6 +129,17 @@ region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre so that you do not have to define (or discard) a temporary variable X. +Additionally, the "immediate" variable expression may be followed by a +colon, followed by a C-style format string, e.g. ":%f" or ":%.10g". +The format string must be appropriate for a double-precision +floating-point value. The format string is used to output the result +of the variable expression evaluation. If a format string is not +specified a high-precision "%.20g" is used as the default. + +This can be useful for formatting print output to a desired precion: + +print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre + Note that neither the curly-bracket or immediate form of variables can contain nested $ characters for other variables to substitute for. Thus you cannot do this: @@ -193,10 +204,10 @@ allowed, but that should be sufficient for most use cases. 3.3 Input script structure :h3,link(cmd_3) This section describes the structure of a typical LAMMPS input script. -The "examples" directory in the LAMMPS distribution contains many -sample input scripts; the corresponding problems are discussed in -"Section 7"_Section_example.html, and animated on the "LAMMPS -WWW Site"_lws. +The examples directory in the LAMMPS distribution contains many sample +input scripts; the corresponding problems are discussed on the +"Examples"_Examples.html doc page, and animated on the "LAMMPS WWW +Site"_lws. A LAMMPS input script typically has 4 parts: @@ -543,8 +554,8 @@ Fix styles :h3 See the "fix"_fix.html command for one-line descriptions of each style or click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built -with the "appropriate accelerated package"_Section_accelerate.html. -This is indicated by additional letters in parenthesis: g = GPU, i = +with the "appropriate accelerated package"_Speed_packages.html. This +is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "adapt"_fix_adapt.html, @@ -571,7 +582,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "dt/reset"_fix_dt_reset.html, "efield"_fix_efield.html, "ehex"_fix_ehex.html, -"enforce2d"_fix_enforce2d.html, +"enforce2d (k)"_fix_enforce2d.html, "evaporate"_fix_evaporate.html, "external"_fix_external.html, "freeze"_fix_freeze.html, @@ -583,6 +594,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "indent"_fix_indent.html, "latte"_fix_latte.html, "langevin (k)"_fix_langevin.html, +"langevin/spin"_fix_langevin_spin.hmtl, "lineforce"_fix_lineforce.html, "momentum (k)"_fix_momentum.html, "move"_fix_move.html, @@ -606,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "nve/line"_fix_nve_line.html, "nve/noforce"_fix_nve_noforce.html, "nve/sphere (o)"_fix_nve_sphere.html, +"nve/spin"_fix_nve_spin.html, "nve/tri"_fix_nve_tri.html, "nvt (iko)"_fix_nh.html, "nvt/asphere (o)"_fix_nvt_asphere.html, @@ -618,6 +631,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "planeforce"_fix_planeforce.html, "poems"_fix_poems.html, "pour"_fix_pour.html, +"precession/spin"_fix_precession_spin.html, "press/berendsen"_fix_press_berendsen.html, "print"_fix_print.html, "property/atom (k)"_fix_property_atom.html, @@ -664,6 +678,8 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "vector"_fix_vector.html, "viscosity"_fix_viscosity.html, "viscous"_fix_viscous.html, +"wall/body/polygon"_fix_wall_body_polygon.html, +"wall/body/polyhedron"_fix_wall_body_polyhedron.html, "wall/colloid"_fix_wall.html, "wall/gran"_fix_wall_gran.html, "wall/gran/region"_fix_wall_gran_region.html, @@ -684,6 +700,7 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, +"bond/react"_fix_bond_react.html, "colvars"_fix_colvars.html, "dpd/energy (k)"_fix_dpd_energy.html, "drude"_fix_drude.html, @@ -758,9 +775,9 @@ See the "compute"_compute.html command for one-line descriptions of each style or click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. +package"_Speed_packages.html. This is indicated by additional letters +in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. "aggregate/atom"_compute_cluster_atom.html, "angle"_compute_angle.html, @@ -823,6 +840,7 @@ KOKKOS, o = USER-OMP, t = OPT. "sna/atom"_compute_sna_atom.html, "snad/atom"_compute_sna_atom.html, "snav/atom"_compute_sna_atom.html, +"spin"_compute_spin.html, "stress/atom"_compute_stress_atom.html, "temp (k)"_compute_temp.html, "temp/asphere"_compute_temp_asphere.html, @@ -851,6 +869,7 @@ package"_Section_start.html#start_3. "dpd"_compute_dpd.html, "dpd/atom"_compute_dpd_atom.html, "edpd/temp/atom"_compute_edpd_temp_atom.html, +"entropy/atom"_compute_entropy_atom.html, "fep"_compute_fep.html, "force/tally"_compute_tally.html, "heat/flux/tally"_compute_tally.html, @@ -901,9 +920,9 @@ See the "pair_style"_pair_style.html command for an overview of pair potentials. Click on the style itself for a full description. Many of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. +package"_Speed_packages.html. This is indicated by additional letters +in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. "none"_pair_none.html, "zero"_pair_zero.html, @@ -913,7 +932,9 @@ KOKKOS, o = USER-OMP, t = OPT. "airebo (oi)"_pair_airebo.html, "airebo/morse (oi)"_pair_airebo.html, "beck (go)"_pair_beck.html, -"body"_pair_body.html, +"body/nparticle"_pair_body_nparticle.html, +"body/rounded/polygon"_pair_body_rounded/polygon.html, +"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html, "bop"_pair_bop.html, "born (go)"_pair_born.html, "born/coul/dsf"_pair_born.html, @@ -948,6 +969,7 @@ KOKKOS, o = USER-OMP, t = OPT. "dsmc"_pair_dsmc.html, "eam (gikot)"_pair_eam.html, "eam/alloy (gikot)"_pair_eam.html, +"eam/cd (o)"_pair_eam.html, "eam/fs (gikot)"_pair_eam.html, "eim (o)"_pair_eim.html, "gauss (go)"_pair_gauss.html, @@ -1016,6 +1038,10 @@ KOKKOS, o = USER-OMP, t = OPT. "snap (k)"_pair_snap.html, "soft (go)"_pair_soft.html, "sw (giko)"_pair_sw.html, +"spin/dmi"_pair_spin_dmi.html, +"spin/exchange"_pair_spin_exchange.html, +"spin/magelec"_pair_spin_magelec.html, +"spin/neel"_pair_spin_neel.html, "table (gko)"_pair_table.html, "tersoff (giko)"_pair_tersoff.html, "tersoff/mod (gko)"_pair_tersoff_mod.html, @@ -1044,7 +1070,6 @@ package"_Section_start.html#start_3. "coul/shield"_pair_coul_shield.html, "dpd/fdt"_pair_dpd_fdt.html, "dpd/fdt/energy (k)"_pair_dpd_fdt.html, -"eam/cd (o)"_pair_eam.html, "edip (o)"_pair_edip.html, "edip/multi"_pair_edip.html, "edpd"_pair_meso.html, @@ -1117,9 +1142,9 @@ See the "bond_style"_bond_style.html command for an overview of bond potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. +package"_Speed_packages.html. This is indicated by additional letters +in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. "none"_bond_none.html, "zero"_bond_zero.html, @@ -1151,9 +1176,9 @@ See the "angle_style"_angle_style.html command for an overview of angle potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. +package"_Speed_packages.html. This is indicated by additional letters +in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. "none"_angle_none.html, "zero"_angle_zero.html, @@ -1187,7 +1212,7 @@ See the "dihedral_style"_dihedral_style.html command for an overview of dihedral potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional +package"_Speed_packages.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. @@ -1211,7 +1236,8 @@ package"_Section_start.html#start_3. "nharmonic (o)"_dihedral_nharmonic.html, "quadratic (o)"_dihedral_quadratic.html, "spherical (o)"_dihedral_spherical.html, -"table (o)"_dihedral_table.html :tb(c=4,ea=c) +"table (o)"_dihedral_table.html, +"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) :line @@ -1221,9 +1247,9 @@ See the "improper_style"_improper_style.html command for an overview of improper potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. +package"_Speed_packages.html. This is indicated by additional letters +in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. "none"_improper_none.html, "zero"_improper_zero.html, @@ -1250,9 +1276,9 @@ See the "kspace_style"_kspace_style.html command for an overview of Kspace solvers. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. +package"_Speed_packages.html. This is indicated by additional letters +in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. "ewald (o)"_kspace_style.html, "ewald/disp"_kspace_style.html, diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt index 7b9041062855136866e909b7c37a451c41460256..6bbd1e4d99a8d02e89147b5a240f1479252c2940 100644 --- a/doc/src/Section_history.txt +++ b/doc/src/Section_history.txt @@ -1,4 +1,4 @@ -"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws - +"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Manual.html :c diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index e852e0abd452b707fc0eb25f0783cfb14bf85507..337880ccee186f3b7c3500627b8d5c6f43af8224 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -1,4 +1,4 @@ -"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c +"Previous Section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Examples.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -36,10 +36,11 @@ This section describes how to perform common tasks using LAMMPS. 6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24 6.25 "Polarizable models"_#howto_25 6.26 "Adiabatic core/shell model"_#howto_26 -6.27 "Drude induced dipoles"_#howto_27 :all(b) +6.27 "Drude induced dipoles"_#howto_27 +6.28 "Magnetic spins"_#howto_28 :all(b) The example input scripts included in the LAMMPS distribution and -highlighted in "Section 7"_Section_example.html also show how to +highlighted on the "Examples"_Examples.html doc page also show how to setup and run various kinds of simulations. :line @@ -187,9 +188,9 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting coefficients is done in the input data file via the "read_data"_read_data.html command or in the input script with commands like "pair_coeff"_pair_coeff.html or -"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html -for additional tools that can use CHARMM or AMBER to assign force -field coefficients and convert their output into LAMMPS input. +"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for +additional tools that can use CHARMM or AMBER to assign force field +coefficients and convert their output into LAMMPS input. See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force @@ -671,10 +672,10 @@ this scenario, LAMMPS is the driver code. During its timestepping, the fix is invoked, and can make library calls to the other code, which has been linked to LAMMPS as a library. This is the way the "POEMS"_poems package that performs constrained rigid-body motion on -groups of atoms is hooked to LAMMPS. See the -"fix poems"_fix_poems.html command for more details. See "this -section"_Section_modify.html of the documentation for info on how to add -a new fix to LAMMPS. +groups of atoms is hooked to LAMMPS. See the "fix +poems"_fix_poems.html command for more details. See the +"Modify"_Modify.html doc page for info on how to add a new fix to +LAMMPS. :link(poems,http://www.rpi.edu/~anderk5/lab) @@ -695,8 +696,8 @@ processors to start up another program). In the latter case the stand-alone code could communicate with LAMMPS thru files that the command writes and reads. -See "Section 10"_Section_modify.html of the documentation for how -to add a new command to LAMMPS. +See the "Modify"_Modify.html doc page for how to add a new command to +LAMMPS. (3) Use LAMMPS as a library called by another code. In this case the other code is the driver and calls LAMMPS as needed. Or a wrapper @@ -730,10 +731,10 @@ any other language that supports a vanilla C-like interface). For example, from C++ you could create one (or more) "instances" of LAMMPS, pass it an input script to process, or execute individual commands, all by invoking the correct class methods in LAMMPS. From C -or Fortran you can make function calls to do the same things. See -"Section 11"_Section_python.html of the manual for a description -of the Python wrapper provided with LAMMPS that operates through the -LAMMPS library interface. +or Fortran you can make function calls to do the same things. See the +"Python"_Python.html doc page for a description of the Python wrapper +provided with LAMMPS that operates through the LAMMPS library +interface. The files src/library.cpp and library.h contain the C-style interface to LAMMPS. See "Section 6.19"_Section_howto.html#howto_19 of the @@ -761,12 +762,12 @@ simulations can be visualized (and analyzed) in a variety of ways. LAMMPS snapshots are created by the "dump"_dump.html command which can create files in several formats. The native LAMMPS dump format is a text file (see "dump atom" or "dump custom") which can be visualized -by several popular visualization tools. The "dump image"_dump_image.html -and "dump movie"_dump_image.html styles can output internally rendered -images and convert a sequence of them to a movie during the MD run. -Several programs included with LAMMPS as auxiliary tools can convert -between LAMMPS format files and other formats. -See the "Section 9"_Section_tools.html doc page for details. +by several popular visualization tools. The "dump +image"_dump_image.html and "dump movie"_dump_image.html styles can +output internally rendered images and convert a sequence of them to a +movie during the MD run. Several programs included with LAMMPS as +auxiliary tools can convert between LAMMPS format files and other +formats. See the "Tools"_Tools.html doc page for details. A Python-based toolkit distributed by our group can read native LAMMPS dump files, including custom dump files with additional columns of @@ -1056,7 +1057,7 @@ rigid bodies composed of finite-size particles :ul Example input scripts for these kinds of models are in the body, colloid, dipole, ellipse, line, peri, pour, and tri directories of the -"examples directory"_Section_example.html in the LAMMPS distribution. +"examples directory"_Examples.html in the LAMMPS distribution. Atom styles :h4 @@ -1157,7 +1158,7 @@ styles"_pair_style.html that generate torque: "pair_style lubricate"_pair_lubricate.html "pair_style line/lj"_pair_line_lj.html "pair_style tri/lj"_pair_tri_lj.html -"pair_style body"_pair_body.html :ul +"pair_style body"_pair_body_nparticle.html :ul The granular pair styles are used with spherical particles. The dipole pair style is used with the dipole atom style, which could be @@ -1268,7 +1269,7 @@ list of sub-particles. Individual body partices are typically treated as rigid bodies, and their motion integrated with a command like "fix nve/body"_fix_nve_body.html. Interactions between pairs of body particles are computed via a command like "pair_style -body"_pair_body.html. +body"_pair_body_nparticle.html. :line @@ -1301,8 +1302,8 @@ As discussed below, LAMMPS gives you a variety of ways to determine what quantities are computed and printed when the thermodynamics, dump, or fix commands listed above perform output. Throughout this discussion, note that users can also "add their own computes and fixes -to LAMMPS"_Section_modify.html which can then generate values that can -then be output with these commands. +to LAMMPS"_Modify.html which can then generate values that can then be +output with these commands. The following sub-sections discuss different LAMMPS command related to output and the kind of data they operate on and produce: @@ -1823,8 +1824,8 @@ At zero temperature, it is easy to estimate these derivatives by deforming the simulation box in one of the six directions using the "change_box"_change_box.html command and measuring the change in the stress tensor. A general-purpose script that does this is given in the -examples/elastic directory described in "this -section"_Section_example.html. +examples/elastic directory described on the "Examples"_Examples.html +doc page. Calculating elastic constants at finite temperature is more challenging, because it is necessary to run a simulation that perfoms @@ -1842,10 +1843,10 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda1 6.19 Library interface to LAMMPS :link(howto_19),h4 -As described in "Section 2.5"_Section_start.html#start_5, LAMMPS -can be built as a library, so that it can be called by another code, -used in a "coupled manner"_Section_howto.html#howto_10 with other -codes, or driven through a "Python interface"_Section_python.html. +As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can +be built as a library, so that it can be called by another code, used +in a "coupled manner"_Section_howto.html#howto_10 with other codes, or +driven through a "Python interface"_Python.html. All of these methodologies use a C-style interface to LAMMPS that is provided in the files src/library.cpp and src/library.h. The @@ -1868,9 +1869,9 @@ details. NOTE: You can write code for additional functions as needed to define how your code talks to LAMMPS and add them to src/library.cpp and -src/library.h, as well as to the "Python -interface"_Section_python.html. The added functions can access or -change any internal LAMMPS data you wish. +src/library.h, as well as to the "Python interface"_Python.html. The +added functions can access or change any internal LAMMPS data you +wish. void lammps_open(int, char **, MPI_Comm, void **) void lammps_open_no_mpi(int, char **, void **) @@ -2321,11 +2322,10 @@ Note that this compute allows the per-atom output of other "computes"_compute.html, "fixes"_fix.html, and "variables"_variable.html to be used to define chunk IDs for each atom. This means you can write your own compute or fix to output a -per-atom quantity to use as chunk ID. See -"Section 10"_Section_modify.html of the documentation for how to -do this. You can also define a "per-atom variable"_variable.html in -the input script that uses a formula to generate a chunk ID for each -atom. +per-atom quantity to use as chunk ID. See the "Modify"_Modify.html +doc page for how to do this. You can also define a "per-atom +variable"_variable.html in the input script that uses a formula to +generate a chunk ID for each atom. Fix ave/chunk command: :h4 @@ -2906,6 +2906,54 @@ with a Coulomb pair style. It may be useful to use {coul/long/cs} or similar from the CORESHELL package if the core and Drude particle come too close, which can cause numerical issues. +:line + +6.28 Magnetic spins :link(howto_28),h4 + +Classical magnetic spin simualtions can be performed via the SPIN +package. The algrorithmic and implementation details are described in +"Tranchida"_#Tranchida7. + +The model representents the simulation of atomic magnetic spins +coupled to lattice vibrations. The dynamics of those magnetic spins +can be used to simulate a broad range a phenomena related to +magneto-elasticity, or or to study the influence of defects on the +magnetic properties of materials. + +The magnetic spins are interacting with each others and with the +lattice via pair interactions. Typically, the magnetic exchange +interaction can be defined using the +"pair/spin/exchange"_pair_spin_exchange.html command. This exchange +applies a magnetic torque to a given spin, considering the orientation +of its neighboring spins and their relative distances. +It also applies a force on the atoms as a function of the spin +orientations and their associated inter-atomic distances. + +The command "fix precession/spin"_fix_precession_spin.html allows to +apply a constant magnetic torque on all the spins in the system. This +torque can be an external magnetic field (Zeeman interaction), or an +uniaxial magnetic anisotropy. + +A Langevin thermostat can be applied to those magnetic spins using +"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat +can be coupled to another Langevin thermostat applied to the atoms +using "fix langevin"_fix_langevin.html in order to simulate +thermostated spin-lattice system. + +The magnetic Gilbert damping can also be applied using "fix +langevin/spin"_fix_langevin_spin.html. It allows to either dissipate +the thermal energy of the Langevin thermostat, or to perform a +relaxation of the magnetic configuration toward an equilibrium state. + +All the computed magnetic properties can be outputed by two main +commands. The first one is "compute spin"_compute_spin.html, that +enables to evaluate magnetic averaged quantities, such as the total +magnetization of the system along x, y, or z, the spin temperature, or +the magnetic energy. The second command is "compute +property/atom"_compute_property_atom.html. It enables to output all the +per atom magnetic quantities. Typically, the orientation of a given +magnetic spin, or the magnetic force acting on this spin. + :line :line @@ -2957,3 +3005,7 @@ Phys, 79, 926 (1983). :link(howto-Lamoureux) [(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) + +:link(Tranchida7) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +arXiv preprint arXiv:1801.10233, (2018). diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index e1ca0ce62fcce3ceb514a71dcde332df478d7d71..36a1181ca7b731ca48c6ec995c8578f5fe94611b 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -1,4 +1,6 @@ -"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_start.html :c +"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Section_start.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -54,8 +56,8 @@ brief discussion of the open-source philosophy. LAMMPS is designed to be easy to modify or extend with new capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See "Section 10"_Section_modify.html -for more details. +conditions, or diagnostics. See the "Modify"_Modify.html doc page for +more details. The current version of LAMMPS is written in C++. Earlier versions were written in F77 and F90. See @@ -94,8 +96,8 @@ LAMMPS are listed in "this section"_#intro_5. This section highlights LAMMPS features, with pointers to specific commands which give more details. If LAMMPS doesn't have your favorite interatomic potential, boundary condition, or atom type, see -"Section 10"_Section_modify.html, which describes how you can add -it to LAMMPS. +the "Modify"_Modify.html doc page, which describes how you can add it +to LAMMPS. General features :h4 @@ -234,8 +236,8 @@ Multi-replica models :h4 Pre- and post-processing :h4 -Various pre- and post-processing serial tools are packaged -with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l +Various pre- and post-processing serial tools are packaged with +LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, @@ -251,7 +253,7 @@ Specialized features :h4 LAMMPS can be built with optional packages which implement a variety of additional capabilities. An overview of all the packages is "given -here"_Section_packages.html. +here"_Packages.html. These are some LAMMPS capabilities which you may not think of as typical classical molecular dynamics options: @@ -296,9 +298,9 @@ visualize your MD simulation plot your output data :ul A few tools for pre- and post-processing tasks are provided as part of -the LAMMPS package; they are described in "this -section"_Section_tools.html. However, many people use other codes or -write their own tools for these tasks. +the LAMMPS package; they are described on the "Tools"_Tools.html doc +page. However, many people use other codes or write their own tools +for these tasks. As noted above, our group has also written and released a separate toolkit called "Pizza.py"_pizza which addresses some of the listed @@ -327,15 +329,15 @@ topology information and hundreds of force-field coefficients must typically be specified. We suggest you use a program like "CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup such problems and dump its information to a file. You can then -reformat the file as LAMMPS input. Some of the tools in "this -section"_Section_tools.html can assist in this process. +reformat the file as LAMMPS input. Some of the tools described on the +"Tools"_Tools.html doc page can assist in this process. Similarly, LAMMPS creates output files in a simple format. Most users post-process these files with their own analysis tools or re-format them for input into other programs, including visualization packages. If you are convinced you need to compute something on-the-fly as -LAMMPS runs, see "Section 10"_Section_modify.html for a discussion -of how you can use the "dump"_dump.html and "compute"_compute.html and +LAMMPS runs, see the "Modify"_Modify.html doc page for a discussion of +how you can use the "dump"_dump.html and "compute"_compute.html and "fix"_fix.html commands to print out data of your choosing. Keep in mind that complicated computations can slow down the molecular dynamics timestepping, particularly if the computations are not @@ -429,7 +431,7 @@ Site"_lws, or have a suggestion for something to clarify or include, send an email to the "developers"_http://lammps.sandia.gov/authors.html. :l -If you find a bug, "Section 12.2"_Section_errors.html#err_2 +If you find a bug, the "Errors bugs"_Errors_bugs.html doc page describes how to report it. :l If you publish a paper using LAMMPS results, send the citation (and @@ -442,15 +444,14 @@ directory. :l The tools sub-directory of the LAMMPS distribution has various stand-alone codes for pre- and post-processing of LAMMPS data. More -details are given in "Section 9"_Section_tools.html. If you write -a new tool that users will find useful, it can be added to the LAMMPS +details are given on the "Tools"_Tools.html doc page. If you write a +new tool that users will find useful, it can be added to the LAMMPS distribution. :l LAMMPS is designed to be easy to extend with new code for features like potentials, boundary conditions, diagnostic computations, etc. -"This section"_Section_modify.html gives details. If you add a -feature of general interest, it can be added to the LAMMPS -distribution. :l +The "Modify"_Modify.html doc page gives details. If you add a feature +of general interest, it can be added to the LAMMPS distribution. :l The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS performance on various platforms. The files needed to run the @@ -526,14 +527,14 @@ and efforts. Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages Roy Pollock (LLNL), Ewald and PPPM solvers Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package -Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential +Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC) Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD -Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages +Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field -Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling +Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt deleted file mode 100644 index f1d55758c8b0b498710d2f9c2e83eb9834817481..0000000000000000000000000000000000000000 --- a/doc/src/Section_modify.txt +++ /dev/null @@ -1,827 +0,0 @@ - "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_python.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -10. Modifying & extending LAMMPS :h2 - -This section describes how to customize LAMMPS by modifying -and extending its source code. - -10.1 "Atom styles"_#mod_1 -10.2 "Bond, angle, dihedral, improper potentials"_#mod_2 -10.3 "Compute styles"_#mod_3 -10.4 "Dump styles"_#mod_4 -10.5 "Dump custom output options"_#mod_5 -10.6 "Fix styles"_#mod_6 which include integrators, \ - temperature and pressure control, force constraints, \ - boundary conditions, diagnostic output, etc -10.7 "Input script commands"_#mod_7 -10.8 "Kspace computations"_#mod_8 -10.9 "Minimization styles"_#mod_9 -10.10 "Pairwise potentials"_#mod_10 -10.11 "Region styles"_#mod_11 -10.12 "Body styles"_#mod_12 -10.13 "Thermodynamic output options"_#mod_13 -10.14 "Variable options"_#mod_14 -10.15 "Submitting new features for inclusion in LAMMPS"_#mod_15 :all(b) - -LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% of its source code -is files added in this fashion. - -In this section, changes and additions users can make are listed along -with minimal instructions. If you add a new feature to LAMMPS and -think it will be of interest to general users, we encourage you to -submit it to the developers for inclusion in the released version of -LAMMPS. Information about how to do this is provided -"below"_#mod_14. - -The best way to add a new feature is to find a similar feature in -LAMMPS and look at the corresponding source and header files to figure -out what it does. You will need some knowledge of C++ to be able to -understand the hi-level structure of LAMMPS and its class -organization, but functions (class methods) that do actual -computations are written in vanilla C-style code and operate on simple -C-style data structures (vectors and arrays). - -Most of the new features described in this section require you to -write a new C++ derived class (except for exceptions described below, -where you can make small edits to existing files). Creating a new -class requires 2 files, a source code file (*.cpp) and a header file -(*.h). The derived class must provide certain methods to work as a -new option. Depending on how different your new feature is compared -to existing features, you can either derive from the base class -itself, or from a derived class that already exists. Enabling LAMMPS -to invoke the new class is as simple as putting the two source -files in the src dir and re-building LAMMPS. - -The advantage of C++ and its object-orientation is that all the code -and variables needed to define the new feature are in the 2 files you -write, and thus shouldn't make the rest of LAMMPS more complex or -cause side-effect bugs. - -Here is a concrete example. Suppose you write 2 files pair_foo.cpp -and pair_foo.h that define a new class PairFoo that computes pairwise -potentials described in the classic 1997 "paper"_#Foo by Foo, et al. -If you wish to invoke those potentials in a LAMMPS input script with a -command like - -pair_style foo 0.1 3.5 :pre - -then your pair_foo.h file should be structured as follows: - -#ifdef PAIR_CLASS -PairStyle(foo,PairFoo) -#else -... -(class definition for PairFoo) -... -#endif :pre - -where "foo" is the style keyword in the pair_style command, and -PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h -files. - -When you re-build LAMMPS, your new pairwise potential becomes part of -the executable and can be invoked with a pair_style command like the -example above. Arguments like 0.1 and 3.5 can be defined and -processed by your new class. - -As illustrated by this pairwise example, many kinds of options are -referred to in the LAMMPS documentation as the "style" of a particular -command. - -The instructions below give the header file for the base class that -these styles are derived from. Public variables in that file are ones -used and set by the derived classes which are also used by the base -class. Sometimes they are also used by the rest of LAMMPS. Virtual -functions in the base class header file which are set = 0 are ones you -must define in your new derived class to give it the functionality -LAMMPS expects. Virtual functions that are not set to 0 are functions -you can optionally define. - -Additionally, new output options can be added directly to the -thermo.cpp, dump_custom.cpp, and variable.cpp files as explained -below. - -Here are additional guidelines for modifying LAMMPS and adding new -functionality: - -Think about whether what you want to do would be better as a pre- or -post-processing step. Many computations are more easily and more -quickly done that way. :ulb,l - -Don't do anything within the timestepping of a run that isn't -parallel. E.g. don't accumulate a bunch of data on a single processor -and analyze it. You run the risk of seriously degrading the parallel -efficiency. :l - -If your new feature reads arguments or writes output, make sure you -follow the unit conventions discussed by the "units"_units.html -command. :l - -If you add something you think is truly useful and doesn't impact -LAMMPS performance when it isn't used, send an email to the -"developers"_http://lammps.sandia.gov/authors.html. We might be -interested in adding it to the LAMMPS distribution. See further -details on this at the bottom of this page. :l -:ule - -:line -:line - -10.1 Atom styles :link(mod_1),h4 - -Classes that define an "atom style"_atom_style.html are derived from -the AtomVec class and managed by the Atom class. The atom style -determines what attributes are associated with an atom. A new atom -style can be created if one of the existing atom styles does not -define all the attributes you need to store and communicate with -atoms. - -Atom_vec_atomic.cpp is a simple example of an atom style. - -Here is a brief description of methods you define in your new derived -class. See atom_vec.h for details. - -init: one time setup (optional) -grow: re-allocate atom arrays to longer lengths (required) -grow_reset: make array pointers in Atom and AtomVec classes consistent (required) -copy: copy info for one atom to another atom's array locations (required) -pack_comm: store an atom's info in a buffer communicated every timestep (required) -pack_comm_vel: add velocity info to communication buffer (required) -pack_comm_hybrid: store extra info unique to this atom style (optional) -unpack_comm: retrieve an atom's info from the buffer (required) -unpack_comm_vel: also retrieve velocity info (required) -unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) -pack_reverse: store an atom's info in a buffer communicating partial forces (required) -pack_reverse_hybrid: store extra info unique to this atom style (optional) -unpack_reverse: retrieve an atom's info from the buffer (required) -unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) -pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) -pack_border_vel: add velocity info to buffer (required) -pack_border_hybrid: store extra info unique to this atom style (optional) -unpack_border: retrieve an atom's info from the buffer (required) -unpack_border_vel: also retrieve velocity info (required) -unpack_border_hybrid: retrieve extra info unique to this atom style (optional) -pack_exchange: store all an atom's info to migrate to another processor (required) -unpack_exchange: retrieve an atom's info from the buffer (required) -size_restart: number of restart quantities associated with proc's atoms (required) -pack_restart: pack atom quantities into a buffer (required) -unpack_restart: unpack atom quantities from a buffer (required) -create_atom: create an individual atom of this style (required) -data_atom: parse an atom line from the data file (required) -data_atom_hybrid: parse additional atom info unique to this atom style (optional) -data_vel: parse one line of velocity information from data file (optional) -data_vel_hybrid: parse additional velocity data unique to this atom style (optional) -memory_usage: tally memory allocated by atom arrays (required) :tb(s=:) - -The constructor of the derived class sets values for several variables -that you must set when defining a new atom style, which are documented -in atom_vec.h. New atom arrays are defined in atom.cpp. Search for -the word "customize" and you will find locations you will need to -modify. - -NOTE: It is possible to add some attributes, such as a molecule ID, to -atom styles that do not have them via the "fix -property/atom"_fix_property_atom.html command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the "fix -property/atom"_fix_property_atom.html doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. - -New "pair styles"_pair_style.html, "fixes"_fix.html, or -"computes"_compute.html can be added to LAMMPS, as discussed below. -The code for these classes can use the per-atom properties defined by -fix property/atom. The Atom class has a find_custom() method that is -useful in this context: - -int index = atom->find_custom(char *name, int &flag); :pre - -The "name" of a custom attribute, as specified in the "fix -property/atom"_fix_property_atom.html command, is checked to verify -that it exists and its index is returned. The method also sets flag = -0/1 depending on whether it is an integer or floating-point attribute. -The vector of values associated with the attribute can then be -accessed using the returned index as - -int *ivector = atom->ivector\[index\]; -double *dvector = atom->dvector\[index\]; :pre - -Ivector or dvector are vectors of length Nlocal = # of owned atoms, -which store the attributes of individual atoms. - -:line - -10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4 - -Classes that compute molecular interactions are derived from the Bond, -Angle, Dihedral, and Improper classes. New styles can be created to -add new potentials to LAMMPS. - -Bond_harmonic.cpp is the simplest example of a bond style. Ditto for -the harmonic forms of the angle, dihedral, and improper style -commands. - -Here is a brief description of common methods you define in your -new derived class. See bond.h, angle.h, dihedral.h, and improper.h -for details and specific additional methods. - -init: check if all coefficients are set, calls {init_style} (optional) -init_style: check if style specific conditions are met (optional) -compute: compute the molecular interactions (required) -settings: apply global settings for all types (optional) -coeff: set coefficients for one type (required) -equilibrium_distance: length of bond, used by SHAKE (required, bond only) -equilibrium_angle: opening of angle, used by SHAKE (required, angle only) -write & read_restart: writes/reads coeffs to restart files (required) -single: force and energy of a single bond or angle (required, bond or angle only) -memory_usage: tally memory allocated by the style (optional) :tb(s=:) - -:line - -10.3 Compute styles :link(mod_3),h4 - -Classes that compute scalar and vector quantities like temperature -and the pressure tensor, as well as classes that compute per-atom -quantities like kinetic energy and the centro-symmetry parameter -are derived from the Compute class. New styles can be created -to add new calculations to LAMMPS. - -Compute_temp.cpp is a simple example of computing a scalar -temperature. Compute_ke_atom.cpp is a simple example of computing -per-atom kinetic energy. - -Here is a brief description of methods you define in your new derived -class. See compute.h for details. - -init: perform one time setup (required) -init_list: neighbor list setup, if needed (optional) -compute_scalar: compute a scalar quantity (optional) -compute_vector: compute a vector of quantities (optional) -compute_peratom: compute one or more quantities per atom (optional) -compute_local: compute one or more quantities per processor (optional) -pack_comm: pack a buffer with items to communicate (optional) -unpack_comm: unpack the buffer (optional) -pack_reverse: pack a buffer with items to reverse communicate (optional) -unpack_reverse: unpack the buffer (optional) -remove_bias: remove velocity bias from one atom (optional) -remove_bias_all: remove velocity bias from all atoms in group (optional) -restore_bias: restore velocity bias for one atom after remove_bias (optional) -restore_bias_all: same as before, but for all atoms in group (optional) -pair_tally_callback: callback function for {tally}-style computes (optional). -memory_usage: tally memory usage (optional) :tb(s=:) - -Tally-style computes are a special case, as their computation is done -in two stages: the callback function is registered with the pair style -and then called from the Pair::ev_tally() function, which is called for -each pair after force and energy has been computed for this pair. Then -the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The USER-TALLY package -provides {examples}_compute_tally.html for utilizing this mechanism. - -:line - -10.4 Dump styles :link(mod_4),h4 -10.5 Dump custom output options :link(mod_5),h4 - -Classes that dump per-atom info to files are derived from the Dump -class. To dump new quantities or in a new format, a new derived dump -class can be added, but it is typically simpler to modify the -DumpCustom class contained in the dump_custom.cpp file. - -Dump_atom.cpp is a simple example of a derived dump class. - -Here is a brief description of methods you define in your new derived -class. See dump.h for details. - -write_header: write the header section of a snapshot of atoms -count: count the number of lines a processor will output -pack: pack a proc's output data into a buffer -write_data: write a proc's data to a file :tb(s=:) - -See the "dump"_dump.html command and its {custom} style for a list of -keywords for atom information that can already be dumped by -DumpCustom. It includes options to dump per-atom info from Compute -classes, so adding a new derived Compute class is one way to calculate -new quantities to dump. - -Alternatively, you can add new keywords to the dump custom command. -Search for the word "customize" in dump_custom.cpp to see the -half-dozen or so locations where code will need to be added. - -:line - -10.6 Fix styles :link(mod_6),h4 - -In LAMMPS, a "fix" is any operation that is computed during -timestepping that alters some property of the system. Essentially -everything that happens during a simulation besides force computation, -neighbor list construction, and output, is a "fix". This includes -time integration (update of coordinates and velocities), force -constraints or boundary conditions (SHAKE or walls), and diagnostics -(compute a diffusion coefficient). New styles can be created to add -new options to LAMMPS. - -Fix_setforce.cpp is a simple example of setting forces on atoms to -prescribed values. There are dozens of fix options already in LAMMPS; -choose one as a template that is similar to what you want to -implement. - -Here is a brief description of methods you can define in your new -derived class. See fix.h for details. - -setmask: determines when the fix is called during the timestep (required) -init: initialization before a run (optional) -setup_pre_exchange: called before atom exchange in setup (optional) -setup_pre_force: called before force computation in setup (optional) -setup: called immediately before the 1st timestep and after forces are computed (optional) -min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional) -min_setup: like setup, but for minimizations instead of MD runs (optional) -initial_integrate: called at very beginning of each timestep (optional) -pre_exchange: called before atom exchange on re-neighboring steps (optional) -pre_neighbor: called before neighbor list build (optional) -pre_force: called before pair & molecular forces are computed (optional) -post_force: called after pair & molecular forces are computed and communicated (optional) -final_integrate: called at end of each timestep (optional) -end_of_step: called at very end of timestep (optional) -write_restart: dumps fix info to restart file (optional) -restart: uses info from restart file to re-initialize the fix (optional) -grow_arrays: allocate memory for atom-based arrays used by fix (optional) -copy_arrays: copy atom info when an atom migrates to a new processor (optional) -pack_exchange: store atom's data in a buffer (optional) -unpack_exchange: retrieve atom's data from a buffer (optional) -pack_restart: store atom's data for writing to restart file (optional) -unpack_restart: retrieve atom's data from a restart file buffer (optional) -size_restart: size of atom's data (optional) -maxsize_restart: max size of atom's data (optional) -setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional) -initial_integrate_respa: same as initial_integrate, but for rRESPA (optional) -post_integrate_respa: called after the first half integration step is done in rRESPA (optional) -pre_force_respa: same as pre_force, but for rRESPA (optional) -post_force_respa: same as post_force, but for rRESPA (optional) -final_integrate_respa: same as final_integrate, but for rRESPA (optional) -min_pre_force: called after pair & molecular forces are computed in minimizer (optional) -min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) -min_store: store extra data for linesearch based minimization on a LIFO stack (optional) -min_pushstore: push the minimization LIFO stack one element down (optional) -min_popstore: pop the minimization LIFO stack one element up (optional) -min_clearstore: clear minimization LIFO stack (optional) -min_step: reset or move forward on line search minimization (optional) -min_dof: report number of degrees of freedom {added} by this fix in minimization (optional) -max_alpha: report maximum allowed step size during linesearch minimization (optional) -pack_comm: pack a buffer to communicate a per-atom quantity (optional) -unpack_comm: unpack a buffer to communicate a per-atom quantity (optional) -pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional) -unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional) -dof: report number of degrees of freedom {removed} by this fix during MD (optional) -compute_scalar: return a global scalar property that the fix computes (optional) -compute_vector: return a component of a vector property that the fix computes (optional) -compute_array: return a component of an array property that the fix computes (optional) -deform: called when the box size is changed (optional) -reset_target: called when a change of the target temperature is requested during a run (optional) -reset_dt: is called when a change of the time step is requested during a run (optional) -modify_param: called when a fix_modify request is executed (optional) -memory_usage: report memory used by fix (optional) -thermo: compute quantities for thermodynamic output (optional) :tb(s=:) - -Typically, only a small fraction of these methods are defined for a -particular fix. Setmask is mandatory, as it determines when the fix -will be invoked during the timestep. Fixes that perform time -integration ({nve}, {nvt}, {npt}) implement initial_integrate() and -final_integrate() to perform velocity Verlet updates. Fixes that -constrain forces implement post_force(). - -Fixes that perform diagnostics typically implement end_of_step(). For -an end_of_step fix, one of your fix arguments must be the variable -"nevery" which is used to determine when to call the fix and you must -set this variable in the constructor of your fix. By convention, this -is the first argument the fix defines (after the ID, group-ID, style). - -If the fix needs to store information for each atom that persists from -timestep to timestep, it can manage that memory and migrate the info -with the atoms as they move from processors to processor by -implementing the grow_arrays, copy_arrays, pack_exchange, and -unpack_exchange methods. Similarly, the pack_restart and -unpack_restart methods can be implemented to store information about -the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the "run_style"_run_style.html -command), the initial_integrate, post_force_integrate, and -final_integrate_respa methods can be implemented. The thermo method -enables a fix to contribute values to thermodynamic output, as printed -quantities and/or to be summed to the potential energy of the system. - -:line - -10.7 Input script commands :link(mod_7),h4 - -New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. - -The single method your new class must define is as follows: - -command: operations performed by the new command :tb(s=:) - -Of course, the new class can define other methods and variables as -needed. - -:line - -10.8 Kspace computations :link(mod_8),h4 - -Classes that compute long-range Coulombic interactions via K-space -representations (Ewald, PPPM) are derived from the KSpace class. New -styles can be created to add new K-space options to LAMMPS. - -Ewald.cpp is an example of computing K-space interactions. - -Here is a brief description of methods you define in your new derived -class. See kspace.h for details. - -init: initialize the calculation before a run -setup: computation before the 1st timestep of a run -compute: every-timestep computation -memory_usage: tally of memory usage :tb(s=:) - -:line - -10.9 Minimization styles :link(mod_9),h4 - -Classes that perform energy minimization derived from the Min class. -New styles can be created to add new minimization algorithms to -LAMMPS. - -Min_cg.cpp is an example of conjugate gradient minimization. - -Here is a brief description of methods you define in your new derived -class. See min.h for details. - -init: initialize the minimization before a run -run: perform the minimization -memory_usage: tally of memory usage :tb(s=:) - -:line - -10.10 Pairwise potentials :link(mod_10),h4 - -Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include manybody potentials -such as EAM or Tersoff where particles interact without a static bond -topology. New styles can be created to add new pair potentials to -LAMMPS. - -Pair_lj_cut.cpp is a simple example of a Pair class, though it -includes some optional methods to enable its use with rRESPA. - -Here is a brief description of the class methods in pair.h: - -compute: workhorse routine that computes pairwise interactions -settings: reads the input script line with arguments you define -coeff: set coefficients for one i,j type pair -init_one: perform initialization for one i,j type pair -init_style: initialization specific to this pair style -write & read_restart: write/read i,j pair coeffs to restart files -write & read_restart_settings: write/read global settings to restart files -single: force and energy of a single pairwise interaction between 2 atoms -compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:) - -The inner/middle/outer routines are optional. - -:line - -10.11 Region styles :link(mod_11),h4 - -Classes that define geometric regions are derived from the Region -class. Regions are used elsewhere in LAMMPS to group atoms, delete -atoms to create a void, insert atoms in a specified region, etc. New -styles can be created to add new region shapes to LAMMPS. - -Region_sphere.cpp is an example of a spherical region. - -Here is a brief description of methods you define in your new derived -class. See region.h for details. - -inside: determine whether a point is in the region -surface_interior: determine if a point is within a cutoff distance inside of surc -surface_exterior: determine if a point is within a cutoff distance outside of surf -shape_update : change region shape if set by time-dependent variable :tb(s=:) - -:line - -10.12 Body styles :link(mod_12),h4 - -Classes that define body particles are derived from the Body class. -Body particles can represent complex entities, such as surface meshes -of discrete points, collections of sub-particles, deformable objects, -etc. - -See "Section 6.14"_Section_howto.html#howto_14 of the manual for -an overview of using body particles and the "body"_body.html doc page -for details on the various body styles LAMMPS supports. New styles -can be created to add new kinds of body particles to LAMMPS. - -Body_nparticle.cpp is an example of a body particle that is treated as -a rigid body containing N sub-particles. - -Here is a brief description of methods you define in your new derived -class. See body.h for details. - -data_body: process a line from the Bodies section of a data file -noutrow: number of sub-particles output is generated for -noutcol: number of values per-sub-particle output is generated for -output: output values for the Mth sub-particle -pack_comm_body: body attributes to communicate every timestep -unpack_comm_body: unpacking of those attributes -pack_border_body: body attributes to communicate when reneighboring is done -unpack_border_body: unpacking of those attributes :tb(s=:) - -:line - -10.13 Thermodynamic output options :link(mod_13),h4 - -There is one class that computes and prints thermodynamic information -to the screen and log file; see the file thermo.cpp. - -There are two styles defined in thermo.cpp: "one" and "multi". There -is also a flexible "custom" style which allows the user to explicitly -list keywords for quantities to print when thermodynamic info is -output. See the "thermo_style"_thermo_style.html command for a list -of defined quantities. - -The thermo styles (one, multi, etc) are simply lists of keywords. -Adding a new style thus only requires defining a new list of keywords. -Search for the word "customize" with references to "thermo style" in -thermo.cpp to see the two locations where code will need to be added. - -New keywords can also be added to thermo.cpp to compute new quantities -for output. Search for the word "customize" with references to -"keyword" in thermo.cpp to see the several locations where code will -need to be added. - -Note that the "thermo_style custom"_thermo.html command already allows -for thermo output of quantities calculated by "fixes"_fix.html, -"computes"_compute.html, and "variables"_variable.html. Thus, it may -be simpler to compute what you wish via one of those constructs, than -by adding a new keyword to the thermo command. - -:line - -10.14 Variable options :link(mod_14),h4 - -There is one class that computes and stores "variable"_variable.html -information in LAMMPS; see the file variable.cpp. The value -associated with a variable can be periodically printed to the screen -via the "print"_print.html, "fix print"_fix_print.html, or -"thermo_style custom"_thermo_style.html commands. Variables of style -"equal" can compute complex equations that involve the following types -of arguments: - -thermo keywords = ke, vol, atoms, ... -other variables = v_a, v_myvar, ... -math functions = div(x,y), mult(x,y), add(x,y), ... -group functions = mass(group), xcm(group,x), ... -atom values = x\[123\], y\[3\], vx\[34\], ... -compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre - -Adding keywords for the "thermo_style custom"_thermo_style.html command -(which can then be accessed by variables) was discussed -"here"_Section_modify.html#mod_13 on this page. - -Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaluate() method. Search for -the word "customize" to find the appropriate location. - -Adding a new group function can be done by editing one section of the -Variable::evaluate() method. Search for the word "customize" to find -the appropriate location. You may need to add a new method to the -Group class as well (see the group.cpp file). - -Accessing a new atom-based vector can be done by editing one section -of the Variable::evaluate() method. Search for the word "customize" -to find the appropriate location. - -Adding new "compute styles"_compute.html (whose calculated values can -then be accessed by variables) was discussed -"here"_Section_modify.html#mod_3 on this page. - -:line -:line - -10.15 Submitting new features for inclusion in LAMMPS :link(mod_15),h4 - -We encourage users to submit new features or modifications for -LAMMPS to "the core developers"_http://lammps.sandia.gov/authors.html -so they can be added to the LAMMPS distribution. The preferred way to -manage and coordinate this is as of Fall 2016 via the LAMMPS project on -"GitHub"_https://github.com/lammps/lammps. An alternative is to contact -the LAMMPS developers or the indicated developer of a package or feature -directly and send in your contribution via e-mail. - -For any larger modifications or programming project, you are encouraged -to contact the LAMMPS developers ahead of time, in order to discuss -implementation strategies and coding guidelines, that will make it -easier to integrate your contribution and result in less work for -everybody involved. You are also encouraged to search through the list -of "open issues on GitHub"_https://github.com/lammps/lammps/issues and -submit a new issue for a planned feature, so you would not duplicate -the work of others (and possibly get scooped by them) or have your work -duplicated by others. - -How quickly your contribution will be integrated -depends largely on how much effort it will cause to integrate and test -it, how much it requires changes to the core codebase, and of how much -interest it is to the larger LAMMPS community. Please see below for a -checklist of typical requirements. Once you have prepared everything, -see "this tutorial"_tutorial_github.html for instructions on how to -submit your changes or new files through a GitHub pull request. If you -prefer to submit patches or full files, you should first make certain, -that your code works correctly with the latest patch-level version of -LAMMPS and contains all bugfixes from it. Then create a gzipped tar -file of all changed or added files or a corresponding patch file using -'diff -u' or 'diff -c' and compress it with gzip. Please only use -gzip compression, as this works well on all platforms. - -If the new features/files are broadly useful we may add them as core -files to LAMMPS or as part of a "standard -package"_Section_start.html#start_3. Else we will add them as a -user-contributed file or package. Examples of user packages are in -src sub-directories that start with USER. The USER-MISC package is -simply a collection of (mostly) unrelated single files, which is the -simplest way to have your contribution quickly added to the LAMMPS -distribution. You can see a list of the both standard and user -packages by typing "make package" in the LAMMPS src directory. - -Note that by providing us files to release, you are agreeing to make -them open-source, i.e. we can release them under the terms of the GPL, -used as a license for the rest of LAMMPS. See "Section -1.4"_Section_intro.html#intro_4 for details. - -With user packages and files, all we are really providing (aside from -the fame and fortune that accompanies having your name in the source -code and on the "Authors page"_http://lammps.sandia.gov/authors.html -of the "LAMMPS WWW site"_lws), is a means for you to distribute your -work to the LAMMPS user community, and a mechanism for others to -easily try out your new feature. This may help you find bugs or make -contact with new collaborators. Note that you're also implicitly -agreeing to support your code which means answer questions, fix bugs, -and maintain it if LAMMPS changes in some way that breaks it (an -unusual event). - -NOTE: If you prefer to actively develop and support your add-on -feature yourself, then you may wish to make it available for download -from your own website, as a user package that LAMMPS users can add to -their copy of LAMMPS. See the "Offsite LAMMPS packages and -tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web -site for examples of groups that do this. We are happy to advertise -your package and web site from that page. Simply email the -"developers"_http://lammps.sandia.gov/authors.html with info about -your package and we will post it there. - -The previous sections of this doc page describe how to add new "style" -files of various kinds to LAMMPS. Packages are simply collections of -one or more new class files which are invoked as a new style within a -LAMMPS input script. If designed correctly, these additions typically -do not require changes to the main core of LAMMPS; they are simply -add-on files. If you think your new feature requires non-trivial -changes in core LAMMPS files, you'll need to "communicate with the -developers"_http://lammps.sandia.gov/authors.html, since we may or may -not want to make those changes. An example of a trivial change is -making a parent-class method "virtual" when you derive a new child -class from it. - -Here is a checklist of steps you need to follow to submit a single file -or user package for our consideration. Following these steps will save -both you and us time. See existing files in packages in the src dir for -examples. If you are uncertain, please ask. - -All source files you provide must compile with the most current -version of LAMMPS with multiple configurations. In particular you -need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG -set in addition to the default -DLAMMPS_SMALLBIG setting. Your code -will need to work correctly in serial and in parallel using MPI. :ulb,l - -For consistency with the rest of LAMMPS and especially, if you want -your contribution(s) to be added to main LAMMPS code or one of its -standard packages, it needs to be written in a style compatible with -other LAMMPS source files. This means: 2-character indentation per -level, [no tabs], no lines over 80 characters. I/O is done via -the C-style stdio library, class header files should not import any -system headers outside , STL containers should be avoided -in headers, and forward declarations used where possible or needed. -All added code should be placed into the LAMMPS_NS namespace or a -sub-namespace; global or static variables should be avoided, as they -conflict with the modular nature of LAMMPS and the C++ class structure. -Header files must [not] import namespaces with {using}. -This all is so the developers can more easily understand, integrate, -and maintain your contribution and reduce conflicts with other parts -of LAMMPS. This basically means that the code accesses data -structures, performs its operations, and is formatted similar to other -LAMMPS source files, including the use of the error class for error -and warning messages. :l - -If you want your contribution to be added as a user-contributed -feature, and it's a single file (actually a *.cpp and *.h file) it can -rapidly be added to the USER-MISC directory. Send us the one-line -entry to add to the USER-MISC/README file in that dir, along with the -2 source files. You can do this multiple times if you wish to -contribute several individual features. :l - -If you want your contribution to be added as a user-contribution and -it is several related features, it is probably best to make it a user -package directory with a name like USER-FOO. In addition to your new -files, the directory should contain a README text file. The README -should contain your name and contact information and a brief -description of what your new package does. If your files depend on -other LAMMPS style files also being installed (e.g. because your file -is a derived class from the other LAMMPS class), then an Install.sh -file is also needed to check for those dependencies. See other README -and Install.sh files in other USER directories as examples. Send us a -tarball of this USER-FOO directory. :l - -Your new source files need to have the LAMMPS copyright, GPL notice, -and your name and email address at the top, like other -user-contributed LAMMPS source files. They need to create a class -that is inside the LAMMPS namespace. If the file is for one of the -USER packages, including USER-MISC, then we are not as picky about the -coding style (see above). I.e. the files do not need to be in the -same stylistic format and syntax as other LAMMPS files, though that -would be nice for developers as well as users who try to read your -code. :l - -You [must] also create a [documentation] file for each new command or -style you are adding to LAMMPS. For simplicity and convenience, the -documentation of groups of closely related commands or styles may be -combined into a single file. This will be one file for a single-file -feature. For a package, it might be several files. These are simple -text files with a specific markup language, that are then auto-converted -to HTML and PDF. The tools for this conversion are included in the -source distribution, and the translation can be as simple as doing -"make html pdf" in the doc folder. -Thus the documentation source files must be in the same format and -style as other *.txt files in the lammps/doc/src directory for similar -commands and styles; use one or more of them as a starting point. -A description of the markup can also be found in -lammps/doc/utils/txt2html/README.html -As appropriate, the text files can include links to equations -(see doc/Eqs/*.tex for examples, we auto-create the associated JPG -files), or figures (see doc/JPG for examples), or even additional PDF -files with further details (see doc/PDF for examples). The doc page -should also include literature citations as appropriate; see the -bottom of doc/fix_nh.txt for examples and the earlier part of the same -file for how to format the cite itself. The "Restrictions" section of -the doc page should indicate that your command is only available if -LAMMPS is built with the appropriate USER-MISC or USER-FOO package. -See other user package doc files for examples of how to do this. The -prerequisite for building the HTML format files are Python 3.x and -virtualenv, the requirement for generating the PDF format manual -is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least -"make html" and carefully inspect and proofread the resulting HTML format -doc page before submitting your code. :l - -For a new package (or even a single command) you should include one or -more example scripts demonstrating its use. These should run in no -more than a couple minutes, even on a single processor, and not require -large data files as input. See directories under examples/USER for -examples of input scripts other users provided for their packages. -These example inputs are also required for validating memory accesses -and testing for memory leaks with valgrind :l - -If there is a paper of yours describing your feature (either the -algorithm/science behind the feature itself, or its initial usage, or -its implementation in LAMMPS), you can add the citation to the *.cpp -source file. See src/USER-EFF/atom_vec_electron.cpp for an example. -A LaTeX citation is stored in a variable at the top of the file and a -single line of code that references the variable is added to the -constructor of the class. Whenever a user invokes your feature from -their input script, this will cause LAMMPS to output the citation to a -log.cite file and prompt the user to examine the file. Note that you -should only use this for a paper you or your group authored. -E.g. adding a cite in the code for a paper by Nose and Hoover if you -write a fix that implements their integrator is not the intended -usage. That kind of citation should just be in the doc page you -provide. :l -:ule - -Finally, as a general rule-of-thumb, the more clear and -self-explanatory you make your documentation and README files, and the -easier you make it for people to get started, e.g. by providing example -scripts, the more likely it is that users will try out your new feature. - -:line -:line - -:link(Foo) -[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt deleted file mode 100644 index 5427cd67f28d36bb0344012e6f7cfe593f7aca88..0000000000000000000000000000000000000000 --- a/doc/src/Section_python.txt +++ /dev/null @@ -1,867 +0,0 @@ -"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_errors.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -11. Python interface to LAMMPS :h2 - -LAMMPS can work together with Python in three ways. First, Python can -wrap LAMMPS through the "LAMMPS library -interface"_Section_howto.html#howto_19, so that a Python script can -create one or more instances of LAMMPS and launch one or more -simulations. In Python lingo, this is "extending" Python with LAMMPS. - -Second, the low-level Python interface can be used indirectly through the -PyLammps and IPyLammps wrapper classes in Python. These wrappers try to -simplify the usage of LAMMPS in Python by providing an object-based interface -to common LAMMPS functionality. It also reduces the amount of code necessary to -parameterize LAMMPS scripts through Python and makes variables and computes -directly accessible. See "PyLammps interface"_#py_9 for more details. - -Third, LAMMPS can use the Python interpreter, so that a LAMMPS input -script can invoke Python code, and pass information back-and-forth -between the input script and Python functions you write. The Python -code can also callback to LAMMPS to query or change its attributes. -In Python lingo, this is "embedding" Python in LAMMPS. - -This section describes how to use these three approaches. - -11.1 "Overview of running LAMMPS from Python"_#py_1 -11.2 "Overview of using Python from a LAMMPS script"_#py_2 -11.3 "Building LAMMPS as a shared library"_#py_3 -11.4 "Installing the Python wrapper into Python"_#py_4 -11.5 "Extending Python with MPI to run in parallel"_#py_5 -11.6 "Testing the Python-LAMMPS interface"_#py_6 -11.7 "Using LAMMPS from Python"_#py_7 -11.8 "Example Python scripts that use LAMMPS"_#py_8 -11.9 "PyLammps interface"_#py_9 :ul - -If you are not familiar with it, "Python"_http://www.python.org is a -powerful scripting and programming language which can essentially do -anything that faster, lower-level languages like C or C++ can do, but -typically with much fewer lines of code. When used in embedded mode, -Python can perform operations that the simplistic LAMMPS input script -syntax cannot. Python can be also be used as a "glue" language to -drive a program through its library interface, or to hook multiple -pieces of software together, such as a simulation package plus a -visualization package, or to run a coupled multiscale or multiphysics -model. - -See "Section 6.10"_Section_howto.html#howto_10 of the manual and -the couple directory of the distribution for more ideas about coupling -LAMMPS to other codes. See "Section -6.19"_Section_howto.html#howto_19 for a description of the LAMMPS -library interface provided in src/library.cpp and src/library.h, and -how to extend it for your needs. As described below, that interface -is what is exposed to Python either when calling LAMMPS from Python or -when calling Python from a LAMMPS input script and then calling back -to LAMMPS from Python code. The library interface is designed to be -easy to add functions to. Thus the Python interface to LAMMPS is also -easy to extend as well. - -If you create interesting Python scripts that run LAMMPS or -interesting Python functions that can be called from a LAMMPS input -script, that you think would be useful to other users, please "email -them to the developers"_http://lammps.sandia.gov/authors.html. We can -include them in the LAMMPS distribution. - -:line -:line - -11.1 Overview of running LAMMPS from Python :link(py_1),h4 - -The LAMMPS distribution includes a python directory with all you need -to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS -library interface, with one wrapper function per LAMMPS library -function. This file makes it is possible to do the following either -from a Python script, or interactively from a Python prompt: create -one or more instances of LAMMPS, invoke LAMMPS commands or give it an -input script, run LAMMPS incrementally, extract LAMMPS results, an -modify internal LAMMPS variables. From a Python script you can do -this in serial or parallel. Running Python interactively in parallel -does not generally work, unless you have a version of Python that -extends standard Python to enable multiple instances of Python to read -what you type. - -To do all of this, you must first build LAMMPS as a shared library, -then insure that your Python can find the python/lammps.py file and -the shared library. These steps are explained in subsequent sections -11.3 and 11.4. Sections 11.5 and 11.6 discuss using MPI from a -parallel Python program and how to test that you are ready to use -LAMMPS from Python. Section 11.7 lists all the functions in the -current LAMMPS library interface and how to call them from Python. - -Section 11.8 gives some examples of coupling LAMMPS to other tools via -Python. For example, LAMMPS can easily be coupled to a GUI or other -visualization tools that display graphs or animations in real time as -LAMMPS runs. Examples of such scripts are included in the python -directory. - -Two advantages of using Python to run LAMMPS are how concise the -language is, and that it can be run interactively, enabling rapid -development and debugging of programs. If you use it to mostly invoke -costly operations within LAMMPS, such as running a simulation for a -reasonable number of timesteps, then the overhead cost of invoking -LAMMPS thru Python will be negligible. - -The Python wrapper for LAMMPS uses the amazing and magical (to me) -"ctypes" package in Python, which auto-generates the interface code -needed between Python and a set of C interface routines for a library. -Ctypes is part of standard Python for versions 2.5 and later. You can -check which version of Python you have installed, by simply typing -"python" at a shell prompt. - -:line - -11.2 Overview of using Python from a LAMMPS script :link(py_2),h4 - -LAMMPS has several commands which can be used to invoke Python -code directly from an input script: - -"python"_python.html -"variable python"_variable.html -"fix python/invoke"_fix_python_invoke.html -"pair_style python"_pair_python.html :ul - -The "python"_python.html command which can be used to define and -execute a Python function that you write the code for. The Python -function can also be assigned to a LAMMPS python-style variable via -the "variable"_variable.html command. Each time the variable is -evaluated, either in the LAMMPS input script itself, or by another -LAMMPS command that uses the variable, this will trigger the Python -function to be invoked. - -The Python code for the function can be included directly in the input -script or in an auxiliary file. The function can have arguments which -are mapped to LAMMPS variables (also defined in the input script) and -it can return a value to a LAMMPS variable. This is thus a mechanism -for your input script to pass information to a piece of Python code, -ask Python to execute the code, and return information to your input -script. - -Note that a Python function can be arbitrarily complex. It can import -other Python modules, instantiate Python classes, call other Python -functions, etc. The Python code that you provide can contain more -code than the single function. It can contain other functions or -Python classes, as well as global variables or other mechanisms for -storing state between calls from LAMMPS to the function. - -The Python function you provide can consist of "pure" Python code that -only performs operations provided by standard Python. However, the -Python function can also "call back" to LAMMPS through its -Python-wrapped library interface, in the manner described in the -previous section 11.1. This means it can issue LAMMPS input script -commands or query and set internal LAMMPS state. As an example, this -can be useful in an input script to create a more complex loop with -branching logic, than can be created using the simple looping and -branching logic enabled by the "next"_next.html and "if"_if.html -commands. - -See the "python"_python.html doc page and the "variable"_variable.html -doc page for its python-style variables for more info, including -examples of Python code you can write for both pure Python operations -and callbacks to LAMMPS. - -The "fix python/invoke"_fix_python_invoke.html command can execute -Python code at selected timesteps during a simulation run. - -The "pair_style python"_pair_python command allows you to define -pairwise potentials as python code which encodes a single pairwise -interaction. This is useful for rapid-developement and debugging of a -new potential. - -To use any of these commands, you only need to build LAMMPS with the -PYTHON package installed: - -make yes-python -make machine :pre - -Note that this will link LAMMPS with the Python library on your -system, which typically requires several auxiliary system libraries to -also be linked. The list of these libraries and the paths to find -them are specified in the lib/python/Makefile.lammps file. You need -to insure that file contains the correct information for your version -of Python and your machine to successfully build LAMMPS. See the -lib/python/README file for more info. - -If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps overviewed in the preceding section (11.1) -for running LAMMPS from Python. I.e. you must build LAMMPS as a -shared library and insure that Python can find the python/lammps.py -file and the shared library. - -:line - -11.3 Building LAMMPS as a shared library :link(py_3),h4 - -Instructions on how to build LAMMPS as a shared library are given in -"Section 2.4"_Section_start.html#start_4. A shared library is one -that is dynamically loadable, which is what Python requires to wrap -LAMMPS. On Linux this is a library file that ends in ".so", not ".a". - -From the src directory, type - -make foo mode=shlib :pre - -where foo is the machine target name, such as linux or g++ or serial. -This should create the file liblammps_foo.so in the src directory, as -well as a soft link liblammps.so, which is what the Python wrapper will -load by default. Note that if you are building multiple machine -versions of the shared library, the soft link is always set to the -most recently built version. - -NOTE: If you are building LAMMPS with an MPI or FFT library or other -auxiliary libraries (used by various packages), then all of these -extra libraries must also be shared libraries. If the LAMMPS -shared-library build fails with an error complaining about this, see -"Section 2.4"_Section_start.html#start_4 for more details. - -:line - -11.4 Installing the Python wrapper into Python :link(py_4),h4 - -For Python to invoke LAMMPS, there are 2 files it needs to know about: - -python/lammps.py -src/liblammps.so :ul - -Lammps.py is the Python wrapper on the LAMMPS library interface. -Liblammps.so is the shared LAMMPS library that Python loads, as -described above. - -You can insure Python can find these files in one of two ways: - -set two environment variables -run the python/install.py script :ul - -If you set the paths to these files as environment variables, you only -have to do it once. For the csh or tcsh shells, add something like -this to your ~/.cshrc file, one line for each of the two files: - -setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python -setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre - -If you use the python/install.py script, you need to invoke it every -time you rebuild LAMMPS (as a shared library) or make changes to the -python/lammps.py file. - -You can invoke install.py from the python directory as - -% python install.py \[libdir\] \[pydir\] :pre - -The optional libdir is where to copy the LAMMPS shared library to; the -default is /usr/local/lib. The optional pydir is where to copy the -lammps.py file to; the default is the site-packages directory of the -version of Python that is running the install script. - -Note that libdir must be a location that is in your default -LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a -location that Python looks in by default for imported modules, like -its site-packages dir. If you want to copy these files to -non-standard locations, such as within your own user space, you will -need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables -accordingly, as above. - -If the install.py script does not allow you to copy files into system -directories, prefix the python command with "sudo". If you do this, -make sure that the Python that root runs is the same as the Python you -run. E.g. you may need to do something like - -% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre - -You can also invoke install.py from the make command in the src -directory as - -% make install-python :pre - -In this mode you cannot append optional arguments. Again, you may -need to prefix this with "sudo". In this mode you cannot control -which Python is invoked by root. - -Note that if you want Python to be able to load different versions of -the LAMMPS shared library (see "this section"_#py_5 below), you will -need to manually copy files like liblammps_g++.so into the appropriate -system directory. This is not needed if you set the LD_LIBRARY_PATH -environment variable as described above. - -:line - -11.5 Extending Python with MPI to run in parallel :link(py_5),h4 - -If you wish to run LAMMPS in parallel from Python, you need to extend -your Python with an interface to MPI. This also allows you to -make MPI calls directly from Python in your script, if you desire. - -There are several Python packages available that purport to wrap MPI -as a library and allow MPI functions to be called from Python. However, -development on most of them seems to be halted except on: - -"mpi4py"_https://bitbucket.org/mpi4py/mpi4py -"PyPar"_https://github.com/daleroberts/pypar :ul - -Both packages, PyPar and mpi4py have been successfully tested with -LAMMPS. PyPar is simpler and easy to set up and use, but supports -only a subset of MPI. Mpi4py is more MPI-feature complete, but also a -bit more complex to use. As of version 2.0.0, mpi4py is the only -python MPI wrapper that allows passing a custom MPI communicator to -the LAMMPS constructor, which means one can easily run one or more -LAMMPS instances on subsets of the total MPI ranks. - -:line - -PyPar requires the ubiquitous "Numpy package"_http://numpy.scipy.org -be installed in your Python. After launching Python, type - -import numpy :pre - -to see if it is installed. If not, here is how to install it (version -1.3.0b1 as of April 2009). Unpack the numpy tarball and from its -top-level directory, type - -python setup.py build -sudo python setup.py install :pre - -The "sudo" is only needed if required to copy Numpy files into your -Python distribution's site-packages directory. - -To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it -and from its "source" directory, type - -python setup.py build -sudo python setup.py install :pre - -Again, the "sudo" is only needed if required to copy PyPar files into -your Python distribution's site-packages directory. - -If you have successfully installed PyPar, you should be able to run -Python and type - -import pypar :pre - -without error. You should also be able to run python in parallel -on a simple test script - -% mpirun -np 4 python test.py :pre - -where test.py contains the lines - -import pypar -print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre - -and see one line of output for each processor you run on. - -NOTE: To use PyPar and LAMMPS in parallel from Python, you must insure -both are using the same version of MPI. If you only have one MPI -installed on your system, this is not an issue, but it can be if you -have multiple MPIs. Your LAMMPS build is explicit about which MPI it -is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. PyPar uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both PyPar and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that PyPar finds -the right one. - -:line - -To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it -and from its main directory, type - -python setup.py build -sudo python setup.py install :pre - -Again, the "sudo" is only needed if required to copy mpi4py files into -your Python distribution's site-packages directory. To install with -user privilege into the user local directory type - -python setup.py install --user :pre - -If you have successfully installed mpi4py, you should be able to run -Python and type - -from mpi4py import MPI :pre - -without error. You should also be able to run python in parallel -on a simple test script - -% mpirun -np 4 python test.py :pre - -where test.py contains the lines - -from mpi4py import MPI -comm = MPI.COMM_WORLD -print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre - -and see one line of output for each processor you run on. - -NOTE: To use mpi4py and LAMMPS in parallel from Python, you must -insure both are using the same version of MPI. If you only have one -MPI installed on your system, this is not an issue, but it can be if -you have multiple MPIs. Your LAMMPS build is explicit about which MPI -it is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both mpi4py and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that mpi4py finds -the right one. - -:line - -11.6 Testing the Python-LAMMPS interface :link(py_6),h4 - -To test if LAMMPS is callable from Python, launch Python interactively -and type: - ->>> from lammps import lammps ->>> lmp = lammps() :pre - -If you get no errors, you're ready to use LAMMPS from Python. If the -2nd command fails, the most common error to see is - -OSError: Could not load LAMMPS dynamic library :pre - -which means Python was unable to load the LAMMPS shared library. This -typically occurs if the system can't find the LAMMPS shared library or -one of the auxiliary shared libraries it depends on, or if something -about the library is incompatible with your Python. The error message -should give you an indication of what went wrong. - -You can also test the load directly in Python as follows, without -first importing from the lammps.py file: - ->>> from ctypes import CDLL ->>> CDLL("liblammps.so") :pre - -If an error occurs, carefully go thru the steps in "Section -2.4"_Section_start.html#start_4 and above about building a shared -library and about insuring Python can find the necessary two files -it needs. - -[Test LAMMPS and Python in serial:] :h4 - -To run a LAMMPS test in serial, type these lines into Python -interactively from the bench directory: - ->>> from lammps import lammps ->>> lmp = lammps() ->>> lmp.file("in.lj") :pre - -Or put the same lines in the file test.py and run it as - -% python test.py :pre - -Either way, you should see the results of running the in.lj benchmark -on a single processor appear on the screen, the same as if you had -typed something like: - -lmp_g++ -in in.lj :pre - -[Test LAMMPS and Python in parallel:] :h4 - -To run LAMMPS in parallel, assuming you have installed the -"PyPar"_https://github.com/daleroberts/pypar package as discussed -above, create a test.py file containing these lines: - -import pypar -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp -pypar.finalize() :pre - -To run LAMMPS in parallel, assuming you have installed the -"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed -above, create a test.py file containing these lines: - -from mpi4py import MPI -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -me = MPI.COMM_WORLD.Get_rank() -nprocs = MPI.COMM_WORLD.Get_size() -print "Proc %d out of %d procs has" % (me,nprocs),lmp -MPI.Finalize() :pre - -You can either script in parallel as: - -% mpirun -np 4 python test.py :pre - -and you should see the same output as if you had typed - -% mpirun -np 4 lmp_g++ -in in.lj :pre - -Note that if you leave out the 3 lines from test.py that specify PyPar -commands you will instantiate and run LAMMPS independently on each of -the P processors specified in the mpirun command. In this case you -should get 4 sets of output, each showing that a LAMMPS run was made -on a single processor, instead of one set of output showing that -LAMMPS ran on 4 processors. If the 1-processor outputs occur, it -means that PyPar is not working correctly. - -Also note that once you import the PyPar module, PyPar initializes MPI -for you, and you can use MPI calls directly in your Python script, as -described in the PyPar documentation. The last line of your Python -script should be pypar.finalize(), to insure MPI is shut down -correctly. - -[Running Python scripts:] :h4 - -Note that any Python script (not just for LAMMPS) can be invoked in -one of several ways: - -% python foo.script -% python -i foo.script -% foo.script :pre - -The last command requires that the first line of the script be -something like this: - -#!/usr/local/bin/python -#!/usr/local/bin/python -i :pre - -where the path points to where you have Python installed, and that you -have made the script file executable: - -% chmod +x foo.script :pre - -Without the "-i" flag, Python will exit when the script finishes. -With the "-i" flag, you will be left in the Python interpreter when -the script finishes, so you can type subsequent commands. As -mentioned above, you can only run Python interactively when running -Python on a single processor, not in parallel. - -:line -:line - -11.7 Using LAMMPS from Python :link(py_7),h4 - -As described above, the Python interface to LAMMPS consists of a -Python "lammps" module, the source code for which is in -python/lammps.py, which creates a "lammps" object, with a set of -methods that can be invoked on that object. The sample Python code -below assumes you have first imported the "lammps" module in your -Python script, as follows: - -from lammps import lammps :pre - -These are the methods defined by the lammps module. If you look at -the files src/library.cpp and src/library.h you will see they -correspond one-to-one with calls you can make to the LAMMPS library -from a C++ or C or Fortran program, and which are described in -"Section 6.19"_Section_howto.html#howto_19 of the manual. - -The python/examples directory has Python scripts which show how Python -can run LAMMPS, grab data, change it, and put it back into LAMMPS. - -lmp = lammps() # create a LAMMPS object using the default liblammps.so library - # 4 optional args are allowed: name, cmdargs, ptr, comm -lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object -lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later -lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library -lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre - -lmp.close() # destroy a LAMMPS object :pre - -version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre - -lmp.file(file) # run an entire input script, file = "in.lj" -lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" -lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"] -lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre - -size = lmp.extract_setting(name) # return data type info :pre - -xlo = lmp.extract_global(name,type) # extract a global quantity - # name = "boxxlo", "nlocal", etc - # type = 0 = int - # 1 = double :pre - -boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre - -coords = lmp.extract_atom(name,type) # extract a per-atom quantity - # name = "x", "type", etc - # type = 0 = vector of ints - # 1 = array of ints - # 2 = vector of doubles - # 3 = array of doubles :pre - -eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute -v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix - # id = ID of compute or fix - # style = 0 = global data - # 1 = per-atom data - # 2 = local data - # type = 0 = scalar - # 1 = vector - # 2 = array - # i,j = indices of value in global vector or array :pre - -var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable - # name = name of variable - # group = group ID (ignored for equal-style variables) - # flag = 0 = equal-style variable - # 1 = atom-style variable :pre - -value = lmp.get_thermo(name) # return current value of a thermo keyword -natoms = lmp.get_natoms() # total # of atoms as int :pre - -flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful -lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre - -data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID - # name = "x", "charge", "type", etc -data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered) -data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre - -lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID - # name = "x", "charge", "type", etc - # count = # of per-atom values, 1 or 3, etc :pre -lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre - -lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre - -:line - -The lines - -from lammps import lammps -lmp = lammps() :pre - -create an instance of LAMMPS, wrapped in a Python class by the lammps -Python module, and return an instance of the Python class as lmp. It -is used to make all subsequent calls to the LAMMPS library. - -Additional arguments to lammps() can be used to tell Python the name -of the shared library to load or to pass arguments to the LAMMPS -instance, the same as if LAMMPS were launched from a command-line -prompt. - -If the ptr argument is set like this: - -lmp = lammps(ptr=lmpptr) :pre - -then lmpptr must be an argument passed to Python via the LAMMPS -"python"_python.html command, when it is used to define a Python -function that is invoked by the LAMMPS input script. This mode of -using Python with LAMMPS is described above in 11.2. The variable -lmpptr refers to the instance of LAMMPS that called the embedded -Python interpreter. Using it as an argument to lammps() allows the -returned Python class instance "lmp" to make calls to that instance of -LAMMPS. See the "python"_python.html command doc page for examples -using this syntax. - -Note that you can create multiple LAMMPS objects in your Python -script, and coordinate and run multiple simulations, e.g. - -from lammps import lammps -lmp1 = lammps() -lmp2 = lammps() -lmp1.file("in.file1") -lmp2.file("in.file2") :pre - -The file(), command(), commands_list(), commands_string() methods -allow an input script, a single command, or multiple commands to be -invoked. - -The extract_setting(), extract_global(), extract_box(), -extract_atom(), extract_compute(), extract_fix(), and -extract_variable() methods return values or pointers to data -structures internal to LAMMPS. - -For extract_global() see the src/library.cpp file for the list of -valid names. New names could easily be added. A double or integer is -returned. You need to specify the appropriate data type via the type -argument. - -For extract_atom(), a pointer to internal LAMMPS atom-based data is -returned, which you can use via normal Python subscripting. See the -extract() method in the src/atom.cpp file for a list of valid names. -Again, new names could easily be added if the property you want is not -listed. A pointer to a vector of doubles or integers, or a pointer to -an array of doubles (double **) or integers (int **) is returned. You -need to specify the appropriate data type via the type argument. - -For extract_compute() and extract_fix(), the global, per-atom, or -local data calculated by the compute or fix can be accessed. What is -returned depends on whether the compute or fix calculates a scalar or -vector or array. For a scalar, a single double value is returned. If -the compute or fix calculates a vector or array, a pointer to the -internal LAMMPS data is returned, which you can use via normal Python -subscripting. The one exception is that for a fix that calculates a -global vector or array, a single double value from the vector or array -is returned, indexed by I (vector) or I and J (array). I,J are -zero-based indices. The I,J arguments can be left out if not needed. -See "Section 6.15"_Section_howto.html#howto_15 of the manual for a -discussion of global, per-atom, and local data, and of scalar, vector, -and array data types. See the doc pages for individual -"computes"_compute.html and "fixes"_fix.html for a description of what -they calculate and store. - -For extract_variable(), an "equal-style or atom-style -variable"_variable.html is evaluated and its result returned. - -For equal-style variables a single double value is returned and the -group argument is ignored. For atom-style variables, a vector of -doubles is returned, one value per atom, which you can use via normal -Python subscripting. The values will be zero for atoms not in the -specified group. - -The get_thermo() method returns returns the current value of a thermo -keyword as a float. - -The get_natoms() method returns the total number of atoms in the -simulation, as an int. - -The set_variable() methosd sets an existing string-style variable to a -new string value, so that subsequent LAMMPS commands can access the -variable. - -The reset_box() emthods resets the size and shape of the simulation -box, e.g. as part of restoring a previously extracted and saved state -of a simulation. - -The gather methods collect peratom info of the requested type (atom -coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each callling processor. The scatter -functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to invididual atoms, which may be -owned by different processos. - -Note that the data returned by the gather methods, -e.g. gather_atoms("x"), is different from the data structure returned -by extract_atom("x") in four ways. (1) Gather_atoms() returns a -vector which you index as x\[i\]; extract_atom() returns an array -which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms -by atom ID while extract_atom() does not. (3) Gather_atoms() returns -a list of all atoms in the simulation; extract_atoms() returns just -the atoms local to each processor. (4) Finally, the gather_atoms() -data structure is a copy of the atom coords stored internally in -LAMMPS, whereas extract_atom() returns an array that effectively -points directly to the internal data. This means you can change -values inside LAMMPS from Python by assigning a new values to the -extract_atom() array. To do this with the gather_atoms() vector, you -need to change values in the vector, then invoke the scatter_atoms() -method. - -For the scatter methods, the array of coordinates passed to must be a -ctypes vector of ints or doubles, allocated and initialized something -like this: - -from ctypes import * -natoms = lmp.get_natoms() -n3 = 3*natoms -x = (n3*c_double)() -x\[0\] = x coord of atom with ID 1 -x\[1\] = y coord of atom with ID 1 -x\[2\] = z coord of atom with ID 1 -x\[3\] = x coord of atom with ID 2 -... -x\[n3-1\] = z coord of atom with ID natoms -lmp.scatter_atoms("x",1,3,x) :pre - -Alternatively, you can just change values in the vector returned by -the gather methods, since they are also ctypes vectors. - -:line - -As noted above, these Python class methods correspond one-to-one with -the functions in the LAMMPS library interface in src/library.cpp and -library.h. This means you can extend the Python wrapper via the -following steps: - -Add a new interface function to src/library.cpp and -src/library.h. :ulb,l - -Rebuild LAMMPS as a shared library. :l - -Add a wrapper method to python/lammps.py for this interface -function. :l - -You should now be able to invoke the new interface function from a -Python script. Isn't ctypes amazing? :l -:ule - -:line -:line - -11.8 Example Python scripts that use LAMMPS :link(py_8),h4 - -These are the Python scripts included as demos in the python/examples -directory of the LAMMPS distribution, to illustrate the kinds of -things that are possible when Python wraps LAMMPS. If you create your -own scripts, send them to us and we can include them in the LAMMPS -distribution. - -trivial.py, read/run a LAMMPS input script thru Python, -demo.py, invoke various LAMMPS library interface routines, -simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, -split.py, same as simple.py but running in parallel on a subset of procs, -gui.py, GUI go/stop/temperature-slider to control LAMMPS, -plot.py, real-time temperature plot with GnuPlot via Pizza.py, -viz_tool.py, real-time viz via some viz package, -vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) - -:line - -For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" -with "gl" or "atomeye" or "pymol" or "vmd", depending on what -visualization package you have installed. - -Note that for GL, you need to be able to run the Pizza.py GL tool, -which is included in the pizza sub-directory. See the "Pizza.py doc -pages"_pizza for more info: - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) - -Note that for AtomEye, you need version 3, and there is a line in the -scripts that specifies the path and name of the executable. See the -AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details: - -http://mt.seas.upenn.edu/Archive/Graphics/A -http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre - -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) -:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) - -The latter link is to AtomEye 3 which has the scriping -capability needed by these Python scripts. - -Note that for PyMol, you need to have built and installed the -open-source version of PyMol in your Python, so that you can import it -from a Python script. See the PyMol WWW pages "here"_pymolhome or -"here"_pymolopen for more details: - -http://www.pymol.org -http://sourceforge.net/scm/?type=svn&group_id=4546 :pre - -:link(pymolhome,http://www.pymol.org) -:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) - -The latter link is to the open-source version. - -Note that for VMD, you need a fairly current version (1.8.7 works for -me) and there are some lines in the pizza/vmd.py script for 4 PIZZA -variables that have to match the VMD installation on your system. - -:line - -See the python/README file for instructions on how to run them and the -source code for individual scripts for comments about what they do. - -Here are screenshots of the vizplotgui_tool.py script in action for -different visualization package options. Click to see larger images: - -:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg) -:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg) -:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg) -:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg) - -11.9 PyLammps interface :link(py_9),h4 - -Please see the "PyLammps Tutorial"_tutorial_pylammps.html. diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 7d456171dc5f26a3362b2bbdbb6fe8634a245802..cd445b3e14fcfc5638b711ed30c4f3c8c0493329 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -1,4 +1,6 @@ -"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_commands.html :c +"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Section_commands.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -117,10 +119,11 @@ lower-case name of the package, e.g. replica or user-misc. If you want to do one of the following: -use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html) -build with a package that requires an extra library -build with an accelerator package that requires special compiler/linker settings -run on a machine that has its own compilers, settings, or libraries :ul +use a LAMMPS command that requires an extra library (e.g. "dump +image"_dump_image.html) build with a package that requires an extra +library build with an accelerator package that requires special +compiler/linker settings run on a machine that has its own compilers, +settings, or libraries :ul then building LAMMPS is more complicated. You may need to find where extra libraries exist on your machine or install them if they don't. @@ -695,8 +698,8 @@ are always included, plus optional packages. Packages are groups of files that enable a specific set of features. For example, force fields for molecular systems or granular systems are in packages. -"Section 4"_Section_packages.html in the manual has details about all -the packages, which come in two flavors: [standard] and [user] +The "Packages"_Packages.html doc pages has details about all the +packages, which come in two flavors: [standard] and [user] packages. It also has specific instructions for building LAMMPS with any package which requires an extra library. General instructions are below. @@ -826,45 +829,47 @@ options. Packages that require extra libraries :h4,link(start_3_3) A few of the standard and user packages require extra libraries. See -"Section 4"_Section_packages.html for two tables of packages which -indicate which ones require libraries. For each such package, the -Section 4 doc page gives details on how to build the extra library, -including how to download it if necessary. The basic ideas are -summarized here. +the "Packages"_Packages.html doc pages for two tables of packages +which indicate which ones require libraries. For each such package, +the Section 4 doc page gives details on how to build the extra +library, including how to download it if necessary. The basic ideas +are summarized here. [System libraries:] -Packages in the tables "Section 4"_Section_packages.html with a "sys" -in the last column link to system libraries that typically already -exist on your machine. E.g. the python package links to a system -Python library. If your machine does not have the required library, -you will have to download and install it on your machine, in either -the system or user space. +Packages in the standard and user tables of the +"Packages"_Packages.html doc pages with a "sys" in the last column +link to system libraries that typically already exist on your machine. +E.g. the python package links to a system Python library. If your +machine does not have the required library, you will have to download +and install it on your machine, in either the system or user space. [Internal libraries:] -Packages in the tables "Section 4"_Section_packages.html with an "int" -in the last column link to internal libraries whose source code is -included with LAMMPS, in the lib/name directory where name is the -package name. You must first build the library in that directory -before building LAMMPS with that package installed. E.g. the gpu -package links to a library you build in the lib/gpu dir. You can -often do the build in one step by typing "make lib-name args=..." -from the src dir, with appropriate arguments. You can leave off the -args to see a help message. See "Section 4"_Section_packages.html for -details for each package. +Packages in the standard and user tables of the +"Packages"_Packages.html doc pages with an "int" in the last column +link to internal libraries whose source code is included with LAMMPS, +in the lib/name directory where name is the package name. You must +first build the library in that directory before building LAMMPS with +that package installed. E.g. the gpu package links to a library you +build in the lib/gpu dir. You can often do the build in one step by +typing "make lib-name args=..." from the src dir, with appropriate +arguments. You can leave off the args to see a help message. See the +"Packages details"_Packages_details.html doc page for details for each +package. [External libraries:] -Packages in the tables "Section 4"_Section_packages.html with an "ext" -in the last column link to external libraries whose source code is not -included with LAMMPS. You must first download and install the library -before building LAMMPS with that package installed. E.g. the voronoi -package links to the freely available "Voro++ library"_voro_home2. You -can often do the download/build in one step by typing "make lib-name +Packages in the standard and user tables of the +"Packages"_Packages.html doc pages with an "ext" in the last column +link to external libraries whose source code is not included with +LAMMPS. You must first download and install the library before +building LAMMPS with that package installed. E.g. the voronoi package +links to the freely available "Voro++ library"_voro_home2. You can +often do the download/build in one step by typing "make lib-name args=..." from the src dir, with appropriate arguments. You can leave -off the args to see a help message. See "Section -4"_Section_packages.html for details for each package. +off the args to see a help message. See the "Packages +details"_Packages_details.html doc page for details for each package. :link(voro_home2,http://math.lbl.gov/voro++) @@ -886,9 +891,9 @@ copied from a lib/name/Makefile.lammps.* file when the library is built. If those settings are not correct for your machine you will need to edit or create an appropriate Makefile.lammps file. -Package-specific details for these steps are given in "Section -4"_Section_packages.html an in README files in the lib/name -directories. +Package-specific details for these steps are given on the "Packages +details"_Packages_details.html doc page and in README files in the +lib/name directories. [Compiler options needed for accelerator packages:] @@ -899,14 +904,14 @@ these accelerator packages for optimal performance requires specific settings in the Makefile.machine file you use. A summary of the Makefile.machine settings needed for each of these -packages is given in "Section 4"_Section_packages.html. More info is -given on the doc pages that describe each package in detail: +packages is given on the "Packages"_Packages.html doc pages. More +info is given on the doc pages that describe each package in detail: -5.3.1 "USER-INTEL package"_accelerate_intel.html -5.3.2 "GPU package"_accelerate_intel.html -5.3.3 "KOKKOS package"_accelerate_kokkos.html -5.3.4 "USER-OMP package"_accelerate_omp.html -5.3.5 "OPT package"_accelerate_opt.html :all(b) +"USER-INTEL package"_Speed_intel.html +"GPU package"_Speed_gpu.html +"KOKKOS package"_Speed_kokkos.html +"USER-OMP package"_Speed_omp.html +"OPT package"_Speed_opt.html :all(b) You can also use or examine the following machine Makefiles in src/MAKE/OPTIONS, which include the settings. Note that the @@ -930,8 +935,8 @@ Makefile.opt :ul LAMMPS can be built as either a static or shared library, which can then be called from another application or a scripting language. See "this section"_Section_howto.html#howto_10 for more info on coupling -LAMMPS to other codes. See "this section"_Section_python.html for -more info on wrapping and running LAMMPS from Python. +LAMMPS to other codes. See the "Python"_Python.html doc page for more +info on wrapping and running LAMMPS from Python. Static library :h4 @@ -955,15 +960,15 @@ dynamically loaded, e.g. from Python, type make foo mode=shlib :pre where foo is the machine name. This kind of library is required when -wrapping LAMMPS with Python; see "Section 11"_Section_python.html -for details. This will use the SHFLAGS and SHLIBFLAGS settings in +wrapping LAMMPS with Python; see the "Python"_Python.html doc page for +details. This will use the SHFLAGS and SHLIBFLAGS settings in src/MAKE/Makefile.foo and perform the build in the directory Obj_shared_foo. This is so that each file can be compiled with the -fPIC flag which is required for inclusion in a shared library. The build will create the file liblammps_foo.so which another application -can link to dynamically. It will also create a soft link liblammps.so, -which will point to the most recently built shared library. This is -the file the Python wrapper loads by default. +can link to dynamically. It will also create a soft link +liblammps.so, which will point to the most recently built shared +library. This is the file the Python wrapper loads by default. Note that for a shared library to be usable by a calling program, all the auxiliary libraries it depends on must also exist as shared @@ -1035,10 +1040,10 @@ src/library.cpp and src/library.h. See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS thru its library interface. There are other examples as well in the COUPLE directory which are -discussed in "Section 6.10"_Section_howto.html#howto_10 of the -manual. See "Section 11"_Section_python.html of the manual for a -description of the Python wrapper provided with LAMMPS that operates -through the LAMMPS library interface. +discussed in "Section 6.10"_Section_howto.html#howto_10 of the manual. +See the "Python"_Python.html doc page for a description of the Python +wrapper provided with LAMMPS that operates through the LAMMPS library +interface. The files src/library.cpp and library.h define the C-style API for using LAMMPS as a library. See "Section @@ -1177,7 +1182,7 @@ than your working directory, which is probably not what you want. If LAMMPS encounters errors in the input script or while running a simulation it will print an ERROR message and stop or a WARNING -message and continue. See "Section 12"_Section_errors.html for a +message and continue. See the "Errors"_Errors.html doc page for a discussion of the various kinds of errors LAMMPS can or can't detect, a list of all ERROR and WARNING messages, and what to do about them. @@ -1274,8 +1279,8 @@ Either the full word or an abbreviation can be used for the keywords. Note that the keywords do not use a leading minus sign. I.e. the keyword is "t", not "-t". Also note that each of the keywords has a default setting. Example of when to use these options and what -settings to use on different platforms is given in "Section -5.3"_Section_accelerate.html#acc_3. +settings to use on different platforms is given on the "Speed +kokkos"_Speed_kokkos.html doc page. d or device g or gpus @@ -1459,8 +1464,7 @@ cores within each node are ranked in a desired order. Or when using the "run_style verlet/split"_run_style.html command with 2 partitions to insure that a specific Kspace processor (in the 2nd partition) is matched up with a specific set of processors in the 1st partition. -See the "Section 5"_Section_accelerate.html doc pages for -more details. +See the "Speed tips"_Speed_tips.html doc page for more details. If the keyword {nth} is used with a setting {N}, then it means every Nth processor will be moved to the end of the ranking. This is useful diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e2097ab1d9b99accb71f6bb3d7cd600f1d6e1c9 --- /dev/null +++ b/doc/src/Speed.txt @@ -0,0 +1,64 @@ +"Previous Section"_Package.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Section_howto.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Accelerate performance :h2 + +This section describes various methods for improving LAMMPS +performance for different classes of problems running on different +kinds of machines. + +There are two thrusts to the discussion that follows. The first is +using code options that implement alternate algorithms that can +speed-up a simulation. The second is to use one of the several +accelerator packages provided with LAMMPS that contain code optimized +for certain kinds of hardware, including multi-core CPUs, GPUs, and +Intel Xeon Phi coprocessors. + +The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS +web site gives performance results for the various accelerator +packages discussed on the "Speed packages"_Speed_packages.html doc +page, for several of the standard LAMMPS benchmark problems, as a +function of problem size and number of compute nodes, on different +hardware platforms. + + + + + +"Benchmarks"_Speed_bench.html +"Measuring performance"_Speed_measure.html :all(b) + +"General tips"_Speed_tips.html :all(b) + +"Accelerator packages"_Speed_packages.html +"GPU package"_Speed_gpu.html +"USER-INTEL package"_Speed_intel.html +"KOKKOS package"_Speed_kokkos.html +"USER-OMP package"_Speed_omp.html +"OPT package"_Speed_opt.html +"Comparison of accelerator packages"_Speed_compare.html :all(b) + + diff --git a/doc/src/Section_perf.txt b/doc/src/Speed_bench.txt similarity index 86% rename from doc/src/Section_perf.txt rename to doc/src/Speed_bench.txt index 9998cb0d9a1371fdcca7c6e927c49925bb6f81d2..dc76588c11699822e11030b9db676683492794dd 100644 --- a/doc/src/Section_perf.txt +++ b/doc/src/Speed_bench.txt @@ -1,4 +1,5 @@ -"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -6,12 +7,12 @@ :line -8. Performance & scalability :h2 +Benchmarks :h3 -Current LAMMPS performance is discussed on the Benchmarks page of the -"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are -listed. The page has several sections, which are briefly described -below: +Current LAMMPS performance is discussed on the "Benchmarks +page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws +where timings and parallel efficiencies are listed. The page has +several sections, which are briefly described below: CPU performance on 5 standard problems, strong and weak scaling GPU and Xeon Phi performance on same and related problems @@ -51,8 +52,8 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI and bench/KEPLER dirs have input files and scripts and instructions for running the same (or similar) problems using OpenMP or GPU or Xeon Phi acceleration options. See the README files in those dirs and the -"Section 5.3"_Section_accelerate.html#acc_3 doc pages for -instructions on how to build LAMMPS and run on that kind of hardware. +"Speed packages"_Speed_packages.html doc pages for instructions on how +to build LAMMPS and run on that kind of hardware. The bench/POTENTIALS directory has input files which correspond to the table of results on the diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt new file mode 100644 index 0000000000000000000000000000000000000000..6c947b9662dca8be601ce897c2d1a149a812bbe0 --- /dev/null +++ b/doc/src/Speed_compare.txt @@ -0,0 +1,73 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Comparison of various accelerator packages :h3 + +NOTE: this section still needs to be re-worked with additional KOKKOS +and USER-INTEL information. + +The next section compares and contrasts the various accelerator +options, since there are multiple ways to perform OpenMP threading, +run on GPUs, and run on Intel Xeon Phi coprocessors. + +All 3 of these packages accelerate a LAMMPS calculation using NVIDIA +hardware, but they do it in different ways. + +As a consequence, for a particular simulation on specific hardware, +one package may be faster than the other. We give guidelines below, +but the best way to determine which package is faster for your input +script is to try both of them on your machine. See the benchmarking +section below for examples where this has been done. + +[Guidelines for using each package optimally:] + +The GPU package allows you to assign multiple CPUs (cores) to a single +GPU (a common configuration for "hybrid" nodes that contain multicore +CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l + +The GPU package moves per-atom data (coordinates, forces) +back-and-forth between the CPU and GPU every timestep. The +KOKKOS/CUDA package only does this on timesteps when a CPU calculation +is required (e.g. to invoke a fix or compute that is non-GPU-ized). +Hence, if you can formulate your input script to only use GPU-ized +fixes and computes, and avoid doing I/O too often (thermo output, dump +file snapshots, restart files), then the data transfer cost of the +KOKKOS/CUDA package can be very low, causing it to run faster than the +GPU package. :l + +The GPU package is often faster than the KOKKOS/CUDA package, if the +number of atoms per GPU is smaller. The crossover point, in terms of +atoms/GPU at which the KOKKOS/CUDA package becomes faster depends +strongly on the pair style. For example, for a simple Lennard Jones +system the crossover (in single precision) is often about 50K-100K +atoms per GPU. When performing double precision calculations the +crossover point can be significantly smaller. :l + +Both packages compute bonded interactions (bonds, angles, etc) on the +CPU. If the GPU package is running with several MPI processes +assigned to one GPU, the cost of computing the bonded interactions is +spread across more CPUs and hence the GPU package can run faster. :l + +When using the GPU package with multiple CPUs assigned to one GPU, its +performance depends to some extent on high bandwidth between the CPUs +and the GPU. Hence its performance is affected if full 16 PCIe lanes +are not available for each GPU. In HPC environments this can be the +case if S2050/70 servers are used, where two devices generally share +one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide +full 16 lanes to each of the PCIe 2.0 16x slots. :l +:ule + +[Differences between the two packages:] + +The GPU package accelerates only pair force, neighbor list, and PPPM +calculations. :ulb,l + +The GPU package requires neighbor lists to be built on the CPU when using +exclusion lists, hybrid pair styles, or a triclinic simulation box. :l +:ule diff --git a/doc/src/accelerate_gpu.txt b/doc/src/Speed_gpu.txt similarity index 96% rename from doc/src/accelerate_gpu.txt rename to doc/src/Speed_gpu.txt index 816a31c788e99592a3f70af5e42c786c2ce75410..d6ebbf8069d1adde06b1b52c83fff027a3905377 100644 --- a/doc/src/accelerate_gpu.txt +++ b/doc/src/Speed_gpu.txt @@ -1,5 +1,5 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -7,9 +7,7 @@ :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.1 GPU package :h5 +GPU package :h3 The GPU package was developed by Mike Brown at ORNL and his collaborators, particularly Trung Nguyen (ORNL). It provides GPU @@ -72,10 +70,9 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t [Building LAMMPS with the GPU package:] This requires two steps (a,b): build the GPU library, then build -LAMMPS with the GPU package. - -You can do both these steps in one line as described in -"Section 4"_Section_packages.html of the manual. +LAMMPS with the GPU package. You can do both these steps in one line +as described on the "Packages details"_Packages_details.html#GPU doc +page. Or you can follow these two (a,b) steps: diff --git a/doc/src/accelerate_intel.txt b/doc/src/Speed_intel.txt similarity index 97% rename from doc/src/accelerate_intel.txt rename to doc/src/Speed_intel.txt index 71f5185b154f9f832d0ab5b92bd3d2e49f25df2f..08e3fbc4cc110256f91ac70f4bbe99c428e44734 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/Speed_intel.txt @@ -1,5 +1,5 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -7,9 +7,7 @@ :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.2 USER-INTEL package :h5 +USER-INTEL package :h3 The USER-INTEL package is maintained by Mike Brown at Intel Corporation. It provides two methods for accelerating simulations, @@ -188,8 +186,8 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the -USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or -"KOKKOS package"_accelerate_kokkos.html. In the example above, up +USER-INTEL package, "USER-OMP package"_Speed_omp.html, or +"KOKKOS package"_Speed_kokkos.html. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% performance gain can be achieved. @@ -233,9 +231,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi :pre -Alternatively this can be done as a single command with -suitable make command invocations. This is discussed in "Section -4"_Section_packages.html of the manual. +Alternatively this can be done as a single command with suitable make +command invocations, as described on the "Packages +details"_Packages_details.html#USER-INTEL doc page. Note that if you build with support for a Phi coprocessor, the same binary can be used on nodes with or without coprocessors installed. @@ -391,8 +389,8 @@ performance and/or scalability for simple 2-body potentials such as lj/cut or when using LRT mode on processors supporting AVX-512. Not all styles are supported in the USER-INTEL package. You can mix -the USER-INTEL package with styles from the "OPT"_accelerate_opt.html -package or the "USER-OMP package"_accelerate_omp.html. Of course, +the USER-INTEL package with styles from the "OPT"_Speed_opt.html +package or the "USER-OMP package"_Speed_omp.html. Of course, this requires that these packages were installed at build time. This can performed automatically by using "-sf hybrid intel opt" or "-sf hybrid intel omp" command-line options. Alternatively, the "opt" diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/Speed_kokkos.txt similarity index 97% rename from doc/src/accelerate_kokkos.txt rename to doc/src/Speed_kokkos.txt index 0c9178d6e4f42863003b0a2848f29cd42189620f..8e01db7bdc7b52b3a95f7a5b3e73ccdb97bff1f4 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -1,5 +1,5 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -7,9 +7,7 @@ :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.3 KOKKOS package :h5 +KOKKOS package :h3 Kokkos is a templated C++ library that provides abstractions to allow a single implementation of an application kernel (e.g. a pair style) to run efficiently on @@ -85,10 +83,10 @@ make kokkos_phi :pre [Compile for CPUs and GPUs (with OpenMPI or MPICH):] -NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software -version 7.5 or later must be installed on your system. See the -discussion for the "GPU"_accelerate_gpu.html package for details of -how to check and do this. +NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA +software version 7.5 or later must be installed on your system. See +the discussion for the "GPU package"_Speed_gpu.html for details of how +to check and do this. use a C++11 compatible compiler and set KOKKOS_ARCH variable in /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described @@ -434,8 +432,8 @@ migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP provides alternative methods via environment variables for binding -threads to hardware cores. More info on binding threads to cores is -given in "Section 5.3"_Section_accelerate.html#acc_3. +threads to hardware cores. More info on binding threads to cores is +given on the "Speed omp"_Speed_omp.html doc page. KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism on most Unix platforms. This library is not available on all diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt new file mode 100644 index 0000000000000000000000000000000000000000..03c0345c206c238f3061e714ab935b35a558ccce --- /dev/null +++ b/doc/src/Speed_measure.txt @@ -0,0 +1,55 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Measuring performance :h3 + +Before trying to make your simulation run faster, you should +understand how it currently performs and where the bottlenecks are. + +The best way to do this is run the your system (actual number of +atoms) for a modest number of timesteps (say 100 steps) on several +different processor counts, including a single processor if possible. +Do this for an equilibrium version of your system, so that the +100-step timings are representative of a much longer run. There is +typically no need to run for 1000s of timesteps to get accurate +timings; you can simply extrapolate from short runs. + +For the set of runs, look at the timing data printed to the screen and +log file at the end of each LAMMPS run. "This +section"_Section_start.html#start_7 of the manual has an overview. + +Running on one (or a few processors) should give a good estimate of +the serial performance and what portions of the timestep are taking +the most time. Running the same problem on a few different processor +counts should give an estimate of parallel scalability. I.e. if the +simulation runs 16x faster on 16 processors, its 100% parallel +efficient; if it runs 8x faster on 16 processors, it's 50% efficient. + +The most important data to look at in the timing info is the timing +breakdown and relative percentages. For example, trying different +options for speeding up the long-range solvers will have little impact +if they only consume 10% of the run time. If the pairwise time is +dominating, you may want to look at GPU or OMP versions of the pair +style, as discussed below. Comparing how the percentages change as +you increase the processor count gives you a sense of how different +operations within the timestep are scaling. Note that if you are +running with a Kspace solver, there is additional output on the +breakdown of the Kspace time. For PPPM, this includes the fraction +spent on FFTs, which can be communication intensive. + +Another important detail in the timing info are the histograms of +atoms counts and neighbor counts. If these vary widely across +processors, you have a load-imbalance issue. This often results in +inaccurate relative timing data, because processors have to wait when +communication occurs for other processors to catch up. Thus the +reported times for "Communication" or "Other" may be higher than they +really are, due to load-imbalance. If this is an issue, you can +uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile +LAMMPS, to obtain synchronized timings. + diff --git a/doc/src/accelerate_omp.txt b/doc/src/Speed_omp.txt similarity index 96% rename from doc/src/accelerate_omp.txt rename to doc/src/Speed_omp.txt index fa7bef1a520bd867b4d3cf610d50b5ea8614c865..9685b6d349fe730517f07a5906f8802d094ffb36 100644 --- a/doc/src/accelerate_omp.txt +++ b/doc/src/Speed_omp.txt @@ -1,5 +1,5 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -7,9 +7,7 @@ :line -"Return to Section 5 overview"_Section_accelerate.html - -5.3.4 USER-OMP package :h5 +USER-OMP package :h3 The USER-OMP package was developed by Axel Kohlmeyer at Temple University. It provides multi-threaded versions of most pair styles, @@ -39,7 +37,8 @@ each MPI task running on a CPU. The lines above illustrate how to include/build with the USER-OMP package in two steps, using the "make" command. Or how to do it with -one command as described in "Section 4"_Section_packages.html of the manual. +one command as described on the "Packages +details"_Packages_details.html#USER-OMP doc page. Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must include "-fopenmp". Likewise, if you use an Intel compiler, the @@ -100,7 +99,7 @@ task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This is because many of the USER-OMP styles contain similar optimizations to those used in the OPT package, described in "Section -5.3.5"_accelerate_opt.html. +5.3.5"_Speed_opt.html. With multiple threads/task, the optimal choice of number of MPI tasks/node and OpenMP threads/task can vary a lot and should always be diff --git a/doc/src/accelerate_opt.txt b/doc/src/Speed_opt.txt similarity index 86% rename from doc/src/accelerate_opt.txt rename to doc/src/Speed_opt.txt index 845264b5227ca31493cb582eac91ab5c216427ae..7d0d7169f001682b76fa931a00459df293379101 100644 --- a/doc/src/accelerate_opt.txt +++ b/doc/src/Speed_opt.txt @@ -1,5 +1,5 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -7,9 +7,7 @@ :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.5 OPT package :h5 +OPT package :h3 The OPT package was developed by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge @@ -34,7 +32,8 @@ None. The lines above illustrate how to build LAMMPS with the OPT package in two steps, using the "make" command. Or how to do it with one command -as described in "Section 4"_Section_packages.html of the manual. +as described on the "Packages details"_Packages_details.html#OPT doc +page. Note that if you use an Intel compiler to build with the OPT package, the CCFLAGS setting in your Makefile.machine must include "-restrict". diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt new file mode 100644 index 0000000000000000000000000000000000000000..13b5e183dbbfcac153b09377d8e698b2deca3490 --- /dev/null +++ b/doc/src/Speed_packages.txt @@ -0,0 +1,191 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +Accelerator packages :h3 + +Accelerated versions of various "pair_style"_pair_style.html, +"fixes"_fix.html, "computes"_compute.html, and other commands have +been added to LAMMPS, which will typically run faster than the +standard non-accelerated versions. Some require appropriate hardware +to be present on your system, e.g. GPUs or Intel Xeon Phi +coprocessors. + +All of these commands are in packages provided with LAMMPS. An +overview of packages is give on the "Packages"_Packages.html doc +pages. + +These are the accelerator packages currently in LAMMPS, either as +standard or user packages: + +"GPU Package"_Speed_gpu.html : for NVIDIA GPUs as well as OpenCL support +"USER-INTEL Package"_Speed_intel.html : for Intel CPUs and Intel Xeon Phi +"KOKKOS Package"_Speed_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading +"USER-OMP Package"_Speed_omp.html : for OpenMP threading and generic CPU optimizations +"OPT Package"_Speed_opt.html : generic CPU optimizations :tb(s=:) + + + +Inverting this list, LAMMPS currently has acceleration support for +three kinds of hardware, via the listed packages: + +Many-core CPUs : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html, "USER-OMP"_Speed_omp.html, "OPT"_Speed_opt.html packages +NVIDIA GPUs : "GPU"_Speed_gpu.html, "KOKKOS"_Speed_kokkos.html packages +Intel Phi : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html packages :tb(s=:) + +Which package is fastest for your hardware may depend on the size +problem you are running and what commands (accelerated and +non-accelerated) are invoked by your input script. While these doc +pages include performance guidelines, there is no substitute for +trying out the different packages appropriate to your hardware. + +Any accelerated style has the same name as the corresponding standard +style, except that a suffix is appended. Otherwise, the syntax for +the command that uses the style is identical, their functionality is +the same, and the numerical results it produces should also be the +same, except for precision and round-off effects. + +For example, all of these styles are accelerated variants of the +Lennard-Jones "pair_style lj/cut"_pair_lj.html: + +"pair_style lj/cut/gpu"_pair_lj.html +"pair_style lj/cut/intel"_pair_lj.html +"pair_style lj/cut/kk"_pair_lj.html +"pair_style lj/cut/omp"_pair_lj.html +"pair_style lj/cut/opt"_pair_lj.html :ul + +To see what accelerate styles are currently available, see +"Section 3.5"_Section_commands.html#cmd_5 of the manual. The +doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or +"fix nve"_fix_nve.html) also list any accelerated variants available +for that style. + +To use an accelerator package in LAMMPS, and one or more of the styles +it provides, follow these general steps. Details vary from package to +package and are explained in the individual accelerator doc pages, +listed above: + +build the accelerator library | + only for GPU package | +install the accelerator package | + make yes-opt, make yes-user-intel, etc | +add compile/link flags to Makefile.machine in src/MAKE | + only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | +re-build LAMMPS | + make machine | +prepare and test a regular LAMMPS simulation | + lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | +enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, | + only needed for KOKKOS package | +set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, | + only if defaults need to be changed | +use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu +:tb(c=2,s=|) + +Note that the first 4 steps can be done as a single command with +suitable make command invocations. This is discussed on the +"Packages"_Packages.html doc pages, and its use is illustrated in the +individual accelerator sections. Typically these steps only need to +be done once, to create an executable that uses one or more +accelerator packages. + +The last 4 steps can all be done from the command-line when LAMMPS is +launched, without changing your input script, as illustrated in the +individual accelerator sections. Or you can add +"package"_package.html and "suffix"_suffix.html commands to your input +script. + +NOTE: With a few exceptions, you can build a single LAMMPS executable +with all its accelerator packages installed. Note however that the +USER-INTEL and KOKKOS packages require you to choose one of their +hardware options when building for a specific platform. I.e. CPU or +Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi +option for the KOKKOS package. + +These are the exceptions. You cannot build a single executable with: + +both the USER-INTEL Phi and KOKKOS Phi options +the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul + +See the examples/accelerate/README and make.list files for sample +Make.py commands that build LAMMPS with any or all of the accelerator +packages. As an example, here is a command that builds with all the +GPU related packages installed (GPU, KOKKOS with Cuda), including +settings to build the needed auxiliary GPU libraries for Kepler GPUs: + +Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \ + -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre + +The examples/accelerate directory also has input scripts that can be +used with all of the accelerator packages. See its README file for +details. + +Likewise, the bench directory has FERMI and KEPLER and PHI +sub-directories with Make.py commands and input scripts for using all +the accelerator packages on various machines. See the README files in +those dirs. + +As mentioned above, the "Benchmark +page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives +performance results for the various accelerator packages for several +of the standard LAMMPS benchmark problems, as a function of problem +size and number of compute nodes, on different hardware platforms. + +Here is a brief summary of what the various packages provide. Details +are in the individual accelerator sections. + +Styles with a "gpu" suffix are part of the GPU package, and can be run +on NVIDIA GPUs. The speed-up on a GPU depends on a variety of +factors, discussed in the accelerator sections. :ulb,l + +Styles with an "intel" suffix are part of the USER-INTEL +package. These styles support vectorized single and mixed precision +calculations, in addition to full double precision. In extreme cases, +this can provide speedups over 3.5x on CPUs. The package also +supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) +coprocessors. This can result in additional speedup over 2x depending +on the hardware configuration. :l + +Styles with a "kk" suffix are part of the KOKKOS package, and can be +run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel +Xeon Phi in "native" mode. The speed-up depends on a variety of +factors, as discussed on the KOKKOS accelerator page. :l + +Styles with an "omp" suffix are part of the USER-OMP package and allow +a pair-style to be run in multi-threaded mode using OpenMP. This can +be useful on nodes with high-core counts when using less MPI processes +than cores is advantageous, e.g. when running with PPPM so that FFTs +are run on fewer MPI processors or when the many MPI tasks would +overload the available bandwidth for communication. :l + +Styles with an "opt" suffix are part of the OPT package and typically +speed-up the pairwise calculations of your simulation by 5-25% on a +CPU. :l +:ule + +The individual accelerator package doc pages explain: + +what hardware and software the accelerated package requires +how to build LAMMPS with the accelerated package +how to run with the accelerated package either via command-line switches or modifying the input script +speed-ups to expect +guidelines for best performance +restrictions :ul + diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt new file mode 100644 index 0000000000000000000000000000000000000000..c0d360cd8e2932dd726b19713cb50cf18ef35620 --- /dev/null +++ b/doc/src/Speed_tips.txt @@ -0,0 +1,63 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +General tips :h3 + +NOTE: this section 5.2 is still a work in progress + +Here is a list of general ideas for improving simulation performance. +Most of them are only applicable to certain models and certain +bottlenecks in the current performance, so let the timing data you +generate be your guide. It is hard, if not impossible, to predict how +much difference these options will make, since it is a function of +problem size, number of processors used, and your machine. There is +no substitute for identifying performance bottlenecks, and trying out +various options. + +make individual pages for these, or one for PPPM +one for timestepping, etc +one for balancing +or proc layout + +rRESPA +2-FFT PPPM +Staggered PPPM +single vs double PPPM +partial charge PPPM +verlet/split run style +processor command for proc layout and numa layout +load-balancing: balance and fix balance :ul + +2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses +2 FFTs instead of the 4 FFTs used by the default {ik differentiation} +PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to +achieve the same accuracy as 4-FFT PPPM. For problems where the FFT +cost is the performance bottleneck (typically large problems running +on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. + +Staggered PPPM performs calculations using two different meshes, one +shifted slightly with respect to the other. This can reduce force +aliasing errors and increase the accuracy of the method, but also +doubles the amount of work required. For high relative accuracy, using +staggered PPPM allows one to half the mesh size in each dimension as +compared to regular PPPM, which can give around a 4x speedup in the +kspace time. However, for low relative accuracy, using staggered PPPM +gives little benefit and can be up to 2x slower in the kspace +time. For example, the rhodopsin benchmark was run on a single +processor, and results for kspace time vs. relative accuracy for the +different methods are shown in the figure below. For this system, +staggered PPPM (using ik differentiation) becomes useful when using a +relative accuracy of slightly greater than 1e-5 and above. + +:c,image(JPG/rhodo_staggered.jpg) + +NOTE: Using staggered PPPM may not give the same increase in accuracy +of energy and pressure as it does in forces, so some caution must be +used if energy and/or pressure are quantities of interest, such as +when using a barostat. diff --git a/doc/src/Section_tools.txt b/doc/src/Tools.txt similarity index 88% rename from doc/src/Section_tools.txt rename to doc/src/Tools.txt index 7cc07cbec55a5e7c4f3545c623875be8cc6919cc..7165010da3bee1b7b937ceb798313f99b0c1ee7a 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Tools.txt @@ -1,6 +1,6 @@ "Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_modify.html :c +Section"_Modify.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -8,33 +8,34 @@ Section"_Section_modify.html :c :line -9. Additional tools :h2 +Auxiliary tools :h2 LAMMPS is designed to be a computational kernel for performing molecular dynamics computations. Additional pre- and post-processing -steps are often necessary to setup and analyze a simulation. A -list of such tools can be found on the LAMMPS home page -at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html +steps are often necessary to setup and analyze a simulation. A list +of such tools can be found on the "LAMMPS webpage"_lws at these links: -A few additional tools are provided with the LAMMPS distribution -and are described in this section. +"Pre/Post processing"_http://lammps.sandia.gov/prepost.html +"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html +"Pizza.py toolkit"_pizza :ul -Our group has also written and released a separate toolkit called -"Pizza.py"_pizza which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. +The last link for "Pizza.py"_pizza is a Python-based tool developed at +Sandia which provides tools for doing setup, analysis, plotting, and +visualization for LAMMPS simulations. -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) +:link(pizza,http://pizza.sandia.gov) :link(python,http://www.python.org) +Additional tools included in the LAMMPS distribution are described on +this page. + Note that many users write their own setup or analysis tools or use other existing codes and convert their output to a LAMMPS input format or vice versa. The tools listed here are included in the LAMMPS distribution as examples of auxiliary tools. Some of them are not -actively supported by Sandia, as they were contributed by LAMMPS -users. If you have problems using them, we can direct you to the -authors. +actively supported by the LAMMPS developers, as they were contributed +by LAMMPS users. If you have problems using them, we can direct you +to the authors. The source code for each of these codes is in the tools sub-directory of the LAMMPS distribution. There is a Makefile (which you may need @@ -71,11 +72,12 @@ own sub-directories with their own Makefiles and/or README files. "reax"_#reax_tool "smd"_#smd "vim"_#vim -"xmgrace"_#xmgrace +"xmgrace"_#xmgrace :ul +:line :line -amber2lmp tool :h3,link(amber) +amber2lmp tool :h4,link(amber) The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the @@ -90,7 +92,7 @@ necessary modifications yourself. :line -binary2txt tool :h3,link(binary) +binary2txt tool :h4,link(binary) The file binary2txt.cpp converts one or more binary LAMMPS dump file into ASCII text files. The syntax for running the tool is @@ -103,7 +105,7 @@ since binary files are not compatible across all platforms. :line -ch2lmp tool :h3,link(charmm) +ch2lmp tool :h4,link(charmm) The ch2lmp sub-directory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS. @@ -128,7 +130,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. :line -chain tool :h3,link(chain) +chain tool :h4,link(chain) The file chain.f creates a LAMMPS data file containing bead-spring polymer chains and/or monomer solvent atoms. It uses a text file @@ -145,7 +147,7 @@ system for the "chain benchmark"_Section_perf.html. :line -colvars tools :h3,link(colvars) +colvars tools :h4,link(colvars) The colvars directory contains a collection of tools for postprocessing data produced by the colvars collective variable library. @@ -167,7 +169,7 @@ gmail.com) at ICTP, Italy. :line -createatoms tool :h3,link(createatoms) +createatoms tool :h4,link(createatoms) The tools/createatoms directory contains a Fortran program called createAtoms.f which can generate a variety of interesting crystal @@ -180,7 +182,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. :line -doxygen tool :h3,link(doxygen) +doxygen tool :h4,link(doxygen) The tools/doxygen directory contains a shell script called doxygen.sh which can generate a call graph and API lists using @@ -192,7 +194,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. :line -drude tool :h3,link(drude) +drude tool :h4,link(drude) The tools/drude directory contains a Python script called polarizer.py which can add Drude oscillators to a LAMMPS @@ -205,7 +207,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr :line -eam database tool :h3,link(eamdb) +eam database tool :h4,link(eamdb) The tools/eam_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 @@ -221,7 +223,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, :line -eam generate tool :h3,link(eamgn) +eam generate tool :h4,link(eamgn) The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated "embedded atom @@ -234,7 +236,7 @@ The source files and potentials were provided by Gerolf Ziegenhain :line -eff tool :h3,link(eff) +eff tool :h4,link(eff) The tools/eff directory contains various scripts for generating structures and post-processing output for simulations using the @@ -245,18 +247,18 @@ These tools were provided by Andres Jaramillo-Botero at CalTech :line -emacs tool :h3,link(emacs) +emacs tool :h4,link(emacs) -The tools/emacs directory contains a Lips add-on file for Emacs that -enables a lammps-mode for editing of input scripts when using Emacs, -with various highlighting options setup. +The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs +that enables a lammps-mode for editing input scripts when using GNU Emacs, +with various highlighting options set up. These tools were provided by Aidan Thompson at Sandia (athomps at sandia.gov). :line -fep tool :h3,link(fep) +fep tool :h4,link(fep) The tools/fep directory contains Python scripts useful for post-processing results from performing free-energy perturbation @@ -269,7 +271,7 @@ See README file in the tools/fep directory. :line -i-pi tool :h3,link(ipi) +i-pi tool :h4,link(ipi) The tools/i-pi directory contains a version of the i-PI package, with all the LAMMPS-unrelated files removed. It is provided so that it can @@ -286,7 +288,7 @@ calculations with LAMMPS. :line -ipp tool :h3,link(ipp) +ipp tool :h4,link(ipp) The tools/ipp directory contains a Perl script ipp which can be used to facilitate the creation of a complicated file (say, a lammps input @@ -300,7 +302,7 @@ tools/createatoms tool's input file. :line -kate tool :h3,link(kate) +kate tool :h4,link(kate) The file in the tools/kate directory is an add-on to the Kate editor in the KDE suite that allow syntax highlighting of LAMMPS input @@ -311,7 +313,7 @@ The file was provided by Alessandro Luigi Sellerio :line -lmp2arc tool :h3,link(arc) +lmp2arc tool :h4,link(arc) The lmp2arc sub-directory contains a tool for converting LAMMPS output files to the format for Accelrys' Insight MD code (formerly @@ -327,7 +329,7 @@ Greathouse at Sandia (jagreat at sandia.gov). :line -lmp2cfg tool :h3,link(cfg) +lmp2cfg tool :h4,link(cfg) The lmp2cfg sub-directory contains a tool for converting LAMMPS output files into a series of *.cfg files which can be read into the @@ -338,7 +340,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). :line -matlab tool :h3,link(matlab) +matlab tool :h4,link(matlab) The matlab sub-directory contains several "MATLAB"_matlabhome scripts for post-processing LAMMPS output. The scripts include readers for log @@ -356,7 +358,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ :line -micelle2d tool :h3,link(micelle) +micelle2d tool :h4,link(micelle) The file micelle2d.f creates a LAMMPS data file containing short lipid chains in a monomer solution. It uses a text file containing lipid @@ -369,11 +371,11 @@ micelle2d < def.micelle2d > data.file :pre See the def.micelle2d file in the tools directory for an example of a definition file. This tool was used to create the system for the -"micelle example"_Section_example.html. +"micelle example"_Examples.html. :line -moltemplate tool :h3,link(moltemplate) +moltemplate tool :h4,link(moltemplate) The moltemplate sub-directory contains a Python-based tool for building molecular systems based on a text-file description, and @@ -387,7 +389,7 @@ supports it. It has its own WWW page at :line -msi2lmp tool :h3,link(msi) +msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS template input and data files from BIOVIA's Materias Studio files (formerly Accelrys' @@ -404,7 +406,7 @@ See the README file in the tools/msi2lmp folder for more information. :line -phonon tool :h3,link(phonon) +phonon tool :h4,link(phonon) The phonon sub-directory contains a post-processing tool useful for analyzing the output of the "fix phonon"_fix_phonon.html command in @@ -419,7 +421,7 @@ University. :line -polybond tool :h3,link(polybond) +polybond tool :h4,link(polybond) The polybond sub-directory contains a Python-based tool useful for performing "programmable polymer bonding". The Python file @@ -433,7 +435,7 @@ This tool was written by Zachary Kraus at Georgia Tech. :line -pymol_asphere tool :h3,link(pymol) +pymol_asphere tool :h4,link(pymol) The pymol_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal @@ -451,7 +453,7 @@ This tool was written by Mike Brown at Sandia. :line -python tool :h3,link(pythontools) +python tool :h4,link(pythontools) The python sub-directory contains several Python scripts that perform common LAMMPS post-processing tasks, such as: @@ -467,7 +469,7 @@ README for more info on Pizza.py and how to use these scripts. :line -reax tool :h3,link(reax_tool) +reax tool :h4,link(reax_tool) The reax sub-directory contains stand-alond codes that can post-process the output of the "fix reax/bonds"_fix_reax_bonds.html @@ -478,7 +480,7 @@ These tools were written by Aidan Thompson at Sandia. :line -smd tool :h3,link(smd) +smd tool :h4,link(smd) The smd sub-directory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output @@ -494,7 +496,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). :line -vim tool :h3,link(vim) +vim tool :h4,link(vim) The files in the tools/vim directory are add-ons to the VIM editor that allow easier editing of LAMMPS input scripts. See the README.txt @@ -505,7 +507,7 @@ ziegenhain.com) :line -xmgrace tool :h3,link(xmgrace) +xmgrace tool :h4,link(xmgrace) The files in the tools/xmgrace directory can be used to plot the thermodynamic data in LAMMPS log files via the xmgrace plotting @@ -517,4 +519,3 @@ simulation. See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) - diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt index 7ff7ef8fd417c1118951adcbc0f89b4c7d08540a..fe109d24fb5fa2fd014f06094da8a60ca077ec9c 100644 --- a/doc/src/angle_charmm.txt +++ b/doc/src/angle_charmm.txt @@ -51,10 +51,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt index d4330139c963c12c53dc50aa2312eca93ce068e6..c13a64afb667955a61ca1bc1dae826251f257c85 100644 --- a/doc/src/angle_class2.txt +++ b/doc/src/angle_class2.txt @@ -83,10 +83,9 @@ same value from the Ea formula. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -98,8 +97,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt index c0ce3c9301f735fc69fb1b239d30ddce3150c3b0..99264b02a60adeb79c5f360988edbead0487c66f 100644 --- a/doc/src/angle_cosine.txt +++ b/doc/src/angle_cosine.txt @@ -38,10 +38,9 @@ K (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt index 830fd6db584a67bf7c93082b971e3abb383e69d2..052300412f1449a86f636888e101fac170fb086d 100644 --- a/doc/src/angle_cosine_delta.txt +++ b/doc/src/angle_cosine_delta.txt @@ -43,10 +43,9 @@ internally. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt index b5c53b1b0fb5a81d8ab33d2ebbc8e2087fd26fab..4bedae324647ade4c9a7da9a718b0d79f31fa311 100644 --- a/doc/src/angle_cosine_periodic.txt +++ b/doc/src/angle_cosine_periodic.txt @@ -51,10 +51,9 @@ geometry. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt index 6ed9fe2150b7d7bdcda19e55bc7ca852ceed4a88..185b9f530940d80bf6b63bc5a7cf963ca6f3d590 100644 --- a/doc/src/angle_cosine_shift.txt +++ b/doc/src/angle_cosine_shift.txt @@ -41,10 +41,9 @@ theta (angle) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt index 44a68c1087582357c0d2b27a98ba21184a582531..e5c7fdd7095b029d3618c2d85d6d94f82f1cd74a 100644 --- a/doc/src/angle_cosine_shift_exp.txt +++ b/doc/src/angle_cosine_shift_exp.txt @@ -53,10 +53,9 @@ A (real number) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt index 065cdad5421bf816fd6cb600a023d265e4bbfff8..e85c514d1edf9a5f1c18e4cb818b2299a3d4b620 100644 --- a/doc/src/angle_cosine_squared.txt +++ b/doc/src/angle_cosine_squared.txt @@ -43,10 +43,9 @@ internally. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt index d91f260d51b5d208c8a2d3a182c6fb17fbc0545c..31ae2e9464b0bd6c2b9cab81220a94273490358b 100644 --- a/doc/src/angle_dipole.txt +++ b/doc/src/angle_dipole.txt @@ -71,10 +71,9 @@ gamma0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] @@ -96,16 +95,17 @@ USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3 section for more info on packages. NOTE: In the "Angles" section of the data file, the atom ID 'j' -corresponding to the dipole to restrain must come before the atom ID -of the reference atom 'i'. A third atom ID 'k' must also be provided, -although 'k' is just a 'dummy' atom which can be any atom; it may be -useful to choose a convention (e.g., 'k'='i') and adhere to it. For -example, if ID=1 for the dipolar atom to restrain, and ID=2 for the -reference atom, the corresponding line in the "Angles" section of the -data file would read: X X 1 2 2 +defining the direction of the dipole vector to restrain must come +before the atom ID of the reference atom 'i'. A third atom ID 'k' must +also be provided to comply with the requirement of a valid angle +definition. This atom ID k should be chosen to be that of an atom +bonded to atom 'i' to avoid errors with "lost angle atoms" when running +in parallel. Since the LAMMPS code checks for valid angle definitions, +cannot use the same atom ID of either 'i' or 'j' (this was allowed +and recommended with older LAMMPS versions). The "newton" command for intramolecular interactions must be "on" -(which is the default). +(which is the default except when using some accelerator packages). This angle style should not be used with SHAKE. diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt index da39e7cf326b43afce171e0005c1ef93cde2d5c8..18eb56b478614bfc51391bd54288f8d330bd801d 100644 --- a/doc/src/angle_fourier.txt +++ b/doc/src/angle_fourier.txt @@ -39,10 +39,9 @@ C2 (real) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -54,8 +53,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt index 5adda6cb32f85a00310f5dc62ada7838e84d5715..6faff5f10d60924064badc7b8622541ace5c84f6 100644 --- a/doc/src/angle_fourier_simple.txt +++ b/doc/src/angle_fourier_simple.txt @@ -38,10 +38,9 @@ n (real) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt index 4c74763964832d98cfcae9443866e2db4293ca64..fe803be62320c156185ee30a7bf227e394fa3214 100644 --- a/doc/src/angle_harmonic.txt +++ b/doc/src/angle_harmonic.txt @@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt index f7640bdfbc0f75af1170cb551220d846df1529a0..a31214f4357c2c0c9d1fb9f911904dcd977fd4f4 100644 --- a/doc/src/angle_quartic.txt +++ b/doc/src/angle_quartic.txt @@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt index bd6e167bd8f4dfccc84412c6597e1d2568a1daec..29b56875e7e797c06c6a1b1f597118fd4373b603 100644 --- a/doc/src/angle_table.txt +++ b/doc/src/angle_table.txt @@ -124,10 +124,9 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -139,8 +138,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 49d9dde79119dee8b7b4ab7efa43519ac9910744..0e6aa8a03333c649da9c76d70119c071eb73ed53 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -15,7 +15,7 @@ atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ - {sphere} or {tri} or {template} or {hybrid} :ulb,l + {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l args = none for any style except the following {body} args = bstyle bstyle-args bstyle = style of body particles @@ -38,6 +38,7 @@ atom_style full atom_style body nparticle 2 10 atom_style hybrid charge bond atom_style hybrid charge body nparticle 2 5 +atom_style spin atom_style template myMols atom_style tdpd 2 :pre @@ -89,6 +90,7 @@ quantities. {peri} | mass, volume | mesocopic Peridynamic models | {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | {sphere} | diameter, mass, angular velocity | granular models | +{spin} | magnetic moment | system with magnetic particles | {template} | template index, template atom | small molecules with fixed topology | {tri} | corner points, angular momentum | rigid bodies | {wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|) @@ -175,6 +177,9 @@ used for calculating the field variables (e.g. stress and deformation) and a contact radius for calculating repulsive forces which prevent individual physical bodies from penetrating each other. +For the {spin} style, a magnetic spin is associated to each atom. +Those spins have a norm (their magnetic moment) and a direction. + The {wavepacket} style is similar to {electron}, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate @@ -250,16 +255,16 @@ with another molecular style that stores bond,angle,etc info on a per-atom basis. LAMMPS can be extended with new atom styles as well as new body -styles; see "this section"_Section_modify.html. +styles; see the "Modify"_Modify.html doc page. :line Styles with a {kk} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +run faster, depending on your available hardware, as discussed in on +the "Speed packages"_Speed_packages.html doc page. The accelerated +styles take the same arguments and should produce the same results, +except for round-off and precision issues. Note that other acceleration packages in LAMMPS, specifically the GPU, USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom @@ -274,8 +279,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] @@ -312,6 +317,8 @@ The {meso} style is part of the USER-SPH package for smoothed particle hydrodynamics (SPH). See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. +The {spin} style is part of the SPIN package. + The {wavepacket} style is part of the USER-AWPMD package for the "antisymmetrized wave packet MD method"_pair_awpmd.html. diff --git a/doc/src/body.txt b/doc/src/body.txt index 8d49efdae40eed30f9c7ec82e704adc3aef44771..4a39ac25d8c2719f3c7a24ba8559439c4003c808 100644 --- a/doc/src/body.txt +++ b/doc/src/body.txt @@ -27,19 +27,17 @@ styles supported by LAMMPS are as follows. The name in the first column is used as the {bstyle} argument for the "atom_style body"_atom_style.html command. -{nparticle} | rigid body with N sub-particles | -{rounded/polygon} | 2d convex polygon with N vertices :tb(c=2,s=|) +{nparticle} : rigid body with N sub-particles +{rounded/polygon} : 2d polygons with N vertices +{rounded/polyhedron} : 3d polyhedra with N vertices, E edges and F faces :tb(s=:) The body style determines what attributes are stored for each body and thus how they can be used to compute pairwise body/body or bond/non-body (point particle) interactions. More details of each style are described below. -NOTE: The rounded/polygon style listed in the table above and -described below has not yet been relesed in LAMMPS. It will be soon. - -We hope to add more styles in the future. See "Section -10.12"_Section_modify.html#mod_12 for details on how to add a new body +More styles may be added in the future. See the "Modify +body"_Modify_body.html doc page for details on how to add a new body style to the code. :line @@ -61,7 +59,7 @@ the simple particles. By contrast, when body particles are used, LAMMPS treats an entire body as a single particle for purposes of computing pairwise interactions, building neighbor lists, migrating particles between -processors, outputting particles to a dump file, etc. This means that +processors, output of particles to a dump file, etc. This means that interactions between pairs of bodies or between a body and non-body (point) particle need to be encoded in an appropriate pair style. If such a pair style were to mimic the "fix rigid"_fix_rigid.html model, @@ -72,17 +70,20 @@ single body/body interaction was computed. Thus it only makes sense to use body particles and develop such a pair style, when particle/particle interactions are more complex than what the "fix rigid"_fix_rigid.html command can already calculate. For -example, if particles have one or more of the following attributes: +example, consider particles with one or more of the following +attributes: represented by a surface mesh represented by a collection of geometric entities (e.g. planes + spheres) deformable internal stress that induces fragmentation :ul -then the interaction between pairs of particles is likely to be more -complex than the summation of simple sub-particle interactions. An -example is contact or frictional forces between particles with planar -surfaces that inter-penetrate. +For these models, the interaction between pairs of particles is likely +to be more complex than the summation of simple pairwise interactions. +An example is contact or frictional forces between particles with +planar surfaces that inter-penetrate. Likewise, the body particle may +store internal state, such as a stress tensor used to compute a +fracture criterion. These are additional LAMMPS commands that can be used with body particles of different styles @@ -130,7 +131,9 @@ x1 y1 z1 ... xN yN zN :pre -N is the number of sub-particles in the body particle. M = 6 + 3*N. +where M = 6 + 3*N, and N is the number of sub-particles in the body +particle. + The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N sub-particles (x1 to zN) as 3N values. These values can be listed on @@ -175,15 +178,18 @@ The {bflag2} argument is ignored. [Specifics of body style rounded/polygon:] -NOTE: Aug 2016 - This body style has not yet been added to LAMMPS. -The info below is a placeholder. +The {rounded/polygon} body style represents body particles as a 2d +polygon with a variable number of N vertices. This style can only be +used for 2d models; see the "boundary"_boundary.html command. See the +"pair_style body/rounded/polygon" doc page for a diagram of two +squares with rounded circles at the vertices. Special cases for N = 1 +(circle) and N = 2 (rod with rounded ends) can also be specified. + +One use of this body style is for 2d discrete element models, as +described in "Fraige"_#body-Fraige. -The {rounded/polygon} body style represents body particles as a convex -polygon with a variable number N > 2 of vertices, which can only be -used for 2d models. One example use of this body style is for 2d -discrete element models, as described in "Fraige"_#Fraige. Similar to -body style {nparticle}, the atom_style body command for this body -style takes two additional arguments: +Similar to body style {nparticle}, the atom_style body command for +this body style takes two additional arguments: atom_style body rounded/polygon Nmin Nmax Nmin = minimum # of vertices in any body in the system @@ -203,17 +209,20 @@ x1 y1 z1 ... xN yN zN i j j k k ... -radius :pre +diameter :pre -N is the number of vertices in the body particle. M = 6 + 3*N + 2*N + -1. The integer line has a single value N. The floating point line(s) +where M = 6 + 3*N + 2*N + 1, and N is the number of vertices in the +body particle. + +The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N -vertices (x1 to zN) as 3N values, followed by 2N vertex indices -corresponding to the end points of the N edges, followed by a single -radius value = the smallest circle encompassing the polygon. That -last value is used to facilitate the body/body contact detection. -These floating-point values can be listed on as many lines as you -wish; see the "read_data"_read_data.html command for more details. +vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by +2N vertex indices corresponding to the end points of the N edges, +followed by a single diameter value = the rounded diameter of the +circle that surrounds each vertex. The diameter value can be different +for each body particle. These floating-point values can be listed on +as many lines as you wish; see the "read_data"_read_data.html command +for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body @@ -225,8 +234,11 @@ from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the {Atoms} section of the data file. -For example, the following information would specify a square -particles whose edge length is sqrt(2): +For example, the following information would specify a square particle +whose edge length is sqrt(2) and rounded diameter is 1.0. The +orientation of the square is aligned with the xy coordinate axes which +is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz = +1 1 4 0 0 0. Note that only Izz matters in 2D simulations. 3 1 27 4 @@ -235,12 +247,178 @@ particles whose edge length is sqrt(2): -0.7071 0.7071 0 0.7071 0.7071 0 0.7071 -0.7071 0 -0 1 1 2 2 3 3 0 +0 1 +1 2 +2 3 +3 0 1.0 :pre +A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends +by circles of diameter 0.5, is specified as follows: + +1 1 13 +2 +1 1 1.33333 0 0 0 +-2 0 0 +2 0 0 +0.5 :pre + +A disk, whose diameter is 3.0, mass 1.0, is specified as follows: + +1 1 10 +1 +1 1 4.5 0 0 0 +0 0 0 +3.0 :pre + The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html command can be used with this body style to compute body/body -interactions. +interactions. The "fix wall/body/polygon"_fix_wall_body_polygon.html +command can be used with this body style to compute the interaction of +body particles with a wall. + +:line + +[Specifics of body style rounded/polyhedron:] + +The {rounded/polyhedron} body style represents body particles as a 3d +polyhedron with a variable number of N vertices, E edges and F faces. +This style can only be used for 3d models; see the +"boundary"_boundary.html command. See the "pair_style +body/rounded/polygon" doc page for a diagram of a two 2d squares with +rounded circles at the vertices. A 3d cube with rounded spheres at +the 8 vertices and 12 rounded edges would be similar. Special cases +for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be +specified. + +This body style is for 3d discrete element models, as described in +"Wang"_#body-Wang. + +Similar to body style {rounded/polygon}, the atom_style body command +for this body style takes two additional arguments: + +atom_style body rounded/polyhedron Nmin Nmax +Nmin = minimum # of vertices in any body in the system +Nmax = maximum # of vertices in any body in the system :pre + +The Nmin and Nmax arguments are used to bound the size of data +structures used internally by each particle. + +When the "read_data"_read_data.html command reads a data file for this +body style, the following information must be provided for each entry +in the {Bodies} section of the data file: + +atom-ID 3 M +N E F +ixx iyy izz ixy ixz iyz +x1 y1 z1 +... +xN yN zN +0 1 +1 2 +2 3 +... +0 1 2 -1 +0 2 3 -1 +... +1 2 3 4 +diameter :pre + +where M = 6 + 3*N + 2*E + 4*F + 1, and N is the number of vertices in +the body particle, E = number of edges, F = number of faces. + +The integer line has three values: number of vertices (N), number of +edges (E) and number of faces (F). The floating point line(s) list 6 +moments of inertia followed by the coordinates of the N vertices (x1 +to zN) as 3N values, followed by 2N vertex indices corresponding to +the end points of the E edges, then 4*F vertex indices defining F +faces. The last value is the diameter value = the rounded diameter of +the sphere that surrounds each vertex. The diameter value can be +different for each body particle. These floating-point values can be +listed on as many lines as you wish; see the +"read_data"_read_data.html command for more details. Because the +maxmimum vertices per face is hard-coded to be 4 +(i.e. quadrilaterals), faces with more than 4 vertices need to be +split into triangles or quadrilaterals. For triangular faces, the +last vertex index should be set to -1. + +The ordering of the 4 vertices within a face should follow +the right-hand rule so that the normal vector of the face points +outwards from the center of mass. + +The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the principal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. +The coordinates of each vertex are specified as its x,y,z displacement +from the center-of-mass of the body particle. The center-of-mass +position of the particle is specified by the x,y,z values in the +{Atoms} section of the data file. + +For example, the following information would specify a cubic particle +whose edge length is 2.0 and rounded diameter is 0.5. +The orientation of the cube is aligned with the xyz coordinate axes +which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz +iyz = 0.667 0.667 0.667 0 0 0. + +1 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 :pre + +A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends +by circles of diameter 0.5, is specified as follows: + +1 1 13 +2 +0 1.33333 1.33333 0 0 0 +-2 0 0 +2 0 0 +0.5 :pre + +A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: + +1 1 10 +1 +0.9 0.9 0.9 0 0 0 +0 0 0 +3.0 :pre + +The "pair_style +body/rounded/polhedron"_pair_body_rounded_polyhedron.html command can +be used with this body style to compute body/body interactions. The +"fix wall/body/polyhedron"_fix_wall_body_polygon.html command can be +used with this body style to compute the interaction of body particles +with a wall. + +:line For output purposes via the "compute body/local"_compute_body_local.html and "dump local"_dump.html @@ -257,10 +435,10 @@ the body particle itself. These values are calculated using the current COM and orientation of the body particle. For images created by the "dump image"_dump_image.html command, if the -{body} keyword is set, then each body particle is drawn as a convex -polygon consisting of N line segments. Note that the line segments -are drawn between the N vertices, which does not correspond exactly to -the physical extent of the body (because the "pair_style +{body} keyword is set, then each body particle is drawn as a polygon +consisting of N line segments. Note that the line segments are drawn +between the N vertices, which does not correspond exactly to the +physical extent of the body (because the "pair_style rounded/polygon"_pair_body_rounded_polygon.html defines finite-size spheres at those point and the line segments between the spheres are tangent to the spheres). The drawn diameter of each line segment is @@ -269,6 +447,10 @@ determined by the {bflag1} parameter for the {body} keyword. The :line -:link(Fraige) +:link(body-Fraige) [(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008). + +:link(body-Wang) +[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular +Matter, 13, 1 (2011). diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt index 9687a6316805acb77298f74eeb84952e8f4243fe..049482c97394572d6af86fa598c181ece78af16b 100644 --- a/doc/src/bond_class2.txt +++ b/doc/src/bond_class2.txt @@ -44,10 +44,9 @@ K4 (energy/distance^4) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt index 9050c3bf5ccecdd8701f414ef0caea5e39a19c2c..be154a53b1c88a7cfe8409aa3074e0ba0e1890e1 100644 --- a/doc/src/bond_fene.txt +++ b/doc/src/bond_fene.txt @@ -47,10 +47,9 @@ sigma (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -62,8 +61,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt index ff687444a97378373514442bda71a614b74bd821..77ebd977c8d7b067ad6feef461c61ec2639e0899 100644 --- a/doc/src/bond_fene_expand.txt +++ b/doc/src/bond_fene_expand.txt @@ -50,10 +50,9 @@ delta (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt index cc3ff75878f36dd27f2d85b61ae3bfb522f52583..7a56cb3afa8da3c0f274335c74a84e482eb2425c 100644 --- a/doc/src/bond_gromos.txt +++ b/doc/src/bond_gromos.txt @@ -40,10 +40,9 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt index c18a7e0fd4d35a337a832255b64b4daf8f07392f..54e89fcc72d05d89e01382d7e9d55fd6bae11b2f 100644 --- a/doc/src/bond_harmonic.txt +++ b/doc/src/bond_harmonic.txt @@ -42,10 +42,9 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -57,8 +56,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt index bf3b3c115adeb59fcbd0a7a51e36a4612e6c020d..0213b5cc6fb5e82b07917a96ce5ad239a251a9bd 100644 --- a/doc/src/bond_harmonic_shift.txt +++ b/doc/src/bond_harmonic_shift.txt @@ -43,10 +43,9 @@ rc (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt index 1918ce00b6210468a119d332762ed85f8f2bad0e..d907bf4a629a4ebebde1e8c8552a3f0960d613fa 100644 --- a/doc/src/bond_harmonic_shift_cut.txt +++ b/doc/src/bond_harmonic_shift_cut.txt @@ -43,10 +43,9 @@ rc (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt index 4f6a32e341b57a7977e4aaabc83d8dd1a1282137..66f2d08cabe033b1864a4558a2a8e058ca8e53ad 100644 --- a/doc/src/bond_morse.txt +++ b/doc/src/bond_morse.txt @@ -41,10 +41,9 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt index 434af625061a45679e9f01630c3999743d6d77ee..e0aa5629b3ec496c1700009b59615b989a992c8d 100644 --- a/doc/src/bond_nonlinear.txt +++ b/doc/src/bond_nonlinear.txt @@ -41,10 +41,9 @@ lamda (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 2add6f4c2f0fb1f31aabaccca596cddbb41c5687..927fea64031d5422615d1251b9332e4e66120d3a 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. + +Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool +and the performance of the LAMMPS-implementation of oxDNA. +The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line @@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line +:link(Henrich2) +[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). + :link(oxdna_fene) [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt index 4dc7ad4a3693e8d0ed492514fbaaf5f15deaecd0..760a5d7f07b65cfab5c8e4cbc99419922c8b0eba 100644 --- a/doc/src/bond_quartic.txt +++ b/doc/src/bond_quartic.txt @@ -76,10 +76,9 @@ delete_bonds all bond 0 remove :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -91,8 +90,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt index 906d3e5d7639eb08e211554b2817195dd383bcf1..fe0b3ce22bbc388b405e6cce32b7be6466559451 100644 --- a/doc/src/bond_table.txt +++ b/doc/src/bond_table.txt @@ -121,10 +121,9 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -136,8 +135,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/compute.txt b/doc/src/compute.txt index c06735d28e3dbe0091b3426eebbf264f1e147ad0..532a5414e38a4f2d3fe7b70790d048703d8987b5 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -153,8 +153,8 @@ via the "compute_modify"_compute_modify.html command. Computes can be deleted with the "uncompute"_uncompute.html command. -Code for new computes can be added to LAMMPS (see "this -section"_Section_modify.html of the manual) and the results of their +Code for new computes can be added to LAMMPS; see the +"Modify"_Modify.html doc page for details. The results of their calculations accessed in the various ways described above. :line diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt index b75d100112b9f3a9a5e49d1ec282f275e56a9014..3fd838d95775ae9e97f7ad8da792112b9890d80d 100644 --- a/doc/src/compute_ackland_atom.txt +++ b/doc/src/compute_ackland_atom.txt @@ -10,19 +10,29 @@ compute ackland/atom command :h3 [Syntax:] -compute ID group-ID ackland/atom :pre +compute ID group-ID ackland/atom keyword/value :pre -ID, group-ID are documented in "compute"_compute.html command -ackland/atom = style name of this compute command :ul +ID, group-ID are documented in "compute"_compute.html command :ulb,l +ackland/atom = style name of this compute command :l + +zero or more keyword/value pairs may be appended :l +keyword = {legacy} :l + {legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre +:ule [Examples:] -compute 1 all ackland/atom :pre +compute 1 all ackland/atom +compute 1 all ackland/atom legacy yes :pre [Description:] Defines a computation that calculates the local lattice structure according to the formulation given in "(Ackland)"_#Ackland. +Historically, LAMMPS had two, slightly different implementations of +the algorithm from the paper. With the {legacy} keyword, it is +possible to switch between the pre-2015 ({legacy yes}) and post-2015 +implemention ({legacy no}). The post-2015 variant is the default. In contrast to the "centro-symmetry parameter"_compute_centro_atom.html this method is stable against @@ -66,7 +76,8 @@ integers defined above. "compute centro/atom"_compute_centro_atom.html -[Default:] none +[Default:] +The keyword {legacy} defaults to {no}. :line diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index 3a46f79d160013e96c177c3939454da9a6f4ecc7..00a75f50c439ad4f0896d9e654f332057eacdb02 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -275,7 +275,7 @@ previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. +their own compute styles and "add them to LAMMPS"_Modify.html. If the style begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed integer is @@ -285,7 +285,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with the timestep on which this compute accesses the fix, else an error results. Users can also write code for their own fix styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If a value begins with "v_", a variable name for an {atom} or {atomfile} style "variable"_variable.html must follow which has been diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 39c301cf911a159089189ee02cef15a5ffae4d1e..00e5f696c118029431bf5a36395bcd906fe432ee 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -15,7 +15,7 @@ compute ID group-ID displace/atom :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l displace/atom = style name of this compute command :l zero or more keyword/arg pairs may be appended :l -keyword = {refresh} : +keyword = {refresh} :l {replace} arg = name of per-atom variable :pre :ule diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt new file mode 100644 index 0000000000000000000000000000000000000000..f7e7b8a66764427cd117c4305920d457efbd7e2b --- /dev/null +++ b/doc/src/compute_entropy_atom.txt @@ -0,0 +1,130 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute entropy/atom command :h3 + +[Syntax:] + +compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre + +ID, group-ID are documented in "compute"_compute.html command :l +entropy/atom = style name of this compute command :l +sigma = width of gaussians used in the g(r) smoothening :l +cutoff = cutoff for the g(r) calculation :l +one or more keyword/value pairs may be appended :l +keyword = {avg} or {local} + {avg} values = {yes} or {no} cutoff2 + {yes} = average the pair entropy over neighbors + {no} = do not average the pair entropy over neighbors + cutoff2 = cutoff for the averaging over neighbors + {local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre +:ule + +[Examples:] + +compute 1 all entropy/atom 0.25 5. +compute 1 all entropy/atom 0.25 5. avg yes 5. +compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre + +[Description:] + +Define a computation that calculates the pair entropy fingerprint for +each atom in the group. The fingerprint is useful to distinguish between +ordered and disordered environments, for instance liquid and solid-like +environments, or glassy and crystalline-like environments. Some +applications could be the identification of grain boundaries, a +melt-solid interface, or a solid cluster emerging from the melt. +The advantage of this parameter over others is that no a priori +information about the solid structure is required. + +This parameter for atom i is computed using the following formula from +"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton , + +:c,image(Eqs/pair_entropy.jpg) + +where r is a distance, g(r) is the radial distribution function of atom +i and rho is the density of the system. The g(r) computed for each +atom i can be noisy and therefore it is smoothened using: + +:c,image(Eqs/pair_entropy2.jpg) + +where the sum in j goes through the neighbors of atom i, and sigma is a +parameter to control the smoothening. + +The input parameters are {sigma} the smoothening parameter, and the +{cutoff} for the calculation of g(r). + +If the keyword {avg} has the setting {yes}, then this compute also +averages the parameter over the neighbors of atom i according to: + +:c,image(Eqs/pair_entropy3.jpg) + +where the sum j goes over the neighbors of atom i and N is the number +of neighbors. This procedure provides a sharper distinction between +order and disorder environments. In this case the input parameter +{cutoff2} is the cutoff for the averaging over the neighbors and +must also be specified. + +If the {avg yes} option is used, the effective cutoff of the neighbor +list should be {cutoff}+{cutoff2} and therefore it might be necessary +to increase the skin of the neighbor list with: + +neighbor skin bin :pre + +See "neighbor"_neighbor.html for details. + +If the {local yes} option is used, the g(r) is normalized by the +local density around each atom, that is to say the density around each +atom is the number of neighbors within the neighbor list cutoff divided +by the corresponding volume. This option can be useful when dealing with +inhomogeneus systems such as those that have surfaces. + +Here are typical input parameters for fcc aluminum (lattice +constant 4.05 Angstroms), + +compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre + +and for bcc sodium (lattice constant 4.23 Angstroms), + +compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre + + +[Output info:] + +By default, this compute calculates the pair entropy value for each +atom as a per-atom vector, which can be accessed by any command that +uses per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. + +The pair entropy values have units of the Boltzmann constant. They are +always negative, and lower values (lower entropy) correspond to more +ordered environments. + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"compute cna/atom"_compute_cna_atom.html +"compute centro/atom"_compute_centro_atom.html + +[Default:] + +The default values for the optional keywords are avg = no and local = no. + +:line + +:link(Piaggi) +[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017). + +:link(Nettleton) +[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958). diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt index 3136b1fd18f849bcf6c69b328983b8aa135d5c50..28b4aa2461b9be2841c5a8cb1253228ab922a5b3 100644 --- a/doc/src/compute_global_atom.txt +++ b/doc/src/compute_global_atom.txt @@ -130,7 +130,7 @@ page for details. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute -styles and "add them to LAMMPS"_Section_modify.html. See the +styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -143,7 +143,7 @@ references the values, else an error results. If no bracketed integer is appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Section_modify.html. See the +own fix style and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -168,7 +168,7 @@ page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. See the discussion above for how +them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -181,7 +181,7 @@ global/atom references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Section_modify.html. See the +own fix style and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt index e8adac3deb5e71a5cd3ed3c15088868b3b8768f5..39a1470201fc3f6705ee222e9719261aeae5dd4f 100644 --- a/doc/src/compute_heat_flux.txt +++ b/doc/src/compute_heat_flux.txt @@ -26,14 +26,16 @@ compute myFlux all heat/flux myKE myPE myStress :pre Define a computation that calculates the heat flux vector based on contributions from atoms in the specified group. This can be used by -itself to measure the heat flux into or out of a reservoir of atoms, -or to calculate a thermal conductivity using the Green-Kubo formalism. - -See the "fix thermal/conductivity"_fix_thermal_conductivity.html -command for details on how to compute thermal conductivity in an -alternate way, via the Muller-Plathe method. See the "fix -heat"_fix_heat.html command for a way to control the heat added or -subtracted to a group of atoms. +itself to measure the heat flux through a set of atoms (e.g. a region +between two thermostatted reservoirs held at different temperatures), +or to calculate a thermal conductivity using the equilibrium +Green-Kubo formalism. + +For other non-equilibrium ways to compute a thermal conductivity, see +"this section"_Section_howto.html#howto_20. These include use of the +"fix thermal/conductivity"_fix_thermal_conductivity.html command for +the Muller-Plathe method. Or the "fix heat"_fix_heat.html command +which can add or subtract heat from groups of atoms. The compute takes three arguments which are IDs of other "computes"_compute.html. One calculates per-atom kinetic energy diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index f0691ad20762758234828f976e7519ef47568d57..8b7491da4946891650ceef0cd1c3111cb318b453 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -105,10 +105,9 @@ where "thermo_temp" is the ID of a similarly defined compute of style Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index bac19918ba7ccefedb982449b91db8cd086edae7..c0970d5121cca49705fa5eb5eb02407f490a04e5 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -19,6 +19,7 @@ input = one or more atom attributes :l x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, + sp, spx, spy, spz, fmx, fmy, fmz, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, @@ -46,6 +47,9 @@ input = one or more atom attributes :l q = atom charge mux,muy,muz = orientation of dipole moment of atom mu = magnitude of dipole moment of atom + sp = atomic magnetic spin moment + spx, spy, spz = direction of the atomic magnetic spin + fmx, fmy, fmz = magnetic force radius,diameter = radius,diameter of spherical particle omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle @@ -82,7 +86,8 @@ input = one or more atom attributes :l compute 1 all property/atom xs vx fx mux compute 2 all property/atom type -compute 1 all property/atom ix iy iz :pre +compute 1 all property/atom ix iy iz +compute 3 all property/atom sp spx spy spz :pre [Description:] @@ -152,6 +157,10 @@ The vector or array values will be in whatever "units"_units.html the corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc. +For the spin quantities, sp is in the units of the Bohr magneton, spx, +spy, and spz are adimentional quantities, and fmx, fmy and fmz are +given in rad.THz. + [Restrictions:] none [Related commands:] diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 07d3c3bda7b88e277f36cb2e839398763488ca40..48115a08861e6e272ea71cb86fdb0276c00aedee 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -116,7 +116,7 @@ per-atom or local quantities. See the individual is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own -compute styles and "add them to LAMMPS"_Section_modify.html. See the +compute styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -129,9 +129,9 @@ references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. See the discussion above for how -I can be specified with a wildcard asterisk to effectively specify -multiple values. +them to LAMMPS"_Modify.html. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an diff --git a/doc/src/compute_slice.txt b/doc/src/compute_slice.txt index e89c05a0f95a0e2b39d2545a512fe158c4bd39e3..13f40ecf9220c3245f6956c2c4d5908d974bb29e 100644 --- a/doc/src/compute_slice.txt +++ b/doc/src/compute_slice.txt @@ -58,7 +58,7 @@ page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates a global @@ -69,7 +69,7 @@ the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If an input value begins with "v_", a variable name must follow which has been previously defined in the input script. Only vector-style diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 1c3787e696638191373d0b563f461c37d42dddad..268e23ac2808d82f8750b95bd652cd4d50f6b9d2 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -161,9 +161,9 @@ function. The keyword {bzeroflag} determines whether or not {B0}, the bispectrum components of an atom with no neighbors, are subtracted from -the calculated bispectrum components. This optional keyword is only -available for compute {sna/atom}, as {snad/atom} and {snav/atom} -are unaffected by the removal of constant terms. +the calculated bispectrum components. This optional keyword +normally only affects compute {sna/atom}. However, when +{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}. The keyword {quadraticflag} determines whether or not the quadratic analogs to the bispectrum quantities are generated. @@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1, the numbers of columns are 930, 2790, and 5580, respectively. If the {quadratic} keyword value is set to 1, then additional -columns are appended to each per-atom array, corresponding to +columns are generated, corresponding to the products of all distinct pairs of bispectrum components. If the number of bispectrum components is {K}, then the number of distinct pairs -is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same -ordering of sub-blocks as was used for the bispectrum -components. Within each sub-block, the ordering is upper-triangular, -(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}) +is {K}({K}+1)/2. +For compute {sna/atom} these columns are appended to existing {K} columns. +The ordering of quadratic terms is upper-triangular, +(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}). +For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2 +additional columns is inserted directly after each of sub-block +of linear terms i.e. linear and quadratic terms are contiguous. +So the nesting order from inside to outside is bispectrum component, +linear then quadratic, vector/tensor component, type. These values can be accessed by any command that uses per-atom values from a compute as input. See "Section diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..fcc764c14cb0f7cc88869655bf8d2df1f745c777 --- /dev/null +++ b/doc/src/compute_spin.txt @@ -0,0 +1,78 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute spin command :h3 + +[Syntax:] + +compute ID group-ID compute/spin :pre + +ID, group-ID are documented in "compute"_compute.html command +compute/spin = style name of this compute command :ul + +[Examples:] + +compute out_mag all compute/spin :pre + +[Description:] + +Define a computation that calculates magnetic quantities for a system +of atoms having spins. + +This compute calculates 6 magnetic quantities. + +The three first quantities are the x,y and z coordinates of the total magnetization. + +The fourth quantity is the norm of the total magnetization. + +The fifth quantity is the magnetic energy. + +The sixth one is referred to as the spin temperature, according +to the work of "(Nurdin)"_#Nurdin1. + +The simplest way to output the results of the compute spin calculation +is to define some of the quantities as variables, and to use the thermo and +thermo_style commands, for example: + +compute out_mag all compute/spin :pre + +variable mag_z equal c_out_mag\[3\] +variable mag_norm equal c_out_mag\[4\] +variable temp_mag equal c_out_mag\[6\] :pre + +thermo 10 +thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre + +This serie of commands evaluates the total magnetization along z, the norm of +the total magnetization, and the magnetic temperature. Three variables are +assigned to those quantities. The thermo and thermo_style commands print them +every 10 timesteps. + + +[Output info:] + +The array values are "intensive". The array values will be in +metal units ("units"_units.html). + +[Restrictions:] + +The {spin} compute is part of the SPIN package. +This compute is only enabled if LAMMPS was built with this package. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. +The atom_style has to be "spin" for this compute to be valid. + +[Related commands:] none + + +[Default:] none + +:line + +:link(Nurdin1) +[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000) + diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt index b88be79e20704a41482ad444668ca8b81d0c4b32..f9fa56c88283e1082704b8622a831982736c3861 100644 --- a/doc/src/compute_temp.txt +++ b/doc/src/compute_temp.txt @@ -67,10 +67,9 @@ thermostatting. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -82,8 +81,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt index fe2420b4e40d8d28e0b824d8022b8322596877f6..59ec8cf20b6f38949df74c993f667b1733d7088e 100644 --- a/doc/src/compute_temp_partial.txt +++ b/doc/src/compute_temp_partial.txt @@ -74,10 +74,9 @@ thermostatting. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -89,8 +88,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 1b64e2e5b46393313fc74099ef9bbf04da946b74..46dd30f7570f7a87d9874367f67f1d4af85a2fca 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -31,6 +31,7 @@ Computes :h1 compute_dpd compute_dpd_atom compute_edpd_temp_atom + compute_entropy_atom compute_erotate_asphere compute_erotate_rigid compute_erotate_sphere @@ -95,6 +96,7 @@ Computes :h1 compute_smd_ulsph_stress compute_smd_vol compute_sna_atom + compute_spin compute_stress_atom compute_tally compute_tdpd_cc_atom diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index 6af69214d3c4523318945c3bf70ac0547621dd64..6700ed29d3f3f6d9b3c7d5094b182a1bf6235a82 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -37,8 +37,8 @@ keyword = {special} :l create_bonds many all all 1 1.0 1.2 create_bonds many surf solvent 3 2.0 2.4 -create_bond single/bond 1 1 2 -create_bond single/angle 5 52 98 107 special no :pre +create_bonds single/bond 1 1 2 +create_bonds single/angle 5 52 98 107 special no :pre [Description:] diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 06abe054e4819e7c7e9ea9e248e7f2285e423572..f808649a44da0c3ef018ba279c38ec4228e7fc9c 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -116,10 +116,9 @@ computed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -131,8 +130,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt index cb9fc72c223b2293990764db4b0dffb59dc249b5..41282b22a3149d59bc72dc1cfb87267a41cde38d 100644 --- a/doc/src/dihedral_class2.txt +++ b/doc/src/dihedral_class2.txt @@ -141,10 +141,9 @@ r3 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -156,8 +155,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt index 715682affc010e657556ba9221ca68a093b5259a..483745be4181cea4d59631f0d7f9711abbdecd0d 100644 --- a/doc/src/dihedral_cosine_shift_exp.txt +++ b/doc/src/dihedral_cosine_shift_exp.txt @@ -52,10 +52,9 @@ A (real number) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -67,8 +66,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt index 0accbb22bf80bfb89e1b77bd7fa8760e56ad3e55..0270139f68197e4217fa3f089a1c03dd4de4fbc3 100644 --- a/doc/src/dihedral_fourier.txt +++ b/doc/src/dihedral_fourier.txt @@ -44,10 +44,9 @@ dm (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt index d9a48ff384d9df3dd9228a05be3c523302b80362..a25a7969fe70b8402c1719caf312fc113ca97544 100644 --- a/doc/src/dihedral_harmonic.txt +++ b/doc/src/dihedral_harmonic.txt @@ -53,10 +53,9 @@ Some force fields let {n} be positive or negative which corresponds to Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt index 1e907557b28564f74e3f080160997a107941d4b5..814962a472b7b240ec61eae4ca3dc41762771552 100644 --- a/doc/src/dihedral_helix.txt +++ b/doc/src/dihedral_helix.txt @@ -46,10 +46,9 @@ C (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -61,8 +60,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt index 7d3c2ea083d0ef78b7e275caa9ca51e1305e8e49..62cad4141a6a27283eb725715de91dbbcf4721b7 100644 --- a/doc/src/dihedral_multi_harmonic.txt +++ b/doc/src/dihedral_multi_harmonic.txt @@ -40,10 +40,9 @@ A5 (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt index 8392d83899de8c41cd855e6a038f3e7a585ec08a..a49979fa66ac13a24dbc22e75868337cda771b05 100644 --- a/doc/src/dihedral_nharmonic.txt +++ b/doc/src/dihedral_nharmonic.txt @@ -40,10 +40,9 @@ An (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt index d1a6ba3ff2865db905b97bf72b70d343f509e06e..9b33173da4fe35a9890de29e601d812ff83505ec 100644 --- a/doc/src/dihedral_opls.txt +++ b/doc/src/dihedral_opls.txt @@ -48,10 +48,9 @@ K4 (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt index ca2f5aed40f2f67512a255813689a50e35a4c7d7..f90c4b79f159591a0e6d639ae720da32a4be61e3 100644 --- a/doc/src/dihedral_quadratic.txt +++ b/doc/src/dihedral_quadratic.txt @@ -41,10 +41,9 @@ phi0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt index 0b88f26a61076c6b10750ea419b947fb88a0dd8f..6a480fec93397fa262f39b42eee0e45c18bcf774 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -174,10 +174,9 @@ that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -189,8 +188,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt new file mode 100644 index 0000000000000000000000000000000000000000..1c83d4ffa09f7221ac8c3859594abc754b9b28c4 --- /dev/null +++ b/doc/src/dihedral_table_cut.txt @@ -0,0 +1,205 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +dihedral_style table/cut command :h3 + +[Syntax:] + +dihedral_style table/cut style Ntable :pre + +style = {linear} or {spline} = method of interpolation +Ntable = size of the internal lookup table :ul + +[Examples:] + +dihedral_style table/cut spline 400 +dihedral_style table/cut linear 1000 +dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1 +dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 :pre + +[Description:] + +The {table/cut} dihedral style creates interpolation tables of length +{Ntable} from dihedral potential and derivative values listed in a +file(s) as a function of the dihedral angle "phi". In addition, an +analytic cutoff that is quadratic in the bond-angle (theta) is applied +in order to regularize the dihedral interaction. The dihedral table +files are read by the "dihedral_coeff"_dihedral_coeff.html command. + +The interpolation tables are created by fitting cubic splines to the +file values and interpolating energy and derivative values at each of +{Ntable} dihedral angles. During a simulation, these tables are used +to interpolate energy and force values on individual atoms as +needed. The interpolation is done in one of 2 styles: {linear} or +{spline}. + +For the {linear} style, the dihedral angle (phi) is used to find 2 +surrounding table values from which an energy or its derivative is +computed by linear interpolation. + +For the {spline} style, cubic spline coefficients are computed and +stored at each of the {Ntable} evenly-spaced values in the +interpolated table. For a given dihedral angle (phi), the appropriate +coefficients are chosen from this list, and a cubic polynomial is used +to compute the energy and the derivative at this angle. + +The following coefficients must be defined for each dihedral type via +the "dihedral_coeff"_dihedral_coeff.html command as in the example +above. + +style (aat) +cutoff prefactor +cutoff angle1 +cutoff angle2 +filename +keyword :ul + +The cutoff dihedral style uses a tabulated dihedral interaction with a +cutoff function: + +:c,image(Eqs/dihedral_table_cut.jpg) + +The cutoff specifies an prefactor to the cutoff function. While this value +would ordinarily equal 1 there may be situations where the value should change. + +The cutoff angle1 specifies the angle (in degrees) below which the dihedral +interaction is unmodified, i.e. the cutoff function is 1. + +The cutoff function is applied between angle1 and angle2, which is the angle at +which the cutoff function drops to zero. The value of zero effectively "turns +off" the dihedral interaction. + +The filename specifies a file containing tabulated energy and +derivative values. The keyword specifies a section of the file. The +format of this file is described below. + +:line + +The format of a tabulated file is as follows (without the +parenthesized comments). It can begin with one or more comment +or blank lines. + +# Table of the potential and its negative derivative :pre + +DIH_TABLE1 (keyword is the first text on line) +N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F) + (blank line) +1 -168.0 -1.40351172223 0.0423346818422 +2 -156.0 -1.70447981034 0.00811786522531 +3 -144.0 -1.62956100432 -0.0184129719987 +... +30 180.0 -0.707106781187 0.0719306095245 :pre + +# Example 2: table of the potential. Forces omitted :pre + +DIH_TABLE2 +N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre + +1 -168.0 -1.40351172223 +2 -156.0 -1.70447981034 +3 -144.0 -1.62956100432 +... +30 180.0 -0.707106781187 :pre + +A section begins with a non-blank line whose 1st character is not a +"#"; blank lines or lines starting with "#" can be used as comments +between sections. The first line begins with a keyword which +identifies the section. The line can contain additional text, but the +initial text must match the argument specified in the +"dihedral_coeff"_dihedral_coeff.html command. The next line lists (in +any order) one or more parameters for the table. Each parameter is a +keyword followed by one or more numeric values. + +Following a blank line, the next N lines list the tabulated values. On +each line, the 1st value is the index from 1 to N, the 2nd value is +the angle value, the 3rd value is the energy (in energy units), and +the 4th is -dE/d(phi) also in energy units). The 3rd term is the +energy of the 4-atom configuration for the specified angle. The 4th +term (when present) is the negative derivative of the energy with +respect to the angle (in degrees, or radians depending on whether the +user selected DEGREES or RADIANS). Thus the units of the last term +are still energy, not force. The dihedral angle values must increase +from one line to the next. + +Dihedral table splines are cyclic. There is no discontinuity at 180 +degrees (or at any other angle). Although in the examples above, the +angles range from -180 to 180 degrees, in general, the first angle in +the list can have any value (positive, zero, or negative). However +the {range} of angles represented in the table must be {strictly} less +than 360 degrees (2pi radians) to avoid angle overlap. (You may not +supply entries in the table for both 180 and -180, for example.) If +the user's table covers only a narrow range of dihedral angles, +strange numerical behavior can occur in the large remaining gap. + +[Parameters:] + +The parameter "N" is required and its value is the number of table +entries that follow. Note that this may be different than the N +specified in the "dihedral_style table"_dihedral_style.html command. +Let {Ntable} is the number of table entries requested dihedral_style +command, and let {Nfile} be the parameter following "N" in the +tabulated file ("30" in the sparse example above). What LAMMPS does +is a preliminary interpolation by creating splines using the {Nfile} +tabulated values as nodal points. It uses these to interpolate as +needed to generate energy and derivative values at {Ntable} different +points (which are evenly spaced over a 360 degree range, even if the +angles in the file are not). The resulting tables of length {Ntable} +are then used as described above, when computing energy and force for +individual dihedral angles and their atoms. This means that if you +want the interpolation tables of length {Ntable} to match exactly what +is in the tabulated file (with effectively nopreliminary +interpolation), you should set {Ntable} = {Nfile}. To insure the +nodal points in the user's file are aligned with the interpolated +table entries, the angles in the table should be integer multiples of +360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your +choice of angle units). + +The optional "NOF" keyword allows the user to omit the forces +(negative energy derivatives) from the table file (normally located in +the 4th column). In their place, forces will be calculated +automatically by differentiating the potential energy function +indicated by the 3rd column of the table (using either linear or +spline interpolation). + +The optional "DEGREES" keyword allows the user to specify angles in +degrees instead of radians (default). + +The optional "RADIANS" keyword allows the user to specify angles in +radians instead of degrees. (Note: This changes the way the forces +are scaled in the 4th column of the data file.) + +The optional "CHECKU" keyword is followed by a filename. This allows +the user to save all of the the {Ntable} different entries in the +interpolated energy table to a file to make sure that the interpolated +function agrees with the user's expectations. (Note: You can +temporarily increase the {Ntable} parameter to a high value for this +purpose. "{Ntable}" is explained above.) + +The optional "CHECKF" keyword is analogous to the "CHECKU" keyword. +It is followed by a filename, and it allows the user to check the +interpolated force table. This option is available even if the user +selected the "NOF" option. + +Note that one file can contain many sections, each with a tabulated +potential. LAMMPS reads the file section by section until it finds one +that matches the specified keyword. + +[Restrictions:] + +This dihedral style can only be used if LAMMPS was built with the +USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info on packages. + +[Related commands:] + +"dihedral_coeff"_dihedral_coeff.html, "dihedral_style table"_dihedral_table.html + +[Default:] none + +:link(dihedralcut-Salerno) +[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018). diff --git a/doc/src/dihedrals.txt b/doc/src/dihedrals.txt index 500a6a52bf69b7beb641c414f6dee354d6ca6b7b..a862bf50a0a9c357ffeed1129e3b67423259447c 100644 --- a/doc/src/dihedrals.txt +++ b/doc/src/dihedrals.txt @@ -19,6 +19,7 @@ Dihedral Styles :h1 dihedral_quadratic dihedral_spherical dihedral_table + dihedral_table_cut dihedral_zero dihedral_charmm dihedral_class2 diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 438ff1d4e074779f22217e851799a81f1f7ff857..ff1bf6424df10a43ffcefa95cae512ecfbf2f631 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -1,4 +1,4 @@ - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) @@ -184,10 +184,10 @@ file and in what format. Settings made via the individual values and the file itself. The {atom}, {local}, and {custom} styles create files in a simple text -format that is self-explanatory when viewing a dump file. Many of the -LAMMPS "post-processing tools"_Section_tools.html, including -"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this -format, as does the "rerun"_rerun.html command. +format that is self-explanatory when viewing a dump file. Some of the +LAMMPS post-processing tools described on the "Tools"_Tools.html doc +page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, +work with this format, as does the "rerun"_rerun.html command. For post-processing purposes the {atom}, {local}, and {custom} text files are self-describing in the following sense. @@ -413,10 +413,10 @@ If the filename ends with ".bin", the dump file (or files, if "*" or will be about the same size as a text version, but will typically write out much faster. Of course, when post-processing, you will need to convert it back to text format (see the "binary2txt -tool"_Section_tools.html#binary) or write your own code to read the -binary file. The format of the binary file can be understood by -looking at the tools/binary2txt.cpp file. This option is only -available for the {atom} and {custom} styles. +tool"_Tools.html#binary) or write your own code to read the binary +file. The format of the binary file can be understood by looking at +the tools/binary2txt.cpp file. This option is only available for the +{atom} and {custom} styles. If the filename ends with ".gz", the dump file (or files, if "*" or "%" is also used) is written in gzipped format. A gzipped dump file will @@ -625,9 +625,9 @@ The {d_name} and {i_name} attributes allow to output custom per atom floating point or integer properties that are managed by "fix property/atom"_fix_property_atom.html. -See "Section 10"_Section_modify.html of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. +See the "Modify"_Modify.html doc page for information on how to add +new compute and fix styles to LAMMPS to calculate per-atom quantities +which could then be output into dump files. :line diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index 3fa267d2b099a252bce78e49d24c69609dffac2a..c1732be972f6502111c71fbc411152e223c9053f 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -606,9 +606,9 @@ supported. :l :line -See "Section 10"_Section_modify.html of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. +See the "Modify"_Modify.html doc page for information on how to add +new compute and fix styles to LAMMPS to calculate per-atom quantities +which could then be output into dump files. :line diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 6de6de545e720d518316ea9d31c82fb825fd8c9c..5365610d640ab7598a11554d6c20bb47de8cf442 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre dump-ID = ID of dump to modify :ulb,l one or more keyword/value pairs may be appended :l these keywords apply to various dump styles :l -keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l +keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l {append} arg = {yes} or {no} {at} arg = N N = index of frame written upon first dump @@ -37,6 +37,8 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi {image} arg = {yes} or {no} {label} arg = string string = character string (e.g. BONDS) to use in header of dump local file + {maxfiles} arg = Fmax + Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file) {nfile} arg = Nf Nf = write this many files, one from each of Nf processors {pad} arg = Nchar = # of characters to convert timestep to @@ -364,6 +366,20 @@ e.g. BONDS or ANGLES. :line +The {maxfiles} keyword can only be used when a '*' wildcard is +included in the dump file name, i.e. when writing a new file(s) for +each snapshot. The specified {Fmax} is how many snapshots will be +kept. Once this number is reached, the file(s) containing the oldest +snapshot is deleted before a new dump file is written. If the +specified {Fmax} <= 0, then all files are retained. + +This can be useful for debugging, especially if you don't know on what +timestep something bad will happen, e.g. when LAMMPS will exit with an +error. You can dump every timestep, and limit the number of dump +files produced, even if you run for 1000s of steps. + +:line + The {nfile} or {fileper} keywords can be used in conjunction with the "%" wildcard character in the specified dump file name, for all dump styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles @@ -470,7 +486,7 @@ to respond to the call from the dump command, and update the appropriate reference positions. This is done be defining an "atom-style variable"_variable.html, {check} in this example, which calculates a Boolean value (0 or 1) for each atom, based on the same -criterion used by dump_modify thresh. +criterion used by dump_modify thresh. See the "compute displace/atom"_compute_displace_atom.html command for more details, including an example of how to produce output that @@ -584,13 +600,13 @@ included.) region foo sphere 10 20 10 15 variable inregion atom rmask(foo) -dump_modify ... thresh v_inregion |^ LAST +dump_modify ... thresh v_inregion |^ LAST :pre This will dump atoms which crossed the boundary of the spherical region since the last dump. variable charge atom "(q > 0.5) || (q < -0.5)" -dump_modify ... thresh v_charge |^ LAST +dump_modify ... thresh v_charge |^ LAST :pre This will dump atoms whose charge has changed from an absolute value less than 1/2 to greater than 1/2 (or vice versa) since the last dump. @@ -901,6 +917,7 @@ flush = yes format = %d and %g for each integer or floating point value image = no label = ENTRIES +maxifiles = -1 nfile = 1 pad = 0 pbc = no diff --git a/doc/src/fix.txt b/doc/src/fix.txt index e54a918cd0e2d876088f9cc76a4a52136df71a7e..ba2088576f1b4137d61d89509d2e6089026864f4 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -30,9 +30,9 @@ Set a fix that will be applied to a group of atoms. In LAMMPS, a timestepping or minimization. Examples include updating of atom positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary -conditions, computing diagnostics, etc. There are dozens of fixes -defined in LAMMPS and new ones can be added; see "this -section"_Section_modify.html for a discussion. +conditions, computing diagnostics, etc. There are hundredes of fixes +defined in LAMMPS and new ones can be added; see the +"Modify"_Modify.html doc page for details. Fixes perform their operations at different stages of the timestep. If 2 or more fixes operate at the same stage of the timestep, they are diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 19d1009b8a838829c0dfee1adde7526134d29053..7a34f2ff4480004c3ff249957b2b36204a087035 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -205,6 +205,14 @@ a bond coefficient over time, very similar to how the {pair} keyword operates. The only difference is that now a bond coefficient for a given bond type is adapted. +A wild-card asterisk can be used in place of or in conjunction with +the bond type argument to set the coefficients for multiple bond types. +This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of +atom types, then an asterisk with no numeric values means all types +from 1 to N. A leading asterisk means all types from 1 to n (inclusive). +A trailing asterisk means all types from n to N (inclusive). A middle +asterisk means all types from m to n (inclusive). + Currently {bond} does not support bond_style hybrid nor bond_style hybrid/overlay as bond styles. The only bonds that currently are working with fix_adapt are diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt index b2ac95eabb0f4e2e49e4af226ae6cc98ea0d0358..5bba9acb3fe6ae5e988bfbc57f5d4dc8cdb07b4a 100644 --- a/doc/src/fix_addforce.txt +++ b/doc/src/fix_addforce.txt @@ -103,12 +103,12 @@ converge properly. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -120,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt index 3251125a5d2f21e8f9cdeea958112a5a23b59506..23e4ed235b2d21c3c9cde5df0207781b448d69c2 100644 --- a/doc/src/fix_ave_atom.txt +++ b/doc/src/fix_ave_atom.txt @@ -124,7 +124,7 @@ appended, the per-atom vector calculated by the compute is used. If a bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. See the discussion above for how I can +LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -136,8 +136,8 @@ the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple +LAMMPS"_Modify.html. See the discussion above for how I can be +specified with a wildcard asterisk to effectively specify multiple values. If a value begins with "v_", a variable name must follow which has diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index a8691d376772f458d5c0ed82376fcd0154b7a69a..8e2a09e33fb4a4da2872780fad28fb3f3dc54769 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -263,7 +263,7 @@ previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. +their own compute styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -274,7 +274,7 @@ bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error results. Users can also write code for their -own fix styles and "add them to LAMMPS"_Section_modify.html. See the +own fix styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index 371f2f66a88f5394bac76c74e18a811939eb6961..98f352cb74ea0ed97e05324d2980c46bd7147ca1 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -176,7 +176,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is @@ -189,7 +189,7 @@ values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Only equal-style or diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index 043f0e22be3c7dda7b85209b9b6c53c3578c5b30..5155f42e7bca0335d29ac16566051255a2ff3a89 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -183,11 +183,11 @@ Note that there is a "compute reduce"_compute_reduce.html command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix ave/histo. Or it can be a compute defined not in your input script, but by "thermodynamic -output"_thermo_style.html or other fixes such as "fix -nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See -the doc pages for these commands which give the IDs of these computes. -Users can also write code for their own compute styles and "add them -to LAMMPS"_Section_modify.html. +output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html +or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for +these commands which give the IDs of these computes. Users can also +write code for their own compute styles and "add them to +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If {mode} = scalar, then if @@ -204,7 +204,7 @@ values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. If {mode} = scalar, then diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 266e3f0e38488694dfce0b442a607a6851483377..b61f56cf0274ef732216e2dcc1020a1bd8f4d4ee 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -168,7 +168,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them -to LAMMPS"_Section_modify.html. +to LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If {mode} = scalar, then if @@ -184,7 +184,7 @@ specify multiple values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. If {mode} = scalar, then diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt index 5d7dec3e6aef7bb804f312546cb15bbe85b0e639..4944996695260f3e6aab65dc5bb109085d6ad9b9 100644 --- a/doc/src/fix_aveforce.txt +++ b/doc/src/fix_aveforce.txt @@ -63,12 +63,12 @@ to it. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -80,8 +80,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt new file mode 100644 index 0000000000000000000000000000000000000000..f53b7c785c251240a0d325b820545f342ce21c06 --- /dev/null +++ b/doc/src/fix_bocs.txt @@ -0,0 +1,112 @@ +<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix bocs command :h3 + +[Syntax:] + +fix ID group-ID bocs keyword values ... :pre + +keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline} + {temp} values = Tstart Tstop Tdamp + {cgiso} values = Pstart Pstop Pdamp + {basis set} + {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N + {linear_spline} values = input_filename + {cubic_spline} values = input_filename :pre +:ule + +[Examples:] + +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre + +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre + +thermo_modify press 1_press :pre + + +[Description:] + +These commands incorporate a pressure correction as described by +Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK +barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna . +The first half of the command mimics a standard fix npt command: + +fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre + +The two differences are replacing {npt} with {bocs}, and replacing +{iso}/{aniso}/{etc} with {cgiso}. +The rest of the command details what form you would like to use for +the pressure correction equation. The choices are: {analytic}, {linear_spline}, +or {cubic_spline}. + +With either spline method, the only argument that needs to follow it +is the name of a file that contains the desired pressure correction +as a function of volume. The file should be formatted so each line has: + +Volume_i, PressureCorrection_i :pre + +Note both the COMMA and the SPACE separating the volume's +value and its corresponding pressure correction. The volumes in the file +should be uniformly spaced. Both the volumes and the pressure corrections +should be provided in the proper units, e.g. if you are using {units real}, +the volumes should all be in cubic angstroms, and the pressure corrections +should all be in atomspheres. Furthermore, the table should start/end at a +volume considerably smaller/larger than you expect your system to sample +during the simulation. If the system ever reaches a volume outside of the +range provided, the simulation will stop. + +With the {analytic} option, the arguments are as follows: + +... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre + +Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you +are using {units real}, {V_avg} should be in cubic angstroms, and the +coefficients should all be in atmospheres * cubic angstroms. + +[Restrictions:] + +As this is computing a (modified) pressure, group-ID should be {all}. + +The pressure correction has only been tested for use with an isotropic +pressure coupling in 3 dimensions. + +By default, LAMMPS will still report the normal value for the pressure +if the pressure is printed via a {thermo} command, or if the pressures +are written to a file every so often. In order to have LAMMPS report the +modified pressure, you must include the {thermo_modify} command given in +the examples. For the last argument in the command, you should put +XXXX_press, where XXXX is the ID given to the fix bocs command (in the +example, the ID of the fix bocs command is 1 ). + +This fix is part of the USER-BOCS package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related:] + +For more details about the pressure correction and the entire BOCS software +package, visit the "BOCS package on github"_bocsgithub and read the release +paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 . + + +:link(bocsgithub,https://github.com/noid-group/BOCS) + +:line + +:link(bocs-Dunn1) +[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015). + +:link(bocs-Martyna) +[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994). + +:link(bocs-Dunn2) +[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018). + + + diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt new file mode 100644 index 0000000000000000000000000000000000000000..f85ef9bc1aa6ea034364e5358ac1eafa2824f0d6 --- /dev/null +++ b/doc/src/fix_bond_react.txt @@ -0,0 +1,332 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix bond/react command :h3 + +[Syntax:] + +fix ID group-ID bond/react common_keyword values ... + react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... + ... :pre + +ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l +bond/react = style name of this fix command :l +zero or more common keyword/value pairs may be appended directly after 'bond/react' :l +these apply to all reaction specifications (below) :l +common_keyword = {stabilization} :l + {stabilization} values = {no} or {yes} {group-ID} {xmax} + {no} = no reaction site stabilization + {yes} = perform reaction site stabilization + {group-ID} = user-assigned ID for all non-reacting atoms (group created internally) + {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre +react = mandatory argument indicating new reaction specification :l + react-ID = user-assigned name for the reaction :l + react-group-ID = only atoms in this group are available for the reaction :l + Nevery = attempt reaction every this many steps :l + Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l + Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l + template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l + template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l + map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l + zero or more individual keyword/value pairs may be appended to each react argument :l + individual_keyword = {prob} or {stabilize_steps} :l + {prob} values = fraction seed + fraction = initiate reaction with this probability if otherwise eligible + seed = random number seed (positive integer) + {stabilize_steps} value = timesteps + timesteps = number of timesteps to apply internally created nve/limit.html :pre +:ule + +[Examples:] + +molecule mol1 pre_reacted_topology.txt +molecule mol2 post_reacted_topology.txt +fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre + +molecule mol1 pre_reacted_rxn1.txt +molecule mol2 post_reacted_rxn1.txt +molecule mol3 pre_reacted_rxn2.txt +molecule mol4 post_reacted_rxn2.txt +fix 5 all bond/react stabilization yes nvt_grp .03 & + react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 & + react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345 +fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre + +[Description:] + +Initiate complex covalent bonding (topology) changes. These topology +changes will be referred to as 'reactions' throughout this +documentation. Topology changes are defined in pre- and post-reaction +molecule templates and can include creation and deletion of bonds, +angles, dihedrals, impropers, bond-types, angle-types, dihedral-types, +atom-types, or atomic charges. + +Fix bond/react does not use quantum mechanical (eg. fix qmmm) or +pairwise bond-order potential (eg. Tersoff or AIREBO) methods to +determine bonding changes a priori. Rather, it uses a distance-based +probabilistic criteria to effect predetermined topology changes in +simulations using standard force fields. + +This fix was created to facilitate the dynamic creation of polymeric, +amorphous or highly-crosslinked systems. A suggested workflow for +using this fix is: 1) identify a reaction to be simulated 2) build a +molecule template of the reaction site before the reaction has +occurred 3) build a molecule template of the reaction site after the +reaction has occurred 4) create a map that relates the +template-atom-IDs of each atom between pre- and post-reaction molecule +templates 5) fill a simulation box with molecules and run a simulation +with fix bond/react. + +Only one 'fix bond/react' command can be used at a time. Multiple +reactions can be simultaneously applied by specifying multiple {react} +arguments to a single 'fix bond/react' command. This syntax is +necessary because the 'common keywords' are applied to all reactions. + +The {stabilization} keyword enables reaction site stabilization. +Reaction site stabilization is performed by including reacting atoms +in an internally created fix "nve/limit"_fix_nve_limit.html time +integrator for a set number of timesteps given by the +{stabilize_steps} keyword. While reacting atoms are being time +integrated by the internal nve/limit, they are prevented from being +involved in any new reactions. The {xmax} value keyword should +typically be set to the maximum distance that non-reacting atoms move +during the simulation. + +The group-ID set using the {stabilization} keyword should be a +previously unused group-ID. It cannot be specified as 'all'. The fix +bond/react command creates a "dynamic group"_group.html of this name +that includes all non-reacting atoms. This dynamic group-ID should +then be used by a subsequent system-wide time integrator such as nvt, +npt, or nve, as shown in the second example above. It is currently +necessary to place the time integration command after the fix +bond/react command due to the internal dynamic grouping performed by +fix bond/react. + +NOTE: The internally created group currently applies to all atoms in +the system, i.e. you should generally not have a separate thermostat +which acts on the 'all' group. + +The following comments pertain to each {react} argument: + +A check for possible new reaction sites is performed every {Nevery} +timesteps. + +Two conditions must be met for a reaction to occur. First a bonding +atom pair must be identified. Second, the topology surrounding the +bonding atom pair must match the topology of the pre-reaction +template. If both these conditions are met, the reaction site is +modified to match the post-reaction template. + +A bonding atom pair will be identified if several conditions are met. +First, a pair of atoms within the specified react-group-ID of type +typei and typej must separated by a distance between {Rmin} and +{Rmax}. It is possible that multiple bonding atom pairs are +identified: if the bonding atoms in the pre-reacted template are not +1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as +its bonding partner; otherwise, the farthest potential partner is +chosen. Then, if both an atomi and atomj have each other as their +nearest bonding partners, these two atoms are identified as the +bonding atom pair of the reaction site. Once this unique bonding atom +pair is identified for each reaction, there could two or more +reactions that involve a given atom on the same timestep. If this is +the case, only one such reaction is permitted to occur. This reaction +is chosen randomly from all potential reactions. This capability +allows e.g. for different reaction pathways to proceed from identical +reaction sites with user-specified probabilities. + +The pre-reacted molecule template is specified by a molecule command. +This molecule template file contains a sample reaction site and its +surrounding topology. As described below, the bonding atom pairs of +the pre-reacted template are specified by atom ID in the map file. The +pre-reacted molecule template should contain as few atoms as possible +while still completely describing the topology of all atoms affected +by the reaction. For example, if the force field contains dihedrals, +the pre-reacted template should contain any atom within three bonds of +reacting atoms. + +Some atoms in the pre-reacted template that are not reacting may have +missing topology with respect to the simulation. For example, the +pre-reacted template may contain an atom that would connect to the +rest of a long polymer chain. These are referred to as edge atoms, and +are also specified in the map file. + +Note that some care must be taken when a building a molecule template +for a given simulation. All atom types in the pre-reacted template +must be the same as those of a potential reaction site in the +simulation. A detailed discussion of matching molecule template atom +types with the simulation is provided on the "molecule"_molecule.html +command page. + +The post-reacted molecule template contains a sample of the reaction +site and its surrounding topology after the reaction has occurred. It +must contain the same number of atoms as the pre-reacted template. A +one-to-one correspondence between the atom IDs in the pre- and +post-reacted templates is specified in the map file as described +below. Note that during a reaction, an atom, bond, etc. type may +change to one that was previously not present in the simulation. These +new types must also be defined during the setup of a given simulation. +A discussion of correctly handling this is also provided on the +"molecule"_molecule.html command page. + +The map file is a text document with the following format: + +A map file has a header and a body. The header of map file the +contains one mandatory keyword and one optional keyword. The mandatory +keyword is 'equivalences' and the optional keyword is 'edgeIDs': + +N {equivalences} = # of atoms N in the reaction molecule templates +N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre + +The body of the map file contains two mandatory sections and one +optional section. The first mandatory section begins with the keyword +'BondingIDs' and lists the atom IDs of the bonding atom pair in the +pre-reacted molecule template. The second mandatory section begins +with the keyword 'Equivalences' and lists a one-to-one correspondence +between atom IDs of the pre- and post-reacted templates. The first +column is an atom ID of the pre-reacted molecule template, and the +second column is the corresponding atom ID of the post-reacted +molecule template. The optional section begins with the keyword +'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted +molecule template. + +A sample map file is given below: + +:line + +# this is a map file :pre + +2 edgeIDs +7 equivalences :pre + +BondingIDs :pre + +3 +5 :pre + +EdgeIDs :pre + +1 +7 :pre + +Equivalences :pre + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 :pre + +:line + +Once a reaction site has been successfully identified, data structures +within LAMMPS that store bond topology are updated to reflect the +post-reacted molecule template. All force fields with fixed bonds, +angles, dihedrals or impropers are supported. + +A few capabilities to note: 1) You may specify as many {react} +arguments as desired. For example, you could break down a complicated +reaction mechanism into several reaction steps, each defined by its +own {react} argument. 2) While typically a bond is formed or removed +between the bonding atom pairs specified in the pre-reacted molecule +template, this is not required. 3) By reversing the order of the pre- +and post- reacted molecule templates in another {react} argument, you +can allow for the possibility of one or more reverse reactions. + +The optional keywords deal with the probability of a given reaction +occurring as well as the stable equilibration of each reaction site as +it occurs. + +The {prob} keyword can affect whether an eligible reaction actually +occurs. The fraction setting must be a value between 0.0 and 1.0. A +uniform random number between 0.0 and 1.0 is generated and the +eligible reaction only occurs if the random number is less than the +fraction. + +The {stabilize_steps} keyword allows for the specification of how many +timesteps a reaction site is stabilized before being returned to the +overall system thermostat. + +In order to produce the most physical behavior, this 'reaction site +equilibration time' should be tuned to be as small as possible while +retaining stability for a given system or reaction step. After a +limited number of case studies, this number has been set to a default +of 60 timesteps. Ideally, it should be individually tuned for each fix +reaction step. Note that in some situations, decreasing rather than +increasing this parameter will result in an increase in stability. + +A few other considerations: + +It may be beneficial to ensure reacting atoms are at a certain +temperature before being released to the overall thermostat. For this, +you can use the internally-created dynamic group named +"bond_react_MASTER_group." For example, adding the following command +would thermostat the group of all atoms currently involved in a +reaction: + +fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre + +NOTE: This command must be added after the fix bond/react command, and +will apply to all reactions. + +Computationally, each timestep this fix operates, it loops over +neighbor lists (for bond-forming reactions) and computes distances +between pairs of atoms in the list. It also communicates between +neighboring processors to coordinate which bonds are created and/or +removed. All of these operations increase the cost of a timestep. Thus +you should be cautious about invoking this fix too frequently. + +You can dump out snapshots of the current bond topology via the dump +local command. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html, aside from internally-created per-atom +properties. None of the "fix_modify"_fix_modify.html options are +relevant to this fix. + +This fix computes one statistic for each {react} argument that it +stores in a global vector, of length 'number of react arguments', that +can be accessed by various "output +commands"_Section_howto.html#howto_15. The vector values calculated by +this fix are "intensive". + +These is 1 quantity for each react argument: + +(1) cumulative # of reactions occurred :ul + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"fix bond/create"_fix_bond_create.html, "fix +bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, +"dump local"_dump.html, "special_bonds"_special_bonds.html + +[Default:] + +The option defaults are stabilization = no, stabilize_steps = 60 + +:line + +:link(Gissinger) +[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017). diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index cfb26138fdaa468c3074b1ef6fa1f1dfe6c6eb8c..b8d2cb43be4b2fbc30d70034531969e4325a4709 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -139,7 +139,7 @@ for details. If no bracketed integer is appended, the scalar calculated by the compute is used. If a bracketed integer is appended, the Ith value of the vector calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If {pvar} begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates a global @@ -150,7 +150,7 @@ references the values, or else an error results. If no bracketed integer is appended, the scalar calculated by the fix is used. If a bracketed integer is appended, the Ith value of the vector calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If {pvar} begins with "v_", a variable name must follow which has been previously defined in the input script. Only equal-style variables diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index c870c73bdccf918288589c5141ba4dbafcc60434..681986561a35e7d36874f10621c5746b4218d705 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -94,7 +94,7 @@ nvt/sllod"_fix_nvt_sllod.html and "compute temp/deform"_compute_temp_deform.html commands for more details. Note that simulation of a continuously extended system (extensional flow) can be modeled using the "USER-UEF -package"_Section_packages.html#USER-UEF and its "fix +package"_Packages_details.html#USER-UEF and its "fix commands"_fix_nh_uef.html. For the {x}, {y}, {z} parameters, the associated dimension cannot be @@ -550,10 +550,9 @@ command if you want to include lattice spacings in a variable formula. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -565,8 +564,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt index 1c10d954d6eb910f5863120a405ace281b12e6da..4f2b5d573f54679a6f8930f7feeb61f4fc59acfa 100644 --- a/doc/src/fix_dpd_energy.txt +++ b/doc/src/fix_dpd_energy.txt @@ -50,10 +50,9 @@ examples/USER/dpd directory. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index 1bed4f9e89271f367dd68257f78f33b76c42f11f..7605395ca05122bbde2a2600e2349b9026be4b56 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -19,7 +19,9 @@ Tmin = minimum dt allowed which can be NULL (time units) Tmax = maximum dt allowed which can be NULL (time units) Xmax = maximum distance for an atom to move in one timestep (distance units) zero or more keyword/value pairs may be appended -keyword = {units} :ul +keyword = {emax} or {units} :ul + {emax} value = Emax + Emax = maximum kinetic energy change for an atom in one timestep (energy units) {units} value = {lattice} or {box} lattice = Xmax is defined in lattice units box = Xmax is defined in simulation box units :pre @@ -27,12 +29,17 @@ keyword = {units} :ul [Examples:] fix 5 all dt/reset 10 1.0e-5 0.01 0.1 -fix 5 all dt/reset 10 0.01 2.0 0.2 units box :pre +fix 5 all dt/reset 10 0.01 2.0 0.2 units box +fix 5 all dt/reset 5 NULL 0.001 0.5 emax 30 units box :pre [Description:] Reset the timestep size every N steps during a run, so that no atom -moves further than Xmax, based on current atom velocities and forces. +moves further than the specified {Xmax} distance, based on current +atom velocities and forces. Optionally an additional criterion is +imposed by the {emax} keyword, so that no atom's kinetic energy +changes by more than the specified {Emax}. + This can be useful when starting from a configuration with overlapping atoms, where forces will be large. Or it can be useful when running an impact simulation where one or more high-energy atoms collide with @@ -48,7 +55,12 @@ current velocity and force. Since performing this calculation exactly would require the solution to a quartic equation, a cheaper estimate is generated. The estimate is conservative in that the atom's displacement is guaranteed not to exceed {Xmax}, though it may be -smaller. +smaller. + +In addition if the {emax} keyword is used, the specified {Emax} value +is enforced as a limit on how much an atom's kinetic energy can +change. If the timestep required is even smaller than for the {Xmax} +displacement, then the smaller timestep is used. Given this putative timestep for each atom, the minimum timestep value across all atoms is computed. Then the {Tmin} and {Tmax} bounds are @@ -87,4 +99,5 @@ minimization"_minimize.html. [Default:] -The option defaults is units = lattice. +The option defaults are units = lattice, and no emax kinetic energy +limit. diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt index 5d04e96677f2adc27c9622b84d97810b23748d7a..67b351e4b820e1c95f54b6cf58d77f74f43dcb7d 100644 --- a/doc/src/fix_enforce2d.txt +++ b/doc/src/fix_enforce2d.txt @@ -7,6 +7,7 @@ :line fix enforce2d command :h3 +fix enforce2d/kk command :h3 [Syntax:] @@ -27,12 +28,12 @@ not move from their initial z coordinate. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -44,8 +45,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index 0c878743471ae03c5bd76fec05f16dbc7631f01e..f74a838c4776aa955128ce0681a99f95cc391e08 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -156,10 +156,9 @@ no 0.93 0.00 0.000 -1.76 :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt index b28d33446fe6df61d6efd46017dc37c4cf6f61ee..30e34b48587f2dd276dcd9bb50f398bc95f80a45 100644 --- a/doc/src/fix_external.txt +++ b/doc/src/fix_external.txt @@ -34,8 +34,7 @@ This fix allows external programs that are running LAMMPS through its "library interface"_Section_howto.html#howto_19 to modify certain LAMMPS properties on specific timesteps, similar to the way other fixes do. The external driver can be a "C/C++ or Fortran -program"_Section_howto.html#howto_19 or a "Python -script"_Section_python.html. +program"_Section_howto.html#howto_19 or a "Python script"_Python.html. :line diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt index a63ee4cb32688c286797292acbaa140fbed18101..9619f4120b415768db568ffffbb1734dd504be27 100644 --- a/doc/src/fix_freeze.txt +++ b/doc/src/fix_freeze.txt @@ -31,12 +31,12 @@ using "fix setforce"_fix_setforce.html. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -48,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 38f0fb95ce0530d425689b0daa9052e6a6995074..191bc32b1499f1f4555330c8347bf49cb2472634 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -349,7 +349,7 @@ in the context of NVT dynamics. NOTE: If the density of the cell is initially very small or zero, and increases to a much larger density after a period of equilibration, then certain quantities that are only calculated once at the start -(kspace parameters, tail corrections) may no longer be accurate. The +(kspace parameters) may no longer be accurate. The solution is to start a new simulation after the equilibrium density has been reached. diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index dae8ac5ed0910fc2c91b776339de840707bf5500..f39955d4f8ed4247967043cf3376784e834a3420 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -90,10 +90,9 @@ field. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 93c73f5a5dd2390f93d80dfe7ce2d4efc7f53e69..6ab236e572d0b46c8d6a1ee6851a4b9c5a0233a4 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -264,10 +264,9 @@ generates an average temperature of 220 K, instead of 300 K. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -279,8 +278,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index afc9c5f257523646906966d89464da26a070023e..c85ff24c96d2982439d67c4ac52fd3bea5083044 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs should be chosen low enough, so as to mimic as closely as possible the self-consistent minimization. It must however be high enough, so that the dipoles can follow the local electric field exerted by the -neighbouring atoms. The optimal value probably depends on the +neighboring atoms. The optimal value probably depends on the temperature of the centers of mass and on the mass of the Drude particles. diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..b089cd7f58148c74a805080cccde0ac2cb600143 --- /dev/null +++ b/doc/src/fix_langevin_spin.txt @@ -0,0 +1,102 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix langevin/spin command :h3 + +[Syntax:] + +fix ID group-ID langevin/spin T Tdamp seed :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +langevin/spin = style name of this fix command :l +T = desired temperature of the bath (temperature units, K in metal units) :l +Tdamp = transverse magnetic damping parameter (adim) :l +seed = random number seed to use for white noise (positive integer) :l +:ule + +[Examples:] + +fix 2 all langevin/spin 300.0 0.01 21 :pre + +[Description:] + +Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the +magnetic spins associated to the atoms. +Used with "fix nve/spin"_fix_nve_spin.html, this command performs +Brownian dynamics (BD). +A random torque and a transverse dissipation are applied to each spin i according to +the following stochastic differential equation: + +:c,image(Eqs/fix_langevin_spin_sLLG.jpg) + +with lambda the transverse damping, and eta a random verctor. +This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) +equation. + +The components of eta are drawn from a Gaussian probability law. Their amplitude +is defined as a proportion of the temperature of the external thermostat T (in K +in metal units). + +More details about this implementation are reported in "(Tranchida)"_#Tranchida2. + +Note: due to the form of the sLLG equation, this fix has to be defined just +before the nve/spin fix (and after all other magnetic fixes). +As an example: + +fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 +fix 2 all langevin/spin 300.0 0.01 21 +fix 3 all nve/spin lattice yes :pre + +is correct, but defining a force/spin command after the langevin/spin command +would give an error message. + +Note: The random # {seed} must be a positive integer. A Marsaglia random +number generator is used. Each processor uses the input seed to +generate its own unique seed and its own stream of random numbers. +Thus the dynamics of the system will not be identical on two runs on +different numbers of processors. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. + +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +The {langevin/spin} fix is part of the SPIN package. +This style is only enabled if LAMMPS was built with this package. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +The numerical integration has to be performed with {fix nve/spin} +when {fix langevin/spin} is enabled. + +This fix has to be the last defined magnetic fix before the time +integration fix (e.g. {fix nve/spin}). + +[Related commands:] + +"fix nve/spin"_fix_nve_spin.html, "fix precession/spin"_fix_precession_spin.html + +[Default:] none + +:line + +:link(Mayergoyz1) +[(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009) + +:link(Tranchida2) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index 1c7dcf77a5dd0c72db2dea22873e0728417e8048..308bba1ac31fdf9a7cbd45ec1da50122cd46bcb9 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -14,14 +14,16 @@ fix_modify fix-ID keyword value ... :pre fix-ID = ID of the fix to modify :ulb,l one or more keyword/value pairs may be appended :l -keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l +keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :l {temp} value = compute ID that calculates a temperature {press} value = compute ID that calculates a pressure {energy} value = {yes} or {no} {virial} value = {yes} or {no} {respa} value = {1} to {max respa level} or {0} (for outermost level) {dynamic/dof} value = {yes} or {no} - yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre + yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature + {bodyforces} value = {early} or {late} + early/late = compute rigid-body forces/torques early or late in the timestep :pre :ule [Examples:] @@ -84,9 +86,8 @@ if you want virial contribution of the fix to be part of the relaxation criteria, although this seems unlikely. NOTE: This option is only supported by fixes that explicitly say -so. For some of these (e.g. the -"fix shake"_fix_shake.html command) the default setting is -{virial yes}, for others it is {virial no}. +so. For some of these (e.g. the "fix shake"_fix_shake.html command) +the default setting is {virial yes}, for others it is {virial no}. For fixes that set or modify forces, it may be possible to select at which "r-RESPA"_run_style.html level the fix operates via the {respa} @@ -120,6 +121,28 @@ compute to calculate temperature. See the "compute_modify dynamic/dof"_compute_modify.html command for a similar way to insure correct temperature normalization for those thermostats. +The {bodyforces} keyword determines whether the forces and torques +acting on rigid bodies are computed {early} at the post-force stage of +each timestep (right after per-atom forces have been computed and +communicated among processors), or {late} at the final-integrate stage +of each timestep (after any other fixes have finished their post-force +tasks). Only the rigid-body integration fixes use this option, which +includes "fix rigid"_fix_rigid.html and "fix +rigid/small"_fix_rigid.html, and their variants, and also "fix +poems"_fix_poems.html. + +The default is {late}. If there are other fixes that add forces to +individual atoms, then the rigid-body constraints will include these +forces when time-integrating the rigid bodies. If {early} is +specified, then new fixes can be written that use or modify the +per-body force and torque, before time-integration of the rigid bodies +occurs. Note however this has the side effect, that fixes such as +"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html, +"fix spring"_fix_spring.html, which add forces to individual atoms +will have no effect on the motion of the rigid bodies if they are +specified in the input script after the fix rigid command. LAMMPS +will give a warning if that is the case. + [Restrictions:] none [Related commands:] @@ -130,4 +153,5 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html [Default:] The option defaults are temp = ID defined by fix, press = ID defined -by fix, energy = no, virial = different for each fix style, respa = 0. +by fix, energy = no, virial = different for each fix style, respa = 0, +bodyforce = late. diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt index bcf4465fb8f5c9bc30626cc3275f422fd2158e9e..aa5199ac14adefa0a6b53bafb55663fcc37bdf3b 100644 --- a/doc/src/fix_momentum.txt +++ b/doc/src/fix_momentum.txt @@ -61,10 +61,9 @@ initial velocities with zero aggregate linear and/or angular momentum. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -76,8 +75,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 41d0e6438fc9e05d08aa43d1548a98c0856ffd90..e3a39c6bc6efbd1ddcd8e49b9296724830aceded 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -484,10 +484,9 @@ the various ways to do this. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -499,8 +498,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt index 8c35b6a1a7a4b8bbd2fc98573764f99f0995249c..ff8c300c475d0770e7a345ecfb7e1282a2ea3bbe 100644 --- a/doc/src/fix_nph_asphere.txt +++ b/doc/src/fix_nph_asphere.txt @@ -81,10 +81,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -96,8 +95,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt index 1e590f1cb3f3d5a46724d86e657d805a6a1906e3..9263470e9eba1d609f98969ae880751606d31db7 100644 --- a/doc/src/fix_nph_body.txt +++ b/doc/src/fix_nph_body.txt @@ -80,10 +80,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt index 62b45edfd7cd5ffbd8fe8ab48d5aefc29d3417ee..ba3b2f6c06f67cf2079f022d13a41c05599ba01a 100644 --- a/doc/src/fix_nph_sphere.txt +++ b/doc/src/fix_nph_sphere.txt @@ -90,10 +90,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt index 292e46f94af6fcfe8e8c8b5b1e04908c2c55c9bc..4f696e9590b43a44333db37bed3fcb6561c2b3d2 100644 --- a/doc/src/fix_nphug.txt +++ b/doc/src/fix_nphug.txt @@ -140,10 +140,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -155,8 +154,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt index 5f3979e36ed9e586f2eee15750364641348c040c..a21caa1042df33ec57a08e5ffa0eb949b62dadaa 100644 --- a/doc/src/fix_npt_asphere.txt +++ b/doc/src/fix_npt_asphere.txt @@ -105,10 +105,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt index d89bf19db24fa7a988923a8cb5822cccc9641ed9..0f678a1b7d422fa910d4b217df7b63698ddaf4d7 100644 --- a/doc/src/fix_npt_body.txt +++ b/doc/src/fix_npt_body.txt @@ -104,10 +104,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -119,8 +118,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt index c4cf2cb08de85d8fe892f240473a0a90daa56de0..862f95603f8ba3fb2e187a8d567147d0241d965b 100644 --- a/doc/src/fix_npt_sphere.txt +++ b/doc/src/fix_npt_sphere.txt @@ -115,10 +115,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -130,8 +129,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt index c04c17858ebdf9b4166827a9cf5f52ed0f43e597..ac9cb53b50830f95acba891153d86f423d6c3f80 100644 --- a/doc/src/fix_nve.txt +++ b/doc/src/fix_nve.txt @@ -34,10 +34,9 @@ ensemble. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -49,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt index 1f31fb96792239de806f99e78744106b0b08c1f7..5be7a7aa68e006c6a06ec23ca8a3ba0aa65c06f7 100644 --- a/doc/src/fix_nve_asphere.txt +++ b/doc/src/fix_nve_asphere.txt @@ -45,10 +45,9 @@ This fix is not invoked during "energy minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index 21dc6cba8a4aa7e067bcb9b0c066879e60b23479..cfe73a854d58d9636c8235ffe1838e50b28e25cd 100644 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -65,10 +65,9 @@ moment of inertia, as used in the time integration. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -80,8 +79,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..f4b38c270bc4b40b73c570ce590f39fc282bad1f --- /dev/null +++ b/doc/src/fix_nve_spin.txt @@ -0,0 +1,76 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix nve/spin command :h3 + +[Syntax:] + +fix ID group-ID nve/spin keyword values :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +nve/spin = style name of this fix command :l +keyword = {lattice} :l + {lattice} value = {no} or {yes} :pre +:ule + +[Examples:] + +fix 3 all nve/spin lattice yes +fix 1 all nve/spin lattice no :pre + +[Description:] + +Perform a symplectic integration for the spin or spin-lattice system. + +The {lattice} keyword defines if the spins are integrated on a lattice +of fixed atoms (lattice = no), or if atoms are moving (lattice = yes). + +By default (lattice = yes), a spin-lattice integration is performed. + +The {nve/spin} fix applies a Suzuki-Trotter decomposition to +the equations of motion of the spin lattice system, following the scheme: + +:c,image(Eqs/fix_integration_spin_stdecomposition.jpg) + +according to the implementation reported in "(Omelyan)"_#Omelyan1. + +A sectoring method enables this scheme for parallel calculations. +The implementation of this sectoring algorithm is reported +in "(Tranchida)"_#Tranchida1. + +:line + +[Restrictions:] + +This fix style can only be used if LAMMPS was built with the +SPIN package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info on packages. + +To use the spin algorithm, it is necessary to define a map with +the atom_modify command. Typically, by adding the command: + +atom_modify map array :pre + +before you create the simulation box. Note that the keyword "hash" +instead of "array" is also valid. + +[Related commands:] + +"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html + +[Default:] none + +:line + +:link(Omelyan1) +[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. +86(5), 898. (2001). + +:link(Tranchida1) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt index 21b900f16ac69d3ef28b7b39fa90f232f43eb290..031c60e4becebe29f3279bbfc2b624d54d45ec0d 100644 --- a/doc/src/fix_nvt_asphere.txt +++ b/doc/src/fix_nvt_asphere.txt @@ -86,10 +86,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -101,8 +100,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt index 6a5e09ba7fb57ef45a91b9bf764e1f2e821fc34f..80de7fd7c3ce275453ecfa3a09b90338dbe6e3c7 100644 --- a/doc/src/fix_nvt_body.txt +++ b/doc/src/fix_nvt_body.txt @@ -85,10 +85,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 392dbc281c6f5eee0fc164f4ed8eb6670bfbcbef..bb3c09293923a9d97d1dbd6469de09c47ffcf4ed 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -109,10 +109,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt index ecf0922b7901a154f0728579b41d6e9502b2f3d0..897d5606d717cd668b997b7b59d352cd86c477f4 100644 --- a/doc/src/fix_nvt_sphere.txt +++ b/doc/src/fix_nvt_sphere.txt @@ -96,10 +96,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -111,8 +110,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt index d90d832cb8e2deed341771ea00e9f0b294e55c8b..03abc058b8b0d6e982f6291e1fecbb887cf2ad9a 100644 --- a/doc/src/fix_poems.txt +++ b/doc/src/fix_poems.txt @@ -106,12 +106,18 @@ off, and there is only a single fix poems defined. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +files"_restart.html. + +The "fix_modify"_fix_modify.html {bodyforces} option is supported by +this fix style to set whether per-body forces and torques are computed +early or late in a timestep, i.e. at the post-force stage or at the +final-integrate stage, respectively. + +No global or per-atom quantities are stored by this fix for access by +various "output commands"_Section_howto.html#howto_15. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..4133d7dd57f42993ad8454d4d3e90973eccad34b --- /dev/null +++ b/doc/src/fix_precession_spin.txt @@ -0,0 +1,87 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix precession/spin command :h3 + +[Syntax:] + +fix ID group precession/spin style args :pre + +ID, group are documented in "fix"_fix.html command :ulb,l +precession/spin = style name of this fix command :l +style = {zeeman} or {anisotropy} :l + {zeeman} args = H x y z + H = intensity of the magnetic field (in Tesla) + x y z = vector direction of the field + {anisotropy} args = K x y z + K = intensity of the magnetic anisotropy (in eV) + x y z = vector direction of the anisotropy :pre +:ule + +[Examples:] + +fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 +fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0 +fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre + +[Description:] + +Impose a force torque to each magnetic spin in the group. + +Style {zeeman} is used for the simulation of the interaction +between the magnetic spins in the defined group and an external +magnetic field: + +:c,image(Eqs/force_spin_zeeman.jpg) + +with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T +in metal units). + +Style {anisotropy} is used to simulate an easy axis or an easy plane +for the magnetic spins in the defined group: + +:c,image(Eqs/force_spin_aniso.jpg) + +with n defining the direction of the anisotropy, and K (in eV) its intensity. +If K>0, an easy axis is defined, and if K<0, an easy plane is defined. + +In both cases, the choice of (x y z) imposes the vector direction for the force. +Only the direction of the vector is important; it's length is ignored. + +Both styles can be combined within one single command line. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +By default, the energy associated to this fix is not added to the potential +energy of the system. +The "fix_modify"_fix_modify.html {energy} option is supported by this fix +to add this magnetic potential energy to the potential energy of the system, + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes :pre + +This fix computes a global scalar which can be accessed by various +"output commands"_Section_howto.html#howto_15. + +No information about this fix is written to "binary restart +files"_restart.html. + +[Restrictions:] + +The {precession/spin} style is part of the SPIN package. +This style is only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html + +[Default:] none diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 10bb89c94cad5b28414578f621cab34c31266165..95fc2c424db6252553a8cd51583a8aa85bbe5d05 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -194,9 +194,9 @@ dump 1 all custom 100 tmp.dump id x y z c_1\[1\] c_1\[2\] :pre If you wish to add new "pair styles"_pair_style.html, "fixes"_fix.html, or "computes"_compute.html that use the per-atom -properties defined by this fix, see "Section -modify"_Section_modify.html#mod_1 of the manual which has some details -on how the properties can be accessed from added classes. +properties defined by this fix, see the "Modify atom"_Modify_atom.html +doc page which has details on how the properties can be accessed from +added classes. :line diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index 7f82404127fc61f6c3225f1c0d9b960bad470e27..783dc3133cb21ab290935cc72c37e1f31b173bb0 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -62,10 +62,9 @@ equilibration calculation is written to the specified file. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index 18450c7cd5c0852c30e2324f3c683d84a2b63479..a534a66c09f15fc9862f3f7b264a6e9b4cd653f7 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -80,10 +80,9 @@ This fix is invoked during "energy minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index 54aa7faef802f3061f795c54a7449d6d93265d0b..50f0b77d524d770345969306f87f7dd8ed5162b5 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -34,6 +34,8 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. +The specified group-ID is ignored by this fix. + The format of the output file should be reasonably self-explanatory. The meaning of the column header abbreviations is as follows: @@ -70,7 +72,7 @@ This fix is not invoked during "energy minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section_accelerate"_Section_accelerate.html +hardware, as discussed in "Speed"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -85,7 +87,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Speed"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt index 7c920791f7b10bd923da0402c35a8215a15bf650..75e4598ca5b4c468ff4774224789468528e2eb65 100644 --- a/doc/src/fix_reaxc_species.txt +++ b/doc/src/fix_reaxc_species.txt @@ -139,7 +139,7 @@ minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section_accelerate"_Section_accelerate.html +hardware, as discussed in "Speed"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -154,7 +154,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Speed"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index c8ec20daaa4ae3953b2660a2770607b15610533e..9de63defb700fb0f713187d87f4077fd35b86e0f 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom Kstart,Kstop = restraint coefficients at start/end of run (energy units) theta0 = equilibrium angle theta (degrees) - {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 + {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order Kstart,Kstop = restraint coefficients at start/end of run (energy units) - phi0 = equilibrium dihedral angle phi (degrees) :pre + phi0 = equilibrium dihedral angle phi (degrees) + keyword/value = optional keyword value pairs. supported keyword/value pairs: + {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre :ule [Examples:] @@ -155,11 +157,13 @@ associated with the restraint is with the following coefficients: K (energy) -n = 1 +n (multiplicity, >= 0) d (degrees) = phi0 + 180 :ul -K and phi0 are specified with the fix. Note that the value of n is -hard-wired to 1. Also note that the energy will be a minimum when the +K and phi0 are specified with the fix. Note that the value of the +dihedral multiplicity {n} is set by default to 1. You can use the +optional {mult} keyword to set it to a different positive integer. +Also note that the energy will be a minimum when the current dihedral angle phi is equal to phi0. :line @@ -183,10 +187,17 @@ added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the "fix_modify"_fix_modify.html {energy} option for this fix. -This fix computes a global scalar, which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy for all the restraints as discussed above. The scalar -value calculated by this fix is "extensive". +This fix computes a global scalar and a global vector of length 3, which +can be accessed by various "output commands"_Section_howto.html#howto_15. +The scalar is the total potential energy for {all} the restraints as +discussed above. The vector values are the sum of contributions to the +following individual categories: + +1 = bond energy +2 = angle energy +3 = dihedral energy :ul + +The scalar and vector values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index eced602c4b3540bf95ef8fe17278e7baf697e4c0..f3dd20daa3504e0f0c898edafa1858139ddb4bf2 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -223,10 +223,10 @@ via several options. NOTE: With the {rigid/small} styles, which require that {bodystyle} be specified as {molecule} or {custom}, you can define a system that has -no rigid bodies initially. This is useful when you are using the {mol} -keyword in conjunction with another fix that is adding rigid bodies -on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or -"fix pour"_fix_pour.html. +no rigid bodies initially. This is useful when you are using the +{mol} keyword in conjunction with another fix that is adding rigid +bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html +or "fix pour"_fix_pour.html. For bodystyle {single} the entire fix group of atoms is treated as one rigid body. This option is only allowed for the {rigid} styles. @@ -241,19 +241,17 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you want. Thus you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies. -Bodystyle {custom} is similar to bodystyle {molecule}, however some -custom properties are used to group atoms into rigid bodies. The -special case for molecule/body ID = 0 is not available. Possible -custom properties are an integer property associated with atoms through -"fix property/atom"_fix_property_atom.html or an atom style variable -or an atomfile style variable. For the latter two, the variable value -will be rounded to an integer and then rigid bodies defined from -those values. - -For bodystyle {group}, each of the listed groups is treated as a -separate rigid body. Only atoms that are also in the fix group are -included in each rigid body. This option is only allowed for the -{rigid} styles. +Bodystyle {custom} is similar to bodystyle {molecule} except that it +is more flexible in using other per-atom properties to define the sets +of atoms that form rigid bodies. An integer vector defined by the +"fix property/atom"_fix_property_atom.txt command can be used. Or an +"atom-style or atomfile-style variable"_variable.html can be used; the +floating-point value produced by the variable is rounded to an +integer. As with bondstyle {molecule}, each set of atoms in the fix +groups with the same integer value is treated as a different rigid +body. Since fix property/atom vectors and atom-style variables +produce values for all atoms, you should be careful to use a fix group +that only includes atoms you want to be part of rigid bodies. NOTE: To compute the initial center-of-mass position and other properties of each rigid body, the image flags for each atom in the @@ -692,10 +690,9 @@ rigid/nvt. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -707,8 +704,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -742,6 +739,11 @@ used to calculate the instantaneous pressure tensor. Note that the 2 NVT rigid fixes do not use any external compute to compute instantaneous temperature. +The "fix_modify"_fix_modify.html {bodyforces} option is supported by +all rigid styles to set whether per-body forces and torques are +computed early or late in a timestep, i.e. at the post-force stage or +at the final-integrate stage or the timestep, respectively. + The 2 NVE rigid fixes compute a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar value calculated by these fixes is "intensive". The scalar is the diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index 0810a347408f33cf20586448cf2141fb4c037275..aff3303f4353b3889edbfd3e72113609983cade5 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -186,10 +186,9 @@ read_data data.dpd fix foo_SPECIES NULL Species Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index f5be0f93a54c459ead80c691dd4905df678760c4..0af1c929228e6fcb1ba8d99589a11ab9084d41a4 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -65,12 +65,12 @@ to it. :line -Styles with a r {kk} suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. The region keyword is also supported by Kokkos, but a Kokkos-enabled region must be used. See the region "region"_region.html command for @@ -85,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 46452a1f7e932eaf2531525f7ee6d557fceffb37..7428b30a146a7053c99c208c05e09c73d881ef78 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -145,12 +145,12 @@ info of atoms in the molecule. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -162,8 +162,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 24726d8610abf0a79db6e14b163731d61ff46404..6d14346334c8beac00d4edbbc206e6213a414ac0 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -56,10 +56,9 @@ examples/USER/dpd directory. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -71,8 +70,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt index 47b3cfc67a2dbe667ce2af1799368b50dc741f50..385d24cff19594096b6193443dd88fc8ad3a2f54 100644 --- a/doc/src/fix_vector.txt +++ b/doc/src/fix_vector.txt @@ -94,7 +94,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is @@ -105,7 +105,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. An equal-style or diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index e814c89a0743af6b7d744ac71d62d71df5c3053d..959a103f02cf87fff21ce36b5f75607c5005c397 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -288,10 +288,9 @@ option for this fix. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -303,8 +302,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ba16b56c79fab2c4cecf6798a71a895b862c5cf --- /dev/null +++ b/doc/src/fix_wall_body_polygon.txt @@ -0,0 +1,104 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix wall/body/polygon command :h3 + +[Syntax:] + +fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/body/polygon = style name of this fix command :l +k_n = normal repulsion strength (force/distance or pressure units) :l +c_n = normal damping coefficient (force/distance or pressure units) :l +c_t = tangential damping coefficient (force/distance or pressure units) :l +wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l +args = list of arguments for a particular style :l + {xplane} or {yplane} args = lo hi + lo,hi = position of lower and upper plane (distance units), either can be NULL) + {zcylinder} args = radius + radius = cylinder radius (distance units) :pre +zero or more keyword/value pairs may be appended to args :l +keyword = {wiggle} :l + {wiggle} values = dim amplitude period + dim = {x} or {y} or {z} + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) :pre +:ule + +[Examples:] + +fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0 + +[Description:] + +This fix is for use with 2d models of body particles of style +{rounded/polygon}. It bounds the simulation domain with wall(s). All +particles in the group interact with the wall when they are close +enough to touch it. The nature of the interaction between the wall +and the polygon particles is the same as that between the polygon +particles themselves, which is similar to a Hookean potential. See +"Section 6.14"_Section_howto.html#howto_14 of the manual and the +"body"_body.html doc page for more details on using body particles. + +The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as +those specified with the "pair_style +body/rounded/polygon"_pair_body_rounded_polygon.html command. + +The {wallstyle} can be planar or cylindrical. The 2 planar options +specify a pair of walls in a dimension. Wall positions are given by +{lo} and {hi}. Either of the values can be specified as NULL if a +single wall is desired. For a {zcylinder} wallstyle, the cylinder's +axis is at x = y = 0.0, and the radius of the cylinder is specified. + +Optionally, the wall can be moving, if the {wiggle} keyword is +appended. + +For the {wiggle} keyword, the wall oscillates sinusoidally, similar to +the oscillations of particles which can be specified by the "fix +move"_fix_move.html command. This is useful in packing simulations of +particles. The arguments to the {wiggle} keyword specify a dimension +for the motion, as well as it's {amplitude} and {period}. Note that +if the dimension is in the plane of the wall, this is effectively a +shearing motion. If the dimension is perpendicular to the wall, it is +more of a shaking motion. A {zcylinder} wall can only be wiggled in +the z dimension. + +Each timestep, the position of a wiggled wall in the appropriate {dim} +is set according to this equation: + +position = coord + A - A cos (omega * delta) :pre + +where {coord} is the specified initial position of the wall, {A} is +the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Section_howto.html#howto_15. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +Any dimension (xy) that has a wall must be non-periodic. + +[Related commands:] + +"atom_style body"_atom_style.html, "pair_style +body/rounded/polygon"_pair_body_rounded_polygon.html + +[Default:] none diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt new file mode 100644 index 0000000000000000000000000000000000000000..c937cbdbbc80a6c711c845212a0a47d85d0800be --- /dev/null +++ b/doc/src/fix_wall_body_polyhedron.txt @@ -0,0 +1,103 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix wall/body/polyhedron command :h3 + +[Syntax:] + +fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/body/polyhedron = style name of this fix command :l +k_n = normal repulsion strength (force/distance units or pressure units - see discussion below) :l +c_n = normal damping coefficient (force/distance units or pressure units - see discussion below) :l +c_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) :l +wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l +args = list of arguments for a particular style :l + {xplane} or {yplane} args = lo hi + lo,hi = position of lower and upper plane (distance units), either can be NULL) + {zcylinder} args = radius + radius = cylinder radius (distance units) :pre +zero or more keyword/value pairs may be appended to args :l +keyword = {wiggle} :l + {wiggle} values = dim amplitude period + dim = {x} or {y} or {z} + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) :pre +:ule + +[Examples:] + +fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0 + +[Description:] + +This fix is for use with 3d models of body particles of style +{rounded/polyhedron}. It bounds the simulation domain with wall(s). +All particles in the group interact with the wall when they are close +enough to touch it. The nature of the interaction between the wall +and the polygon particles is the same as that between the polygon +particles themselves, which is similar to a Hookean potential. See +"Section 6.14"_Section_howto.html#howto_14 of the manual and the +"body"_body.html doc page for more details on using body particles. + +The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as +those specified with the "pair_style +body/rounded/polyhedron"_pair_body_rounded_polyhedron.html command. + +The {wallstyle} can be planar or cylindrical. The 3 planar options +specify a pair of walls in a dimension. Wall positions are given by +{lo} and {hi}. Either of the values can be specified as NULL if a +single wall is desired. For a {zcylinder} wallstyle, the cylinder's +axis is at x = y = 0.0, and the radius of the cylinder is specified. + +Optionally, the wall can be moving, if the {wiggle} keyword is appended. + +For the {wiggle} keyword, the wall oscillates sinusoidally, similar to +the oscillations of particles which can be specified by the "fix +move"_fix_move.html command. This is useful in packing simulations of +particles. The arguments to the {wiggle} keyword specify a dimension +for the motion, as well as it's {amplitude} and {period}. Note that +if the dimension is in the plane of the wall, this is effectively a +shearing motion. If the dimension is perpendicular to the wall, it is +more of a shaking motion. A {zcylinder} wall can only be wiggled in +the z dimension. + +Each timestep, the position of a wiggled wall in the appropriate {dim} +is set according to this equation: + +position = coord + A - A cos (omega * delta) :pre + +where {coord} is the specified initial position of the wall, {A} is +the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Section_howto.html#howto_15. No +parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the BODY package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +Any dimension (xyz) that has a wall must be non-periodic. + +[Related commands:] + +"atom_style body"_atom_style.html, "pair_style +body/rounded/polyhedron"_pair_body_rounded_polyhedron.html + +[Default:] none diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt index 954ec65bf6a1c059226c1beac58bea86fab0fb84..5380bdf738c5435352f090bcff46073ddd2b02a7 100644 --- a/doc/src/fix_wall_reflect.txt +++ b/doc/src/fix_wall_reflect.txt @@ -130,10 +130,9 @@ position = c0 + A (1 - cos(omega*delta)) :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index c3fcc06bf1c53e780b9b7bc3ce9885671fc9f690..7a45ed8086a14cdc201eea9cce5f28f80b4df00e 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -20,9 +20,11 @@ Fixes :h1 fix_ave_time fix_aveforce fix_balance + fix_bocs fix_bond_break fix_bond_create fix_bond_swap + fix_bond_react fix_box_relax fix_cmap fix_colvars @@ -59,6 +61,7 @@ Fixes :h1 fix_langevin fix_langevin_drude fix_langevin_eff + fix_langevin_spin fix_latte fix_lb_fluid fix_lb_momentum @@ -97,6 +100,7 @@ Fixes :h1 fix_nve_manifold_rattle fix_nve_noforce fix_nve_sphere + fix_nve_spin fix_nve_tri fix_nvk fix_nvt_asphere @@ -112,6 +116,7 @@ Fixes :h1 fix_planeforce fix_poems fix_pour + fix_precession_spin fix_press_berendsen fix_print fix_property_atom @@ -163,6 +168,8 @@ Fixes :h1 fix_viscosity fix_viscous fix_wall + fix_wall_body_polygon + fix_wall_body_polyhedron fix_wall_ees fix_wall_gran fix_wall_gran_region diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt index 14ec6258de654a466ec429328014f420e81cb999..ef2abf5091854d6f75c37100b0c626fca48c7121 100644 --- a/doc/src/improper_class2.txt +++ b/doc/src/improper_class2.txt @@ -87,10 +87,9 @@ radians internally; hence the units of M are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -102,8 +101,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt index 138a6a16503b125003b15ec1ceb394f18963e1eb..22ba990ba4885b4eaba923f5672a86d821c5d22e 100644 --- a/doc/src/improper_cossq.txt +++ b/doc/src/improper_cossq.txt @@ -53,10 +53,9 @@ X0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt index 5f69eccc60a1d060b894c89f487d591fa1a8b0b8..1662d93b140420f9b89066a0ba475f6b9b2e224c 100644 --- a/doc/src/improper_cvff.txt +++ b/doc/src/improper_cvff.txt @@ -54,10 +54,9 @@ n (0,1,2,3,4,6) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -69,8 +68,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt index f9062da207b329cb7616ca38420e8878675252b4..99132b893193ba9b7855d4b0a2a75c9dbfd54471 100644 --- a/doc/src/improper_fourier.txt +++ b/doc/src/improper_fourier.txt @@ -48,10 +48,9 @@ all (integer >= 0) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt index bb17e5a641e8da1b4b92f3e1b5ecfe8245fddf1a..f37338e468567487c8409203ae3911e451e2e335 100644 --- a/doc/src/improper_harmonic.txt +++ b/doc/src/improper_harmonic.txt @@ -58,10 +58,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -73,8 +72,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt index c02d39247403622fe51e1ffbc4e47df43e11db77..84c35f9f5c19f998196ab0044af01bdb4ffccf63 100644 --- a/doc/src/improper_ring.txt +++ b/doc/src/improper_ring.txt @@ -57,10 +57,9 @@ theta0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -72,8 +71,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt index d6df9ee6cccc8ec2f391a2583ac495caa0ad07e9..e72cc7f0ad16c293a458e1870c42539f1fd4e983 100644 --- a/doc/src/improper_umbrella.txt +++ b/doc/src/improper_umbrella.txt @@ -51,10 +51,9 @@ omega0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 4f27c9aa78e95cb2819b65d44be17acfb53e4a6f..8dbb3dde49adff950c3f9a035e11575bf6081dac 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -145,8 +145,8 @@ speedup in the KSpace time (8x less mesh points, 2x more expensive). However, for low relative accuracy, the staggered PPPM mesh size may be essentially the same as for regular PPPM, which means the method will be up to 2x slower in the KSpace time (simply 2x more expensive). -For more details and timings, see -"Section 5"_Section_accelerate.html. +For more details and timings, see the "Speed tips"_Speed_tips.html doc +page. NOTE: Using {pppm/stagger} may not give the same increase in the accuracy of energy and pressure as it does in forces, so some caution @@ -267,10 +267,9 @@ relative RMS error. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. More specifically, the {pppm/gpu} style performs charge assignment and force interpolation calculations on the GPU. These processes are @@ -291,8 +290,8 @@ KOKKOS, USER-OMP, and OPT packages respectively. They are only enabled if LAMMPS was built with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/lammps.book b/doc/src/lammps.book index ec34f41872db2aa143628ce3f99c249a8641cda9..f9798da2276f8ecee234a26539c1be75d2070774 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -4,20 +4,56 @@ Manual.html Section_intro.html Section_start.html Section_commands.html -Section_packages.html -Section_accelerate.html -accelerate_gpu.html -accelerate_intel.html -accelerate_kokkos.html -accelerate_omp.html -accelerate_opt.html +Packages.html +Packages_standard.html +Packages_user.html +Packages_details.html +Speed.html +Speed_bench.html +Speed_measure.html +Speed_tips.html +Speed_packages.html +Speed_gpu.html +Speed_intel.html +Speed_kokkos.html +Speed_omp.html +Speed_opt.html +Speed_compare.html Section_howto.html -Section_example.html -Section_perf.html -Section_tools.html -Section_modify.html -Section_python.html -Section_errors.html +Examples.html +Tools.html +Modify.html +Modify_overview.html +Modify_contribute.html +Modify_atom.html +Modify_pair.html +Modify_bond.html +Modify_compute.html +Modify_fix.html +Modify_command.html +Modify_dump.html +Modify_kspace.html +Modify_min.html +Modify_region.html +Modify_body.html +Modify_thermo.html +Modify_variable.html +Python.html +Python_overview.html +Python_run.html +Python_shlib.html +Python_install.html +Python_mpi.html +Python_test.html +Python_library.html +Python_pylammps.html +Python_examples.html +Python_call.html +Errors.html +Errors_common.html +Errors_bugs.html +Errors_messages.html +Errors_warnings.html Section_history.html lammps_tutorials.html @@ -135,8 +171,10 @@ fix_ave_histo.html fix_ave_time.html fix_aveforce.html fix_balance.html +fix_bocs.html fix_bond_break.html fix_bond_create.html +fix_bond_react.html fix_bond_swap.html fix_box_relax.html fix_cmap.html @@ -174,6 +212,7 @@ fix_ipi.html fix_langevin.html fix_langevin_drude.html fix_langevin_eff.html +fix_langevin_spin.html fix_latte.html fix_lb_fluid.html fix_lb_momentum.html @@ -211,6 +250,7 @@ fix_nve_line.html fix_nve_manifold_rattle.html fix_nve_noforce.html fix_nve_sphere.html +fix_nve_spin.html fix_nve_tri.html fix_nvk.html fix_nvt_asphere.html @@ -227,6 +267,7 @@ fix_pimd.html fix_planeforce.html fix_poems.html fix_pour.html +fix_precession_spin.html fix_press_berendsen.html fix_print.html fix_property_atom.html @@ -278,6 +319,8 @@ fix_vector.html fix_viscosity.html fix_viscous.html fix_wall.html +fix_wall_body_polygon.html +fix_wall_body_polyhedron.html fix_wall_ees.html fix_wall_gran.html fix_wall_gran_region.html @@ -315,6 +358,7 @@ compute_displace_atom.html compute_dpd.html compute_dpd_atom.html compute_edpd_temp_atom.html +compute_entropy_atom.html compute_erotate_asphere.html compute_erotate_rigid.html compute_erotate_sphere.html @@ -379,6 +423,7 @@ compute_smd_ulsph_strain_rate.html compute_smd_ulsph_stress.html compute_smd_vol.html compute_sna_atom.html +compute_spin.html compute_stress_atom.html compute_tally.html compute_tdpd_cc_atom.html @@ -417,8 +462,9 @@ pair_agni.html pair_airebo.html pair_awpmd.html pair_beck.html -pair_body.html +pair_body_nparticle.html pair_body_rounded_polygon.html +pair_body_rounded_polyhedron.html pair_bop.html pair_born.html pair_brownian.html @@ -504,6 +550,10 @@ pair_sph_lj.html pair_sph_rhosum.html pair_sph_taitwater.html pair_sph_taitwater_morris.html +pair_spin_dmi.html +pair_spin_exchange.html +pair_spin_magelec.html +pair_spin_neel.html pair_srp.html pair_sw.html pair_table.html @@ -580,6 +630,7 @@ dihedral_opls.html dihedral_quadratic.html dihedral_spherical.html dihedral_table.html +dihedral_table_cut.html dihedral_zero.html lammps_commands_improper.html diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index ecec62256a82a3b2e67f9fe64a2af6f796f0c66e..cd9ecce42c8b8750e52389e6b48c08885a7cae3f 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -98,19 +98,20 @@ molecule (header keyword = inertia). NOTE: The molecule command can be used to define molecules with bonds, angles, dihedrals, imporopers, or special bond lists of neighbors within a molecular topology, so that you can later add the molecules -to your simulation, via one or more of the commands listed above. If -such molecules do not already exist when LAMMPS creates the simulation -box, via the "create_box"_create_box.html or -"read_data"_read_data.html command, when you later add them you may -overflow the pre-allocated data structures which store molecular -topology information with each atom, and an error will be generated. -Both the "create_box"_create_box.html command and the data files read -by the "read_data"_read_data.html command have "extra" options which +to your simulation, via one or more of the commands listed above. +Since this topology-related information requires that suitable storage +is reserved when LAMMPS creates the simulation box (e.g. when using +the "create_box"_create_box.html command or the +"read_data"_read_data.html command) suitable space has to be reserved +so you do not overflow those pre-allocated data structures when adding +molecules later. Both the "create_box"_create_box.html command and +the "read_data"_read_data.html command have "extra" options which insure space is allocated for storing topology info for molecules that are added later. -The format of an individual molecule file is similar to the data file -read by the "read_data"_read_data.html commands, and is as follows. +The format of an individual molecule file is similar but +(not identical) to the data file read by the "read_data"_read_data.html +commands, and is as follows. A molecule file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains @@ -455,7 +456,11 @@ of SHAKE clusters. :line -[Restrictions:] none +[Restrictions:] + +This command must come after the simulation box is define by a +"read_data"_read_data.html, "read_restart"_read_restart.html, or +"create_box"_create_box.html command. [Related commands:] diff --git a/doc/src/package.txt b/doc/src/package.txt index 5c698934e857bfa31bdceac69bb3296ff76961c3..81e1db9bd8116656f328deb10bc6b449a6f049be 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -33,8 +33,10 @@ args = arguments specific to the style :l last = ID of last GPU to be used on each node {tpa} value = Nthreads Nthreads = # of GPU threads used per atom - {device} value = device_type - device_type = {kepler} or {fermi} or {cypress} or {generic} + {device} value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13 + platform_id = numerical OpenCL platform id (default: -1) + device_type = {kepler} or {fermi} or {cypress} or {intel} or {phi} or {generic} or {custom} + val1,val2,... = custom OpenCL tune parameters (see below for details) {blocksize} value = size size = thread block size for pair force computation {intel} args = NPhi keyword value ... @@ -96,6 +98,9 @@ args = arguments specific to the style :l package gpu 1 package gpu 1 split 0.75 package gpu 2 split -1.0 +package gpu 1 device kepler +package gpu 1 device 2:generic +package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128 package kokkos neigh half comm device package omp 0 neigh no package omp 4 @@ -144,9 +149,9 @@ the style options are set, either to default values or to specified settings. I.e. settings from previous invocations do not persist across multiple invocations. -See the "Section 5.3"_Section_accelerate.html#acc_3 section of the -manual for more details about using the various accelerator packages -for speeding up LAMMPS simulations. +See the "Speed packages"_Speed_packages.html doc page for more details +about using the various accelerator packages for speeding up LAMMPS +simulations. :line @@ -244,12 +249,40 @@ the value can improve performance. The number of threads per atom must be a power of 2 and currently cannot be greater than 32. The {device} keyword can be used to tune parameters optimized for a -specific accelerator, when using OpenCL. For CUDA, the {device} -keyword is ignored. Currently, the device type is limited to NVIDIA -Kepler, NVIDIA Fermi, AMD Cypress, or a generic device. More devices -may be added later. The default device type can be specified when -building LAMMPS with the GPU library, via settings in the -lib/gpu/Makefile that is used. +specific accelerator and platform when using OpenCL. OpenCL supports +the concept of a [platform], which represents one or more devices that +share the same driver (e.g. there would be a different platform for +GPUs from different vendors or for CPU based accelerator support). +In LAMMPS only one platform can be active at a time and by default +the first platform with an accelerator is selected. This is equivalent +to using a platform ID of -1. The platform ID is a number corresponding +to the output of the ocl_get_devices tool. The platform ID is passed +to the GPU library, by prefixing the {device} keyword with that number +separated by a colon. For CUDA, the {device} keyword is ignored. +Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA +Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device. +More devices may be added later. The default device type can be +specified when building LAMMPS with the GPU library, via setting a +variable in the lib/gpu/Makefile that is used. + +In addition, a device type {custom} is available, which is followed by +13 comma separated numbers, which allows to set those tweakable parameters +from the package command. It can be combined with the (colon separated) +platform id. The individual settings are: + +MEM_THREADS +THREADS_PER_ATOM +THREADS_PER_CHARGE +BLOCK_PAIR +MAX_SHARED_TYPES +BLOCK_NBOR_BUILD +BLOCK_BIO_PAIR +BLOCK_ELLIPSE +WARP_SIZE +PPPM_BLOCK_1D +BLOCK_CELL_2D +BLOCK_CELL_ID +MAX_BIO_SHARED_TYPES :ul The {blocksize} keyword allows you to tweak the number of threads used per thread block. This number should be a multiple of 32 (for GPUs) diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index 9d2a48dcbca399bc00f09458c56941cf3f622b5e..1ba59b7732e164b7f3643100f20d172833b5151b 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -125,10 +125,9 @@ array tabulated with a scaling by r. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -140,8 +139,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 402e537dadf39bc5728d6001d32a0709d17e54c0..352e00249a4198506ea9cd5b54f6a34d2dc3cea9 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -58,11 +58,11 @@ and input files are provided in the examples/USER/misc/agni directory. :line Styles with {omp} suffix is functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, depending -on your available hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated style takes the same arguments and -should produce the same results, except for round-off and precision -issues. +style without the suffix. They have been optimized to run faster, +depending on your available hardware, as discussed on the "Speed +packages"_Speed_packages.html doc page. The accelerated style takes +the same arguments and should produce the same results, except for +round-off and precision issues. The accelerated style is part of the USER-OMP. They are only enabled if LAMMPS was built with those packages. See the "Making @@ -73,8 +73,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index 1aa017f2786ac95e60556d84b5a900fcab5a1704..b5add21f2431c77cb40406ec98e1cba6509771fc 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -176,10 +176,9 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -191,8 +190,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt index e160f09b3d6fc5764c24bdd367d284e93db55622..1aca4b4f9ac88f93cf20ee110d356db6c7b12c38 100644 --- a/doc/src/pair_beck.txt +++ b/doc/src/pair_beck.txt @@ -51,10 +51,9 @@ Rc is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_body.txt b/doc/src/pair_body_nparticle.txt similarity index 93% rename from doc/src/pair_body.txt rename to doc/src/pair_body_nparticle.txt index 7899da832bdbf722bb1c5403dd547890bae5cdb1..8c5b6e155d801729a72b99276373ef4b0f525185 100644 --- a/doc/src/pair_body.txt +++ b/doc/src/pair_body_nparticle.txt @@ -10,21 +10,21 @@ pair_style body command :h3 [Syntax:] -pair_style body cutoff :pre +pair_style body/nparticle cutoff :pre cutoff = global cutoff for interactions (distance units) [Examples:] -pair_style body 3.0 +pair_style body/nparticle 3.0 pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.0 1.5 2.5 :pre [Description:] -Style {body} is for use with body particles and calculates pairwise -body/body interactions as well as interactions between body and -point-particles. See "Section 6.14"_Section_howto.html#howto_14 +Style {body/nparticle} is for use with body particles and calculates +pairwise body/body interactions as well as interactions between body +and point-particles. See "Section 6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html doc page for more details on using body particles. diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt index b6dc2e37b5a80fce04b7b753ffb7e007c4703ae6..9daeb08e9a9e3310380c4b5e40534aecedd59b09 100644 --- a/doc/src/pair_body_rounded_polygon.txt +++ b/doc/src/pair_body_rounded_polygon.txt @@ -8,12 +8,127 @@ pair_style body/rounded/polygon command :h3 +[Syntax:] + +pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff :pre + +c_n = normal damping coefficient +c_t = tangential damping coefficient +mu = normal friction coefficient during gross sliding +delta_ua = multiple contact scaling factor +cutoff = global separation cutoff for interactions (distance units), see below for definition :pre + +[Examples:] + +pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5 +pair_coeff * * 100.0 1.0 +pair_coeff 1 1 100.0 1.0 :pre + [Description:] -Note: This feature is not yet implemented. +Style {body/rounded/polygon} is for use with 2d models of body +particles of style {rounded/polygon}. It calculates pairwise +body/body interactions which can include body particles modeled as +1-vertex circular disks with a specified diameter. See "Section +6.14"_Section_howto.html#howto_14 of the manual and the +"body"_body.html doc page for more details on using body +rounded/polygon particles. + +This pairwise interaction between rounded polygons is described in +"Fraige"_#pair-Fraige, where a polygon does not have sharp corners, +but is rounded at its vertices by circles centered on each vertex with +a specified diameter. The edges of the polygon are defined between +pairs of adjacent vertices. The circle diameter for each polygon is +specified in the data file read by the "read data"_read_data.html +command. This is a 2d discrete element model (DEM) which allows for +multiple contact points. + +Note that when two particles interact, the effective surface of each +polygon particle is displaced outward from each of its vertices and +edges by half its circle diameter (as in the diagram below of a gray +and yellow square particle). The interaction forces and energies +between two particles are defined with respect to the separation of +their respective rounded surfaces, not by the separation of the +vertices and edges themselves. + +This means that the specified cutoff in the pair_style command is the +cutoff distance, r_c, for the surface separation, \delta_n (see figure +below). This is the distance at which two particles no longer +interact. If r_c is specified as 0.0, then it is a contact-only +interaction. I.e. the two particles must overlap in order to exert a +repulsive force on each other. If r_c > 0.0, then the force between +two particles will be attractive for surface separations from 0 to +r_c, and repulsive once the particles overlap. + +Note that unlike for other pair styles, the specified cutoff is not +the distance between the centers of two particles at which they stop +interacting. This center-to-center distance depends on the shape and +size of the two particles and their relative orientation. LAMMPS +takes that into account when computing the surface separation distance +and applying the r_c cutoff. + +The forces between vertex-vertex, vertex-edge, and edge-edge overlaps +are given by: + +:c,image(Eqs/pair_body_rounded.jpg) + +:c,image(JPG/pair_body_rounded.jpg) + +Note that F_n and F_t are functions of the surface separation \delta_n += d - (R_i + R_j). In this model, when (R_i + R_j) < d < (R_i + R_j) ++ r_c, that is, 0 < \delta_n < r_c, the cohesive region of the two +surfaces overlap and the two surfaces are attractive to each other. + +In "Fraige"_#pair-Fraige, the tangential friction force between two +particles that are in contact is modeled differently prior to gross +sliding (i.e. static friction) and during gross-sliding (kinetic +friction). The latter takes place when the tangential deformation +exceeds the Coulomb frictional limit. In the current implementation, +however, we do not take into account frictional history, i.e. we do +not keep track of how many time steps the two particles have been in +contact nor calculate the tangential deformation. Instead, we assume +that gross sliding takes place as soon as two particles are in +contact. + +The following coefficients must be defined for each pair of atom types +via the "pair_coeff"_pair_coeff.html command as in the examples above, +or in the data file read by the "read_data"_read_data.html command: + +k_n (energy/distance^2 units) +k_na (energy/distance^2 units) :ul + +Effectively, k_n and k_na are the slopes of the red lines in the plot +above for force versus surface separation, for \delta_n < 0 and 0 < +\delta_n < r_c respectively. + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +[Restrictions:] + +These pair styles are part of the BODY package. They are only enabled +if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. [Related commands:] -"pair_style body"_pair_body.html +"pair_coeff"_pair_coeff.html [Default:] none + +:link(pair-Fraige) +[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, +Particuology, 6, 455 (2008). diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt new file mode 100644 index 0000000000000000000000000000000000000000..dc559feaafb6715e7f4b06800103951725078964 --- /dev/null +++ b/doc/src/pair_body_rounded_polyhedron.txt @@ -0,0 +1,130 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style body/rounded/polyhedron command :h3 + +[Syntax:] + +pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff :pre + +c_n = normal damping coefficient +c_t = tangential damping coefficient +mu = normal friction coefficient during gross sliding +delta_ua = multiple contact scaling factor +cutoff = global separation cutoff for interactions (distance units), see below for definition :pre + +[Examples:] + +pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5 +pair_coeff * * 100.0 1.0 +pair_coeff 1 1 100.0 1.0 :pre + +[Description:] + +Style {body/rounded/polygon} is for use with 3d models of body +particles of style {rounded/polyhedron}. It calculates pairwise +body/body interactions which can include body particles modeled as +1-vertex spheres with a specified diameter. See "Section +6.14"_Section_howto.html#howto_14 of the manual and the +"body"_body.html doc page for more details on using body +rounded/polyhedron particles. + +This pairwise interaction between the rounded polyhedra is described +in "Wang"_#pair-Wang, where a polyhedron does not have sharp corners +and edges, but is rounded at its vertices and edges by spheres +centered on each vertex with a specified diameter. The edges if the +polyhedron are defined between pairs of adjacent vertices. Its faces +are defined by a loop of edges. The sphere diameter for each polygon +is specified in the data file read by the "read data"_read_data.html +command. This is a discrete element model (DEM) which allows for +multiple contact points. + +Note that when two particles interact, the effective surface of each +polyhedron particle is displaced outward from each of its vertices, +edges, and faces by half its sphere diameter. The interaction forces +and energies between two particles are defined with respect to the +separation of their respective rounded surfaces, not by the separation +of the vertices, edges, and faces themselves. + +This means that the specified cutoff in the pair_style command is the +cutoff distance, r_c, for the surface separation, \delta_n (see figure +below). This is the distance at which two particles no longer +interact. If r_c is specified as 0.0, then it is a contact-only +interaction. I.e. the two particles must overlap in order to exert a +repulsive force on each other. If r_c > 0.0, then the force between +two particles will be attractive for surface separations from 0 to +r_c, and repulsive once the particles overlap. + +Note that unlike for other pair styles, the specified cutoff is not +the distance between the centers of two particles at which they stop +interacting. This center-to-center distance depends on the shape and +size of the two particles and their relative orientation. LAMMPS +takes that into account when computing the surface separation distance +and applying the r_c cutoff. + +The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge, +and edge-face overlaps are given by: + +:c,image(Eqs/pair_body_rounded.jpg) + +:c,image(JPG/pair_body_rounded.jpg) + +In "Wang"_#pair-Wang, the tangential friction force between two +particles that are in contact is modeled differently prior to gross +sliding (i.e. static friction) and during gross-sliding (kinetic +friction). The latter takes place when the tangential deformation +exceeds the Coulomb frictional limit. In the current implementation, +however, we do not take into account frictional history, i.e. we do +not keep track of how many time steps the two particles have been in +contact nor calculate the tangential deformation. Instead, we assume +that gross sliding takes place as soon as two particles are in +contact. + +The following coefficients must be defined for each pair of atom types +via the "pair_coeff"_pair_coeff.html command as in the examples above, +or in the data file read by the "read_data"_read_data.html command: + +k_n (energy/distance^2 units) +k_na (energy/distance^2 units) :ul + +Effectively, k_n and k_na are the slopes of the red lines in the plot +above for force versus surface separation, for \delta_n < 0 and 0 < +\delta_n < r_c respectively. + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +[Restrictions:] + +These pair styles are part of the BODY package. They are only enabled +if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:link(pair-Wang) +[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular +Matter, 13, 1 (2011). + diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt index a016f77fa3ba6c96ef18fbb7d1094e79a0475aab..2504fb7e25c8e9651eb95963d244e478688b93cb 100644 --- a/doc/src/pair_born.txt +++ b/doc/src/pair_born.txt @@ -12,12 +12,14 @@ pair_style born/omp command :h3 pair_style born/gpu command :h3 pair_style born/coul/long command :h3 pair_style born/coul/long/cs command :h3 +pair_style born/coul/long/cs/gpu command :h3 pair_style born/coul/long/gpu command :h3 pair_style born/coul/long/omp command :h3 pair_style born/coul/msm command :h3 pair_style born/coul/msm/omp command :h3 pair_style born/coul/wolf command :h3 pair_style born/coul/wolf/cs command :h3 +pair_style born/coul/wolf/cs/gpu command :h3 pair_style born/coul/wolf/gpu command :h3 pair_style born/coul/wolf/omp command :h3 pair_style born/coul/dsf command :h3 @@ -143,10 +145,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -158,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt index 79b71e91c73e3d6a99b129472cea4831e6905324..8d30f0cec65628515add8cab9d6897d06a3301d5 100644 --- a/doc/src/pair_brownian.txt +++ b/doc/src/pair_brownian.txt @@ -74,7 +74,7 @@ must be specified. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Section_accelerate.html of +hardware, as discussed in "this section"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -88,7 +88,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "this section"_Section_accelerate.html of the manual for more +See "this section"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index d18b39d5d92b0bf7882f51a3a32149ed5d9e56d6..de247b9c0165595b9e70b8717f62abffbde5ce3d 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -140,10 +140,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -155,8 +154,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index 05e760e1b22b44c5901f9160b9fa4f3eaaa44c5c..94bf6a2d7c4228083f6ed16de5d4a7f82d64f63e 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -102,10 +102,9 @@ global Coulombic cutoff is allowed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 75a8e4bff944f8b6786f61bb50aa7eefe1e082c7..af20661bbd3d50b690927d12dc24739b085ddd0e 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -184,10 +184,9 @@ the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -199,8 +198,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt index 36fae5068b6e055adac9b7a2fb475e0df513968c..e62971a64572099caa98854967e90754ba7942f5 100644 --- a/doc/src/pair_class2.txt +++ b/doc/src/pair_class2.txt @@ -102,10 +102,9 @@ cutoff distance. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt index 83b15b358bf532f6725853f8fc7e7b2329419ac5..a7bb0db08a4f505ed14897e56199fc0f59ee0472 100644 --- a/doc/src/pair_colloid.txt +++ b/doc/src/pair_colloid.txt @@ -127,10 +127,9 @@ commands for efficiency: "neighbor multi"_neighbor.html and Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -142,8 +141,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index f5461b1cbc208ca0c5cd01583416f1821b0a6ec8..6949ca50c20d7a805d6bb41c77d8e1eb84dacb12 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -112,10 +112,9 @@ nor file {ffield.comb3} with style {comb}. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -127,8 +126,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index 4cca5ee0d78a529162e782121855150daa162e06..650575d05515f152d2582897ce38e640df7dca50 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -20,6 +20,7 @@ pair_style coul/dsf/kk command :h3 pair_style coul/dsf/omp command :h3 pair_style coul/long command :h3 pair_style coul/long/cs command :h3 +pair_style coul/long/cs/gpu command :h3 pair_style coul/long/omp command :h3 pair_style coul/long/gpu command :h3 pair_style coul/long/kk command :h3 @@ -267,10 +268,9 @@ command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -282,8 +282,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index 2516e5eae4d00113892dd8e97558b59ca13b97e3..e7d196d599985795a484703d90d609337a63c56d 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -186,10 +186,9 @@ type pair. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index 9e29e93430602fd485bef467602d7001c8534fab..a36029ea63af50a98db8b207c7089317a67f6357 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -110,10 +110,9 @@ random force. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -125,8 +124,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 867f3f2315dcb9d908438f91710016abe4ccf9d8..129d3c84af29af18d35100b27415ec07087c9e40 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -129,10 +129,9 @@ significantly larger timesteps to be taken. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -144,8 +143,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index 03e77f53ab0f291be3054b1464d1936b057e95e6..b3c770179fb948329d4b746b863041a101c83436 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -371,10 +371,9 @@ are listed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -386,7 +385,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for more +See the "Speed packages"_Speed_packages.html doc page for more instructions on how to use the accelerated styles effectively. :line @@ -414,15 +413,10 @@ The eam pair styles can only be used via the {pair} keyword of the [Restrictions:] -All of these styles except the {eam/cd} style are part of the MANYBODY -package. They are only enabled if LAMMPS was built with that package. +All of these styles are part of the MANYBODY package. They are only +enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -The {eam/cd} style is part of the USER-MISC package and also requires -the MANYBODY package. It is only enabled if LAMMPS was built with -those packages. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. - [Related commands:] "pair_coeff"_pair_coeff.html diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index e5b1420b5938eed1008b780fc226e1258d0c3fa5..f0d1927812b263fdcbeadc8b5e5843492c9f7bea 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -109,10 +109,9 @@ the EDIP package. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 75ad2d4683ee64716ebc003ca5267d5733302760..7f94d919f2a62053d6b32142c914b9797f38e607 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -136,10 +136,9 @@ needs. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -151,8 +150,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index 7eafa235434386bcfe3438367cee1cec1852e74b..dec660fd1dbbe2f4ef7c42529a2fac083d120159 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -153,10 +153,9 @@ pair interaction. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -168,8 +167,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index f6f46a2de8ace2a7f982d305728b77f42f350ded..7716f89f174a1d8ce1637c09c13d10c9e4b6b6d5 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -84,10 +84,9 @@ is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -99,8 +98,8 @@ by including their suffix, or you can use the "-suffix command-line switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt index c9235785866f6856ad438fb934afdcc64d4ba781..e9a98a0b8426f1a980ddd508d57fa06b72951a1f 100644 --- a/doc/src/pair_gayberne.txt +++ b/doc/src/pair_gayberne.txt @@ -133,10 +133,9 @@ pair_coeff sigma to 1.0 as well. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index d7e87af013f002a6e6472a4ae45e3f5c27fd3de5..86b04f96dede877734a479a5a6dc8fbfc0f91705 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -179,10 +179,9 @@ potential. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt index ec84a2d57a13d7066fb49624cba932a425447656..7daf805e2bedff4409f44a66022220f2f2aec371 100644 --- a/doc/src/pair_gromacs.txt +++ b/doc/src/pair_gromacs.txt @@ -91,10 +91,9 @@ cutoff(s) specified in the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -106,8 +105,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt index fcf63b1bc4e0da31deef339a15da096b245bd4f1..8f1251cf1f3a96aa50e8f9339a69f20b893336bb 100644 --- a/doc/src/pair_gw.txt +++ b/doc/src/pair_gw.txt @@ -95,9 +95,9 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +This pair style is part of the MANYBODY package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. @@ -117,4 +117,5 @@ appropriate units if your simulation doesn't use "metal" units. :line :link(Gao) -[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504. +[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics +Research B 191 (2012) 504. diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index d3cf90ec14c2172faf4eec91a5247724acc3428a..45f852c25421350665da121175d9f403ac1b0c4b 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -166,10 +166,9 @@ optional parameters. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -181,8 +180,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index d37dedc709b82c43e6c49701f3b7916db93ef6d8..9503256d2696919579fce47f655a853e19c08409 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -315,8 +315,8 @@ off C/C interaction, i.e. by setting the appropriate coefficients to Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. Since the {hybrid} and {hybrid/overlay} styles delegate computation to the individual sub-styles, the suffix versions of the {hybrid} and @@ -334,8 +334,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index 32fe002a306d508de4f3ad7b048df32218e7d856..dbc9c458e2997d372b58b7aae7a87cca389c2168 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -23,15 +23,15 @@ pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 pair_coeff * * rebo CH.airebo NULL NULL C pair_coeff * * tersoff BNC.tersoff B N NULL -pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C pair_coeff 1 1 coul/shield 0.70 pair_coeff 1 2 coul/shield 0.69498201415576216335 -pair_coeff 2 2 coul/shield 0.69 +pair_coeff 2 2 coul/shield 0.69 :pre [Description:] The {ilp/graphene/hbn} style computes the registry-dependent interlayer -potential (RDILP) potential as described in "(Leven)"_#Leven and +potential (ILP) potential as described in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2. The normals are calculated in the way as described in "(Kolmogorov)"_#Kolmogorov2. @@ -61,13 +61,13 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP), are fitted with taper function by setting the cutoff equal to 16.0 Angstrom. Using different cutoff or taper function should be careful. -NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented, -BNCH-old.ILP contains the parameters published in "(Leven)"_#Leven and -"(Maaravi)"_#Maaravi2, which is only suitable for long-range -interaction. The parameters in BNCH.ILP provides a good description both -for short- and long-range interaction. This is useful for simulations in -the high pressure (small interlayer distances) regime. The comparison of -two sets of parameters can be found in "(Ouyang)"_#Ouyang. +NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials +are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description +in both short- and long-range interaction regime, while the old ILP parameters +published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for +long-range interaction regime. This feature is essential for simulations in +high-pressure regime (i.e., the interlayer distance smaller than the equilibrium distance). +The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1. This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. @@ -101,12 +101,12 @@ units, if your simulation does not use {metal} units. [Related commands:] -"pair_coeff"_pair_coeff.html -"pair_none"_pair_none.html -"pair_style hybrid/overlay"_pair_hybrid.html -"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html -"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html -"pair_style pair_coul_shield"_pair_coul_shield.html +"pair_coeff"_pair_coeff.html, +"pair_none"_pair_none.html, +"pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html, +"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html, +"pair_style pair_coul_shield"_pair_coul_shield.html. [Default:] tap_flag = 1 @@ -121,5 +121,5 @@ units, if your simulation does not use {metal} units. :link(Kolmogorov2) [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) -:link(Ouyang) -[(Ouyang)] W. Ouyang, D. Mandelli, O. Hod, M. Urbakh, In preparation. +:link(Ouyang1) +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018). diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index c5d910e27c841f9d71e5e6dfd160bfce0a949b46..fc2c1405af78057496fa7d291e9c3adce7ce0be7 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -46,8 +46,8 @@ are included in the KIM library by default, in the "What is in the KIM API source package?" section. To use this pair style, you must first download and install the KIM -API library from the "OpenKIM website"_https://openkim.org. The "KIM -section of Section packages"_Section_packages.html#KIM has +API library from the "OpenKIM website"_https://openkim.org. The KIM +section of the "Packages details"_Packages_details.html doc page has instructions on how to do this with a simple make command, when building LAMMPS. diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 7df1b4d02d364eeadfdb1eefc2d32ae2aac45c9c..a16d123b89abc938fe172a3a73d123c896687588 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -27,7 +27,7 @@ pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre [Description:] -The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi +The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi (KC) interaction potential as described in "(Kolmogorov)"_#Kolmogorov1. No simplification is made, @@ -51,6 +51,15 @@ and {rcut} are included in the parameter file. {S} is designed to facilitate scaling of energies. {rcut} is designed to build the neighbor list for calculating the normals for each atom pair. +NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC) +is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides +a good description in both short- and long-range interaction regime, +while the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 +are only suitable for long-range interaction regime. +This feature is essential for simulations in high-pressure regime +(i.e., the interlayer distance smaller than the equilibrium distance). +The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2. + This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. @@ -83,11 +92,11 @@ units. [Related commands:] -"pair_coeff"_pair_coeff.html -"pair_none"_pair_none.html -"pair_style hybrid/overlay"_pair_hybrid.html -"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html -"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html +"pair_coeff"_pair_coeff.html, +"pair_none"_pair_none.html, +"pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, +"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. [Default:] tap_flag = 0 @@ -95,3 +104,6 @@ units. :link(Kolmogorov1) [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) + +:link(Ouyang2) +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018). diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index c7e005a591c04b712f0bb2ed3a640b1ea8e3e5e1..97f132eacd41e00cd4318cfde24b09e29b4a6ae1 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -38,7 +38,7 @@ This shift is achieved by the last term in the equation for {Vij} above. This potential is intended for interactions between two layers of graphene. Therefore, to avoid interaction between layers in multi-layered materials, each layer should have a separate atom type and interactions should only -be computed between atom types of neighbouring layers. +be computed between atom types of neighboring layers. The parameter file (e.g. CC.KC), is intended for use with metal "units"_units.html, with energies in meV. An additional parameter, {S}, diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index e297d479bc3ae16d3054130ba67d9bb7fe3a0a97..c2968ffdf3fea69aca87ce0cb726f56515af4011 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -269,10 +269,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -284,8 +283,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt index 83f6ec063d4dd6476555a068a7eac6374544a3be..a0a9971474ac61c14d25d7eb80aac78338146648 100644 --- a/doc/src/pair_lj96.txt +++ b/doc/src/pair_lj96.txt @@ -49,10 +49,9 @@ cutoff specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt index 4ca8c3c141c39c9c874902f96f5178a1b1941d7a..c4e2af506210f3bc1db893101f31239b4698afed 100644 --- a/doc/src/pair_lj_cubic.txt +++ b/doc/src/pair_lj_cubic.txt @@ -63,10 +63,9 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma = Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -78,8 +77,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt index e0838426f637da3e3669fc4c35a17afaa6d6083b..c156fefef250fac814660a90901c948826f70737 100644 --- a/doc/src/pair_lj_expand.txt +++ b/doc/src/pair_lj_expand.txt @@ -53,10 +53,9 @@ optional. If not specified, the global LJ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 6be4562d18849130536383878ac5acc084b20f20..bc851adb746588359bbb724f00fb8e399c15cb04 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -156,10 +156,9 @@ specified in the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index b1678cad5862cf4670a80a68e7c2074337250ba9..653520966b512fc5bb7b8e79e87683303f4b0d48 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -62,10 +62,9 @@ specified, the global values for Rin and Rc are used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt index 5f7c226cee3ccc7b83c6139bf2a6c25dd2c13468..aebde2e65355a27867903d36d96365a09f925477 100644 --- a/doc/src/pair_lj_smooth_linear.txt +++ b/doc/src/pair_lj_smooth_linear.txt @@ -49,10 +49,9 @@ LJ cutoff specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 2ef133da554adf3d141e337e3c1b9f4139f72f35..7add9f623d8276855d80c17f4e4fcd434ed651a0 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -207,10 +207,9 @@ directory tree, under examples/USER/fep. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -222,8 +221,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt index b39c7545c7e2bdbc90f72631eaadeca06cfe40c5..2a16aa2a9dad961966abc8fd85fbb087bca0b7a2 100644 --- a/doc/src/pair_lubricate.txt +++ b/doc/src/pair_lubricate.txt @@ -143,7 +143,7 @@ must be specified. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Section_accelerate.html of +hardware, as discussed in "this section"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -157,7 +157,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "this section"_Section_accelerate.html of the manual for more +See "this section"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index 6653b397a0cd04e7dfb56aa1f4c8df9159a9e4a9..74242e32b9900d01ef67157dd3ded68cc7d63c9f 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -106,10 +106,9 @@ MEAM files. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -121,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 3eb5ac5afe5b8cb089d5dea24ed02cdea1ec0eec..34876011a1c0553999916fb6ba40c41cd70b782d 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -101,10 +101,9 @@ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -116,8 +115,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index 57abcf4a4c30c904b55cd07464ca60118ca13d3c..b043030907f775eb56241b0f3092882e7341f2a0 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -204,10 +204,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -219,8 +218,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 2395707fb45b63425456a1ca612895b90bc289c8..e6e103f517855f1a8b37f6e4c8dc028954e138d0 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -92,10 +92,9 @@ a particular simulation; LAMMPS ignores those entries. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -107,8 +106,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt index 81cea1a38d4a255b6fdd01d080cecc67602c3a89..08c3393993bc15e0d6d851b30c30d2ad7165261b 100644 --- a/doc/src/pair_nm.txt +++ b/doc/src/pair_nm.txt @@ -133,10 +133,9 @@ the "run_style respa"_run_style.html command. They do not support the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index 26a205bcf9b449ee20eea88ce5aff6a3feca024b..f272d15a8680d6499df5f7164186789426589413 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. + +Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool +and the performance of the LAMMPS-implementation of oxDNA. +The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line @@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line +:link(Henrich1) +[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). + :link(Sulc1) [(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 2408c02d101135639561652db8f5e74dae7e037f..1b55031b2c97dc8c935c0ddb83a567f24d64ab6f 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -A technical report with more information on the model, the structure of the input file, -the setup tool and the performance of the LAMMPS-implementation of oxDNA -can be found "here"_PDF/USER-CGDNA-overview.pdf. + +Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool +and the performance of the LAMMPS-implementation of oxDNA. +The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line @@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. :line +:link(Henrich) +[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). + :link(Sulc2) [(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012). diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index deca093e3bb1cebb7183f9bb7b8b0df866c09df8..432700305718db3b0ae720079a7943b7cf81d90f 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -139,10 +139,9 @@ details please see the description in "(Mtchell2011a)". Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -154,8 +153,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt index b9dc6e0ed861dccef018578664c70ba510927222..8d8c7e84e744185c4438a328ad534338d0b6042c 100644 --- a/doc/src/pair_reaxc.txt +++ b/doc/src/pair_reaxc.txt @@ -47,13 +47,14 @@ the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially implemented as a stand-alone C code and is now integrated into LAMMPS as a package. -The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is -derived from the {reax/c} style. The Kokkos version can run on GPUs and -can also use OpenMP multithreading. For more information about the Kokkos package, -see "Section 4"_Section_packages.html#kokkos and "Section 5.3.3"_accelerate_kokkos.html. -One important consideration when using the {reax/c/kk} style is the choice of either -half or full neighbor lists. This setting can be changed using the Kokkos "package"_package.html -command. +The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that +is derived from the {reax/c} style. The Kokkos version can run on GPUs +and can also use OpenMP multithreading. For more information about the +Kokkos package, see "Packages details"_Packages_details.html and +"Speed kokkos"_Speed_kokkos.html doc pages. One important +consideration when using the {reax/c/kk} style is the choice of either +half or full neighbor lists. This setting can be changed using the +Kokkos "package"_package.html command. The {reax/c} style differs from the "pair_style reax"_pair_reax.html command in the lo-level implementation details. The {reax} style is a @@ -80,9 +81,8 @@ parameterizations for different classes of materials. You can submit a contact request at the Materials Computation Center (MCC) website "https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc, describing the material(s) you are interested in modeling with ReaxFF. -They can tell -you what is currently available or what it would take to create a -suitable ReaxFF parameterization. +They can tell you what is currently available or what it would take to +create a suitable ReaxFF parameterization. The {cfile} setting can be specified as NULL, in which case default settings are used. A control file can be specified which defines @@ -120,28 +120,31 @@ assign to each atom will be used for computing the electrostatic interactions in the system. See the "fix qeq/reax"_fix_qeq_reax.html command for details. -Using the optional keyword {lgvdw} with the value {yes} turns on -the low-gradient correction of the ReaxFF/C for long-range -London Dispersion, as described in the "(Liu)"_#Liu_2011 paper. Force field +Using the optional keyword {lgvdw} with the value {yes} turns on the +low-gradient correction of the ReaxFF/C for long-range London +Dispersion, as described in the "(Liu)"_#Liu_2011 paper. Force field file {ffield.reax.lg} is designed for this correction, and is trained for several energetic materials (see "Liu"). When using lg-correction, recommended value for parameter {thb} is 0.01, which can be set in the control file. Note: Force field files are different for the original -or lg corrected pair styles, using wrong ffield file generates an error message. +or lg corrected pair styles, using wrong ffield file generates an +error message. Using the optional keyword {enobonds} with the value {yes}, the energy of atoms with no bonds (i.e. isolated atoms) is included in the total potential energy and the per-atom energy of that atom. If the value -{no} is specified then the energy of atoms with no bonds is set to zero. -The latter behavior is usual not desired, as it causes discontinuities -in the potential energy when the bonding of an atom drops to zero. +{no} is specified then the energy of atoms with no bonds is set to +zero. The latter behavior is usual not desired, as it causes +discontinuities in the potential energy when the bonding of an atom +drops to zero. Optional keywords {safezone} and {mincap} are used for allocating -reax/c arrays. Increasing these values can avoid memory problems, such -as segmentation faults and bondchk failed errors, that could occur under -certain conditions. These keywords aren't used by the Kokkos version, which -instead uses a more robust memory allocation scheme that checks if the sizes of -the arrays have been exceeded and automatically allocates more memory. +reax/c arrays. Increasing these values can avoid memory problems, +such as segmentation faults and bondchk failed errors, that could +occur under certain conditions. These keywords aren't used by the +Kokkos version, which instead uses a more robust memory allocation +scheme that checks if the sizes of the arrays have been exceeded and +automatically allocates more memory. The thermo variable {evdwl} stores the sum of all the ReaxFF potential energy contributions, with the exception of the Coulombic and charge @@ -153,7 +156,8 @@ This pair style tallies a breakdown of the total ReaxFF potential energy into sub-categories, which can be accessed via the "compute pair"_compute_pair.html command as a vector of values of length 14. The 14 values correspond to the following sub-categories (the variable -names in italics match those used in the original FORTRAN ReaxFF code): +names in italics match those used in the original FORTRAN ReaxFF +code): {eb} = bond energy {ea} = atom energy @@ -299,10 +303,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -314,8 +317,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -340,8 +343,8 @@ reax"_pair_reax.html [Default:] -The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone = 1.2, -mincap = 50. +The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, +safezone = 1.2, mincap = 50. :line diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index 9ad95eb5fc4e9ddc0bb3f9eda4a1751b0afba726..6ea5c73c0dd1c3cd7036b7aae2d0b492155b81f5 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -145,10 +145,9 @@ specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -160,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 360136a4eaef3df735b65cfc0f8e7ce5ca78dc16..4cd56bc43d63c88af6a6fb53bfe1e1eede9623c1 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -85,10 +85,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp} or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP, and OPT packages respectively. They are only enabled if @@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index 27dcf6082b892b5a5df64442f2045215c8d5dbd8..c3d6e67e82f24e603fcbe49e77fd9a622ffc78f3 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -175,10 +175,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -190,8 +189,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt index 08fa88c477961677b4aafd786e13ad1b89befed9..adbfa596c9c677506fcc4c273ed5641a7701bed4 100644 --- a/doc/src/pair_soft.txt +++ b/doc/src/pair_soft.txt @@ -82,10 +82,9 @@ variables. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -97,8 +96,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1d0cb2265b9f58a46d33072c9e819acb364c00f --- /dev/null +++ b/doc/src/pair_spin_dmi.txt @@ -0,0 +1,91 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style spin/dmi command :h3 + +[Syntax:] + +pair_style spin/dmi cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/dmi 4.0 +pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0 +pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre + +[Description:] + +Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction +between pairs of magnetic spins. +According to the expression reported in "(Rohart)"_#Rohart, one has +the following DM energy: + +:c,image(Eqs/pair_spin_dmi_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j, +and D is the DM vector defining the intensity (in eV) and the direction +of the interaction. + +In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented +from the high spin-orbit layer to the magnetic ultrathin film. + +The application of a spin-lattice Poisson bracket to this energy (as described +in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a +mechanical force F (for spin-lattice calculations only) for each magnetic +particle i: + +:c,image(Eqs/pair_spin_dmi_forces.jpg) + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida5. + +For the {spin/dmi} pair style, the following coefficients must be defined for +each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: + +rc (distance units) +|D| (energy units) +Dx, Dy, Dz (direction of D) :ul + +Note that rc is the radius cutoff of the considered DM interaction, |D| is +the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction. + +None of those coefficients is optional. If not specified, the {spin/dmi} +pair style cannot be used. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Rohart) +[(Rohart)] Rohart and Thiaville, +Physical Review B, 88(18), 184422. (2013). +:link(Tranchida5) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt new file mode 100644 index 0000000000000000000000000000000000000000..a4f37a98eb4e9a205f8c08842d70ef3b6035276d --- /dev/null +++ b/doc/src/pair_spin_exchange.txt @@ -0,0 +1,98 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style spin/exchange command :h3 + +[Syntax:] + +pair_style spin/exchange cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885 +pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre + +[Description:] + +Style {spin/exchange} computes the exchange interaction between +pairs of magnetic spins: + +:c,image(Eqs/pair_spin_exchange_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +rij = ri - rj is the inter-atomic distance between the two particles, +and J(rij) is a function defining the intensity and the sign of the exchange +interaction for different neighboring shells. This function is defined as: + +:c,image(Eqs/pair_spin_exchange_function.jpg) + +where a, b and d are the three constant coefficients defined in the associated +"pair_coeff" command (see below for more explanations). + +The coefficients a, b, and d need to be fitted so that the function above matches with +the value of the exchange interaction for the N neighbor shells taken into account. +Examples and more explanations about this function and its parametrization are reported +in "(Tranchida)"_#Tranchida3. + +From this exchange interaction, each spin i will be submitted +to a magnetic torque omega, and its associated atom can be submitted to a +force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), +such as: + +:c,image(Eqs/pair_spin_exchange_forces.jpg) + +with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit +vector between sites i and j. + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida3. + +For the {spin/exchange} pair style, the following coefficients must be defined +for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: + +rc (distance units) +a (energy units) +b (adim parameter) +d (distance units) :ul + +Note that rc is the radius cutoff of the considered exchange interaction, +and a, b and d are the three coefficients performing the parametrization +of the function J(rij) defined above. + +None of those coefficients is optional. If not specified, the +{spin/exchange} pair style cannot be used. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Tranchida3) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt new file mode 100644 index 0000000000000000000000000000000000000000..8ba24c46af2b98102e872b16f4c423336410338a --- /dev/null +++ b/doc/src/pair_spin_magelec.txt @@ -0,0 +1,73 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style spin/me command :h3 + +[Syntax:] + +pair_style spin/me cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/me 4.5 +pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre + +[Description:] + +Style {spin/me} computes a magneto-electric interaction between +pairs of magnetic spins. According to the derivation reported in +"(Katsura)"_#Katsura1, this interaction is defined as: + +:c,image(Eqs/pair_spin_me_interaction.jpg) + +where si and sj are neighboring magnetic spins of two particles, +eij = (ri - rj)/|ri-rj| is the normalized separation vector between the +two particles, and E is an electric polarization vector. +The norm and direction of E are giving the intensity and the +direction of a screened dielectric atomic polarization (in eV). + +From this magneto-electric interaction, each spin i will be submitted +to a magnetic torque omega, and its associated atom can be submitted to a +force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), +such as: + +:c,image(Eqs/pair_spin_me_forces.jpg) + +with h the Planck constant (in metal units). + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida4. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_spin_exchange"_pair_spin_exchange.html, "pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Katsura1) +[(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005) + +:link(Tranchida4) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt new file mode 100644 index 0000000000000000000000000000000000000000..8551f8d63650f50fd355903028cefd64eb96ed4c --- /dev/null +++ b/doc/src/pair_spin_neel.txt @@ -0,0 +1,81 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style spin/neel command :h3 + +[Syntax:] + +pair_style spin/neel cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/neel 4.0 +pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 +pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre + +[Description:] + +Style {spin/neel} computes the Neel pair anisotropy model +between pairs of magnetic spins: + +:c,image(Eqs/pair_spin_neel_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +rij = ri - rj is the inter-atomic distance between the two particles, +eij = (ri - rj)/|ri-rj| is their normalized separation vector +and g1, q1 and q2 are three functions defining the intensity of the +dipolar and quadrupolar contributions, with: + +:c,image(Eqs/pair_spin_neel_functions.jpg) + +With the functions g(rij) and q(rij) defined and fitted according to the same +Bethe-Slater function used to fit the exchange interaction: + +:c,image(Eqs/pair_spin_exchange_function.jpg) + +where a, b and d are the three constant coefficients defined in the associated +"pair_coeff" command. + +The coefficients a, b, and d need to be fitted so that the function above matches with +the values of the magneto-elastic constant of the materials at stake. + +Examples and more explanations about this function and its parametrization are reported +in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in +future work. + +From this DM interaction, each spin i will be submitted to a magnetic torque +omega and its associated atom to a force F (for spin-lattice calculations only). + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida6. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Tranchida6) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index 6ed8f00236e2e4a4f441401c39823586802818a3..7c9ce4a4f90728fcc0191caa45fdcfd07ca69723 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -144,10 +144,9 @@ taken from the ij and ik pairs (sigma, a, gamma) Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -164,8 +163,8 @@ additional 5 to 10 percent performance improvement when the Stillinger-Weber parameters p and q are set to 4 and 0 respectively. These parameters are common for modeling silicon and water. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -192,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] This pair style is part of the MANYBODY package. It is only enabled -if LAMMPS was built with that package. See -the "Making LAMMPS"_Section_start.html#start_3 section for more info. +if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This pair style requires the "newton"_newton.html setting to be "on" for pair interactions. diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index b99491b477224e621da4429d10c0b20b84c66c0d..f5e69a6d542110394747848f70a0041d79fe3a79 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -217,10 +217,9 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -232,8 +231,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index cd3a7ef31b87d15268cfe93050889b4699a4adc7..52760c396bb2daf15ca8b2d7d004e9c40dadd1a1 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -227,10 +227,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -242,8 +241,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index 918e88992440045bda099cb2ad9849ab4faeff14..70fe207f0afa1e69b2414ce802a760b894abf1eb 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -179,10 +179,9 @@ defined in various papers. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt index e0c2b5a5cbb07b7c525d58d48eab97cb763971ca..aced6d40d69ed54e3b1aafb415dbff4b8759f6de 100644 --- a/doc/src/pair_tersoff_mod.txt +++ b/doc/src/pair_tersoff_mod.txt @@ -131,10 +131,9 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -146,8 +145,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt index 21d57e4e8841570f44f114961af653ad9dde93b4..838c2f39cf772b2342681a8e70337be2e7f160ef 100644 --- a/doc/src/pair_tersoff_zbl.txt +++ b/doc/src/pair_tersoff_zbl.txt @@ -189,10 +189,9 @@ providing the base ZBL implementation. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -204,8 +203,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index 41a4059cee8d4de828d136343a282310f493403d..11d4b85cff15688fbf5ca15dd3a238de42a48bbe 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -130,10 +130,9 @@ the {pair_style} command line. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Mixing]: diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt index 88a22864ccaf960472dbe5ea3f985ea2d375ab23..5af8741502efdf511657435179ed3ea53f8cb0ad 100644 --- a/doc/src/pair_ufm.txt +++ b/doc/src/pair_ufm.txt @@ -69,10 +69,9 @@ NOTE: The thermodynamic integration procedure can be performed with this potenti Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -84,8 +83,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index d9c66d45c0cae201fa12b3799bdf562dc9f55a91..e90a9d8f5005a0d2bb15658a060800574c79e1eb 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -171,10 +171,9 @@ two-body parameters from the CCC and CSiSi entries. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -186,8 +185,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt index e7c063ded9f41227210e17970dc9fb7cc59ed757..979165dda0e97afb88bfb4c1a00e91193589b076 100644 --- a/doc/src/pair_yukawa.txt +++ b/doc/src/pair_yukawa.txt @@ -49,10 +49,9 @@ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt index 2037a9451f9e77079971382afde16709657c88e7..a1752c261ed65c29e4f25644c40c99fc8da3dfb5 100644 --- a/doc/src/pair_yukawa_colloid.txt +++ b/doc/src/pair_yukawa_colloid.txt @@ -80,10 +80,9 @@ yukawa/colloid cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt index 1984cd831f6bf2fef81c9f2ef39c16b04284e309..0507083295671c1458a485a311629152b432b2fd 100644 --- a/doc/src/pair_zbl.txt +++ b/doc/src/pair_zbl.txt @@ -71,10 +71,9 @@ copper. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 202aaa9c0f8354ebadf7a2f24156e3fb19b02fd2..4c3eef2cd11c32ea4801ebb830a6a985cc5a734b 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -10,8 +10,9 @@ Pair Styles :h1 pair_airebo pair_awpmd pair_beck - pair_body + pair_body_nparticle pair_body_rounded_polygon + pair_body_rounded_polyhedron pair_bop pair_born pair_brownian @@ -97,6 +98,10 @@ Pair Styles :h1 pair_sph_rhosum pair_sph_taitwater pair_sph_taitwater_morris + pair_spin_dmi + pair_spin_exchange + pair_spin_magelec + pair_spin_neel pair_srp pair_sw pair_table diff --git a/doc/src/python.txt b/doc/src/python.txt index 1ac2b48528c073a1b40ea4fd210dfb5dfb91a1ae..d670fcc77f8ef4377c829ae0fa486fa9ba8347a1 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -99,10 +99,9 @@ They can be substituted for directly in an input script. Or they can be passed to various commands as arguments, so that the variable is evaluated during a simulation run. -A broader overview of how Python can be used with LAMMPS is -given in "Section 11"_Section_python.html. There is an -examples/python directory which illustrates use of the python -command. +A broader overview of how Python can be used with LAMMPS is given on +the "Python"_Python.html doc page. There is an examples/python +directory which illustrates use of the python command. :line @@ -331,9 +330,9 @@ to the screen and log file. Note that since the LAMMPS print command itself takes a string in quotes as its argument, the Python string must be delimited with a different style of quotes. -"Section 11.7"_Section_python.html#py_7 describes the syntax for how -Python wraps the various functions included in the LAMMPS library -interface. +The "Pytnon library"_Python_library.html doc page describes the syntax +for how Python wraps the various functions included in the LAMMPS +library interface. A more interesting example is in the examples/python/in.python script which loads and runs the following function from examples/python/funcs.py: @@ -484,15 +483,16 @@ building LAMMPS. LAMMPS must also be built as a shared library and your Python function must be able to to load the Python module in python/lammps.py that wraps the LAMMPS library interface. These are the same steps required to use Python by itself to wrap LAMMPS. -Details on these steps are explained in "Section -python"_Section_python.html. Note that it is important that the -stand-alone LAMMPS executable and the LAMMPS shared library be -consistent (built from the same source code files) in order for this -to work. If the two have been built at different times using -different source files, problems may occur. +Details on these steps are explained on the "Python"_Python.html doc +page. Note that it is important that the stand-alone LAMMPS +executable and the LAMMPS shared library be consistent (built from the +same source code files) in order for this to work. If the two have +been built at different times using different source files, problems +may occur. [Related commands:] -"shell"_shell.html, "variable"_variable.html, "fix python/invoke"_fix_python_invoke.html +"shell"_shell.html, "variable"_variable.html, "fix +python/invoke"_fix_python_invoke.html [Default:] none diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index 23f6274582ee9d1ef579ce96ce9692a892866f29..21c6df5017a50b8bf35ef43198c659f60ae4fb51 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -282,11 +282,11 @@ conditions are applied to remap an atom back into the simulation box. NOTE: If you get a warning about inconsistent image flags after reading in a dump snapshot, it means one or more pairs of bonded atoms -now have inconsistent image flags. As discussed in "Section -errors"_Section_errors.html this may or may not cause problems for -subsequent simulations, One way this can happen is if you read image -flag fields from the dump file but do not also use the dump file box -parameters. +now have inconsistent image flags. As discussed on the "Errors +common"_Errors_common.html doc page this may or may not cause problems +for subsequent simulations. One way this can happen is if you read +image flag fields from the dump file but do not also use the dump file +box parameters. LAMMPS knows how to compute unscaled and remapped coordinates for the snapshot column labels discussed above, e.g. {x}, {xs}, {xu}, {xsu}. diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt index a5a2bfcc9743d7402eeb57bfa3dcda678f357829..6f6a82822929d26afd5d0a10ad9c28aa3bd252f7 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -76,8 +76,7 @@ different than if the run had continued. These pair styles include If a restarted run is immediately different than the run which produced the restart file, it could be a LAMMPS bug, so consider -"reporting it"_Section_errors.html#err_2 if you think the behavior is -wrong. +"reporting it"_Errors_bugs.html if you think the behavior is a bug. Because restart files are binary, they may not be portable to other machines. In this case, you can use the "-restart command-line diff --git a/doc/src/region.txt b/doc/src/region.txt index 5039e4a51615164a410bd85ff6572ac41d3a8bf6..1ac3861e675834c262bbf615764caedfd6e25781 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -358,12 +358,12 @@ sub-regions can be defined with the {open} keyword. :line -Styles with a {kk} suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. The code using the region (such as a fix or compute) must also be supported by Kokkos or no acceleration will occur. Currently, only {block} style @@ -378,8 +378,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/run.txt b/doc/src/run.txt index 311560d66b57585c0dfb9e0fae8c64d8f39ea236..913d81bb4d05c46274d5127bed7e6fb483732507 100644 --- a/doc/src/run.txt +++ b/doc/src/run.txt @@ -126,9 +126,8 @@ and interleaving commands in your input script. For example, a be redefined, e.g. to reset a thermostat temperature. Or this could be useful for invoking a command you have added to LAMMPS that wraps some other code (e.g. as a library) to perform a computation -periodically during a long LAMMPS run. See "this -section"_Section_modify.html of the documentation for info about how -to add new commands to LAMMPS. See "this +periodically during a long LAMMPS run. See the "Modify"_Modify.html +doc page for info about how to add new commands to LAMMPS. See "this section"_Section_howto.html#howto_10 of the documentation for ideas about how to couple LAMMPS to other codes. diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index ba836a07dd1510b48e48ad5c8f2714bd5c6252b9..6f1f719d6445f0d813c732c24790946359b74c3a 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -119,13 +119,13 @@ switches"_Section_start.html#start_6 to change this. The log and screen file for the 2nd partition will not contain thermodynamic output beyond the 1st timestep of the run. -See "Section 5"_Section_accelerate.html of the manual for -performance details of the speed-up offered by the {verlet/split} -style. One important performance consideration is the assignment of -logical processors in the 2 partitions to the physical cores of a -parallel machine. The "processors"_processors.html command has -options to support this, and strategies are discussed in -"Section 5"_Section_accelerate.html of the manual. +See the "Speed packages"_Speed_packages.html doc page for performance +details of the speed-up offered by the {verlet/split} style. One +important performance consideration is the assignment of logical +processors in the 2 partitions to the physical cores of a parallel +machine. The "processors"_processors.html command has options to +support this, and strategies are discussed in "Section +5"_Speed.html of the manual. :line @@ -138,13 +138,19 @@ iterations of level 1 for a single iteration of level 2, N2 is the iterations of level 2 per iteration of level 3, etc. N-1 looping parameters must be specified. -The "timestep"_timestep.html command sets the timestep for the -outermost rRESPA level. Thus if the example command above for a -4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep -would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that -specify number of timesteps (e.g. "neigh_modify"_neigh_modify.html -parameters, "dump"_dump.html every N timesteps, etc) refer to the -outermost timesteps. +Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, +you could choose to have bond interactions computed 8x per large +timestep, angle interactions computed 4x, pair interactions computed +2x, and long-range interactions once per large timestep. + +The "timestep"_timestep.html command sets the large timestep for the +outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for +4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the +inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS +commands that specify number of timesteps (e.g. "thermo"_thermo.html +for thermo output every N steps, "neigh_modify +delay/every"_neigh_modify.html parameters, "dump"_dump.html every N +steps, etc) refer to the outermost timesteps. The rRESPA keywords enable you to specify at what level of the hierarchy various forces will be computed. If not specified, the @@ -167,11 +173,17 @@ have their force go ramped to 0.0 so the overlap with the next regime compute forces for all pairs from 5.0 outward, with those from 5.0 to 6.0 having their value ramped in an inverse manner. -Only some pair potentials support the use of the {inner} and {middle} -and {outer} keywords. If not, only the {pair} keyword can be used -with that pair style, meaning all pairwise forces are computed at the -same rRESPA level. See the doc pages for individual pair styles for -details.i +Note that you can use {inner} and {outer} without using {middle} to +split the pairwise computations into two portions instead of three. +Unless you are using a very long pairwise cutoff, a 2-way split is +often faster than a 3-way split, since it avoids too much duplicate +computation of pairwise interactions near the intermediate cutoffs. + +Also note that only a few pair potentials support the use of the +{inner} and {middle} and {outer} keywords. If not, only the {pair} +keyword can be used with that pair style, meaning all pairwise forces +are computed at the same rRESPA level. See the doc pages for +individual pair styles for details. Another option for using pair potentials with rRESPA is with the {hybrid} keyword, which requires the use of the "pair_style hybrid or @@ -238,42 +250,54 @@ roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a For non-biomolecular simulations, the {respa} style can be advantageous if there is a clear separation of time scales - fast and -slow modes in the simulation. Even a LJ system can benefit from -rRESPA if the interactions are divided by the inner, middle and outer -keywords. A 2-fold or more speedup can be obtained while maintaining -good energy conservation. In real units, for a pure LJ fluid at -liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1 -Kcal/mol, the following settings seem to work well: +slow modes in the simulation. For example, a system of slowly-moving +charged polymer chains could be setup as follows: + +timestep 4.0 +run_style respa 2 8 :pre + +This is two-level rRESPA with an 8x difference between the short and +long timesteps. The bonds, angles, dihedrals will be computed every +0.5 fs (assuming real units), while the pair and kspace interactions +will be computed once every 4 fs. These are the default settings for +each kind of interaction, so no additional keywords are necessary. + +Even a LJ system can benefit from rRESPA if the interactions are +divided by the inner, middle and outer keywords. A 2-fold or more +speedup can be obtained while maintaining good energy conservation. +In real units, for a pure LJ fluid at liquid density, with a sigma of +3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings +seem to work well: timestep 36.0 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre :line -The {respa/omp} styles is a variant of {respa} adapted for use with +The {respa/omp} style is a variant of {respa} adapted for use with pair, bond, angle, dihedral, improper, or kspace styles with an {omp} -suffix. It is functionally equivalent to {respa} but performs additional -operations required for managing {omp} styles. For more on {omp} styles -see the "Section 5"_Section_accelerate.html of the manual. -Accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +suffix. It is functionally equivalent to {respa} but performs +additional operations required for managing {omp} styles. For more on +{omp} styles see the "Speed omp"_Speed_omp.html doc page. Accelerated +styles take the same arguments and should produce the same results, +except for round-off and precision issues. You can specify {respa/omp} explicitly in your input script, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] The {verlet/split} style can only be used if LAMMPS was built with the -REPLICA package. Correspondingly the {respa/omp} style is available only -if the USER-OMP package was included. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +REPLICA package. Correspondingly the {respa/omp} style is available +only if the USER-OMP package was included. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info on packages. Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are @@ -287,6 +311,17 @@ conserving energy to adequate precision. run_style verlet :pre +For run_style respa, the default assignment of interactions +to rRESPA levels is as follows: + +bond forces = level 1 (innermost loop) +angle forces = same level as bond forces +dihedral forces = same level as angle forces +improper forces = same level as dihedral forces +pair forces = leven N (outermost level) +kspace forces = same level as pair forces +inner, middle, outer forces = no default :ul + :line :link(Tuckerman3) diff --git a/doc/src/set.txt b/doc/src/set.txt index 4757d1c5758f9ed027a9932c07452ddcc2567f95..d2235d5c32bc03426c8f7c584c10c5fc2b6a7f1c 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -17,6 +17,7 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l one or more keyword/value pairs may be appended :l keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {charge} or {dipole} or {dipole/random} or {quat} or \ + {spin} or {spin/random} or {quat} or \ {quat/random} or {diameter} or {shape} or \ {length} or {tri} or {theta} or {theta/random} or \ {angmom} or {omega} or \ @@ -35,6 +36,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {x},{y},{z} value = atom coordinate (distance units) value can be an atom-style variable (see below) + {vx},{vy},{vz} value = atom velocity (velocity units) + value can be an atom-style variable (see below) {charge} value = atomic charge (charge units) value can be an atom-style variable (see below) {dipole} values = x y z @@ -43,6 +46,13 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {dipole/random} value = seed Dlen seed = random # seed (positive integer) for dipole moment orientations Dlen = magnitude of dipole moment (dipole units) + {spin} values = g x y z + g = magnitude of magnetic spin vector (in Bohr magneton's unit) + x,y,z = orientation of magnetic spin vector + any of x,y,z can be an atom-style variable (see below) + {spin/random} value = seed Dlen + seed = random # seed (positive integer) for magnetic spin orientations + Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit) {quat} values = a b c theta a,b,c = unit vector to rotate particle around via right-hand rule theta = rotation angle (degrees) @@ -119,6 +129,7 @@ set type 3 charge 0.5 set type 1*3 charge 0.5 set atom * charge v_atomfile set atom 100*200 x 0.5 y 1.0 +set atom 100 vx 0.0 vy 0.0 vz -1.0 set atom 1492 type 3 :pre [Description:] @@ -217,7 +228,8 @@ IDs. Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of all selected atoms. For {charge}, the "atom style"_atom_style.html -being used must support the use of atomic charge. +being used must support the use of atomic charge. Keywords {vx}, {vy}, +and {vz} set the velocities of all selected atoms. Keyword {dipole} uses the specified x,y,z values as components of a vector to set as the orientation of the dipole moment vectors of the @@ -232,6 +244,15 @@ the orientation of a particular atom is the same, regardless of how many processors are being used. This keyword does not allow use of an atom-style variable. +Keyword {spin} uses the specified g value to set the magnitude of the +magnetic spin vectors, and the x,y,z values as components of a vector +to set as the orientation of the magnetic spin vectors of the selected +atoms. + +Keyword {spin/random} randomizes the orientation of the magnetic spin +vectors for the selected atoms and sets the magnitude of each to the +specified {Dlen} value. + Keyword {quat} uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. The particles must define a quaternion for their orientation diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 6102169ee363ca2bdb9dc41d1663f9c1dcb442aa..18c5ad5ba1ce9ecedf74156c8f78a073101e8374 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -108,12 +108,11 @@ Style {custom} is the most general setting and allows you to specify which of the keywords listed above you want printed on each thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to "computes"_compute.html, "fixes"_fix.html, and -equal-style "variables"_variable.html that have been defined -elsewhere in the input script or can even be new styles which users -have added to LAMMPS (see the "Section 10"_Section_modify.html -section of the documentation). Thus the {custom} style provides a -flexible means of outputting essentially any desired quantity as a -simulation proceeds. +equal-style "variables"_variable.html that have been defined elsewhere +in the input script or can even be new styles which users have added +to LAMMPS. See the "Modify"_Modify.html doc page for details on the +latter. Thus the {custom} style provides a flexible means of +outputting essentially any desired quantity as a simulation proceeds. All styles except {custom} have {vol} appended to their list of outputs if the simulation box volume changes during the simulation. diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt index 3e10b821aecf3b8bce1f1f9e54198720bd521ce5..fc261bdb958e18bdb19511f4a0ec8ecad8ad8c3e 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/tutorial_github.txt @@ -25,8 +25,8 @@ or improvements to LAMMPS, as it significantly reduces the amount of work required by the LAMMPS developers. Consequently, creating a pull request will increase your chances to have your contribution included and will reduce the time until the integration is complete. For more -information on the requirements to have your code included into LAMMPS -please see "Section 10.15"_Section_modify.html#mod_15 +information on the requirements to have your code included in LAMMPS, +see the "Modify contribute"_Modify_contribute.html doc page. :line diff --git a/doc/src/variable.txt b/doc/src/variable.txt index c0851464c3f14e11629b8e65ee58a171499a4e45..717c77c07908099a76f4f32991697bfcb8294bc6 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -296,17 +296,24 @@ list of runs (e.g. 1000) without having to list N strings in the input script. For the {string} style, a single string is assigned to the variable. -The only difference between this and using the {index} style with a -single string is that a variable with {string} style can be redefined. -E.g. by another command later in the input script, or if the script is -read again in a loop. +Two differences between this this and using the {index} style exist: +a variable with {string} style can be redefined, e.g. by another command later +in the input script, or if the script is read again in a loop. The other +difference is that {string} performs variable substitution even if the +string parameter is quoted. For the {format} style, an equal-style variable is specified along with a C-style format string, e.g. "%f" or "%.10g", which must be appropriate for formatting a double-precision floating-point value. -This allows an equal-style variable to be formatted specifically for -output as a string, e.g. by the "print"_print.html command, if the -default format "%.15g" has too much precision. +The default format is "%.15g". This variable style allows an +equal-style variable to be formatted precisely when it is evaluated. + +If you simply wish to print a variable value with desired precision to +the screen or logfile via the "print"_print.html or "fix +print"_fix_print.html commands, you can also do this by specifying an +"immediate" variable with a trailing colon and format string, as part +of the string argument of those commands. This is explained in +"Section 3.2"_Section_commands.html#cmd_2. For the {getenv} style, a single string is assigned to the variable which should be the name of an environment variable. When the diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt index 39e5a7f8114627a358350f4b7bb4c799fddb27cc..c76f20319c3182a2d9298d8aada887cb806878f3 100644 --- a/doc/src/write_data.txt +++ b/doc/src/write_data.txt @@ -16,6 +16,7 @@ file = name of data file to write out :ulb,l zero or more keyword/value pairs may be appended :l keyword = {pair} or {nocoeff} :l {nocoeff} = do not write out force field info + {nofix} = do not write out extra sections read by fixes {pair} value = {ii} or {ij} {ii} = write one line of pair coefficient info per atom type {ij} = write one line of pair coefficient info per IJ atom type pair :pre @@ -83,6 +84,12 @@ be written to the data file. This can be very helpful, if one wants to make significant changes to the force field or if the parameters are read in separately anyway, e.g. from an include file. +The {nofix} keyword requests that no extra sections read by fixes +should be written to the data file (see the {fix} option of the +"read_data"_read_data.html command for details). For example, this +option excludes sections for user-created per-atom properties +from "fix property/atom"_fix_property_atom.html. + The {pair} keyword lets you specify in what format the pair coefficient information is written into the data file. If the value is specified as {ii}, then one line per atom type is written, to @@ -120,4 +127,3 @@ setup, atom masses initialized, etc). [Default:] The option defaults are pair = ii. - diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py index 79a75d72f6e4be7796e685e7025adbef0d9eb5ff..ed9f47a4e4ae3cfe4c6363a34ab9b7deb42b8c0c 100755 --- a/doc/utils/converters/lammpsdoc/txt2html.py +++ b/doc/utils/converters/lammpsdoc/txt2html.py @@ -662,14 +662,15 @@ class TxtConverter: parser = self.get_argument_parser() parsed_args = parser.parse_args(args) - write_to_files = len(parsed_args.files) > 1 + write_to_files = parsed_args.output_dir or (len(parsed_args.files) > 1) for filename in parsed_args.files: if parsed_args.skip_files and filename in parsed_args.skip_files: continue with open(filename, 'r') as f: - print("Converting", filename, "...", file=err) + if parsed_args.verbose: + print("Converting", filename, "...", file=err) content = f.read() converter = self.create_converter(parsed_args) @@ -683,7 +684,10 @@ class TxtConverter: result = msg if write_to_files: - output_filename = self.get_output_filename(filename) + if parsed_args.output_dir: + output_filename = os.path.join(parsed_args.output_dir, os.path.basename(self.get_output_filename(filename))) + else: + output_filename = self.get_output_filename(filename) with open(output_filename, "w+t") as outfile: outfile.write(result) else: @@ -698,6 +702,8 @@ class Txt2HtmlConverter(TxtConverter): 'HTML file. useful when set of HTML files' ' will be converted to PDF') parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append') + parser.add_argument('--verbose', '-v', dest='verbose', action='store_true') + parser.add_argument('--output-directory', '-o', dest='output_dir') parser.add_argument('--generate-title', dest='create_title', action='store_true', help='add HTML head page' 'title based on first ' 'h1,h2,h3,h4... element') diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index 17d0916157a4f2d9b07ec655522ac6999b6978cb..8119ad3a7869c5345ffad166536f98ffa7bd20ba 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -395,6 +395,8 @@ class Txt2RstConverter(TxtConverter): parser = argparse.ArgumentParser(description='converts a text file with simple formatting & markup into ' 'Restructured Text for Sphinx.') parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append') + parser.add_argument('--verbose', '-v', dest='verbose', action='store_true') + parser.add_argument('--output-directory', '-o', dest='output_dir') parser.add_argument('files', metavar='file', nargs='+', help='one or more files to convert') return parser diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..2806c164989aa9137a6c1860716ae9abccef75ad --- /dev/null +++ b/doc/utils/requirements.txt @@ -0,0 +1 @@ +Sphinx diff --git a/doc/utils/txt2html/txt2html b/doc/utils/txt2html/txt2html new file mode 100755 index 0000000000000000000000000000000000000000..023631eac1b472cdcaf4e8c4757c72c386446ecf Binary files /dev/null and b/doc/utils/txt2html/txt2html differ diff --git a/examples/COUPLE/lammps_quest/lmpqst.cpp b/examples/COUPLE/lammps_quest/lmpqst.cpp index e7f2d92c1dfeb0d512ab64b24d05ab34f2b42e3a..76a89f1d064b289be0e68b6252dd262a7d8ec549 100644 --- a/examples/COUPLE/lammps_quest/lmpqst.cpp +++ b/examples/COUPLE/lammps_quest/lmpqst.cpp @@ -6,10 +6,10 @@ // in.lammps = LAMMPS input script // in.quest = Quest input script -#include "mpi.h" -#include "stdio.h" -#include "stdlib.h" -#include "string.h" +#include +#include +#include +#include #include "stdint.h" #include "many2one.h" diff --git a/examples/COUPLE/lammps_spparks/lmpspk.cpp b/examples/COUPLE/lammps_spparks/lmpspk.cpp index da6d2523696bebe87c759b56a874ca41f6bd4061..2e234c89f1fadb6bbbcdde2a0c579de1a8c97b54 100644 --- a/examples/COUPLE/lammps_spparks/lmpspk.cpp +++ b/examples/COUPLE/lammps_spparks/lmpspk.cpp @@ -7,10 +7,10 @@ // Sfactor = multiplier on strain effect // in.spparks = SPPARKS input script -#include "mpi.h" -#include "stdio.h" -#include "stdlib.h" -#include "string.h" +#include +#include +#include +#include #include "lammps_data_write.h" #include "many2many.h" diff --git a/examples/COUPLE/library/error.cpp b/examples/COUPLE/library/error.cpp index f538dce23f103035181620a99f4d0e3a27f31f42..b7a59b8c72344159a77fcd7326f0d606035f7110 100644 --- a/examples/COUPLE/library/error.cpp +++ b/examples/COUPLE/library/error.cpp @@ -1,6 +1,6 @@ #include -#include -#include +#include +#include #include "error.h" /* ---------------------------------------------------------------------- */ diff --git a/examples/COUPLE/library/files.cpp b/examples/COUPLE/library/files.cpp index 0d98e69a9e0bb80d4594fef1b2c39ce50f45a777..d4d707a6c91fdfcee12e9c446515ba147019bfb9 100644 --- a/examples/COUPLE/library/files.cpp +++ b/examples/COUPLE/library/files.cpp @@ -1,5 +1,5 @@ -#include -#include +#include +#include #include "files.h" #define MAXLINE 256 diff --git a/examples/COUPLE/library/irregular.cpp b/examples/COUPLE/library/irregular.cpp index aea9b8332ca4b60ab523c44e7f19d1fcd0308c3a..b822fc859d4dbb25de9cfff9eb4924c3d032e471 100644 --- a/examples/COUPLE/library/irregular.cpp +++ b/examples/COUPLE/library/irregular.cpp @@ -1,6 +1,6 @@ -#include "stdio.h" -#include "stdlib.h" -#include "string.h" +#include +#include +#include #include "irregular.h" #include "memory.h" #include "error.h" diff --git a/examples/COUPLE/library/lammps_data_write.cpp b/examples/COUPLE/library/lammps_data_write.cpp index cb525871e20f054e44dafc94dedca9ef6f18f7d2..9d1039ff4732e79b2a6823fe752a894a74cc3173 100644 --- a/examples/COUPLE/library/lammps_data_write.cpp +++ b/examples/COUPLE/library/lammps_data_write.cpp @@ -1,6 +1,6 @@ #include -#include -#include +#include +#include #include "lammps_data_write.h" #include "memory.h" #include "error.h" diff --git a/examples/COUPLE/library/lammps_data_write.h b/examples/COUPLE/library/lammps_data_write.h index 9a6de2b63c3406142c719d00873078a83dc9b8aa..0192c17e2984356c330022b55c7f3124038d1bb1 100644 --- a/examples/COUPLE/library/lammps_data_write.h +++ b/examples/COUPLE/library/lammps_data_write.h @@ -1,7 +1,7 @@ #ifndef LAMMPS_DATA_WRITE_H #define LAMMPS_DATA_WRITE_H -#include +#include #include "send2one.h" class LAMMPSDataWrite : public Send2One { diff --git a/examples/COUPLE/library/many2many.cpp b/examples/COUPLE/library/many2many.cpp index 3ca9ca63bbcb5f36e9193d4eb514d3f05aa580e2..cbf5da8e6ef57dc307940d2894c2e0ef6e9f286f 100644 --- a/examples/COUPLE/library/many2many.cpp +++ b/examples/COUPLE/library/many2many.cpp @@ -1,6 +1,6 @@ #include -#include -#include +#include +#include #include "many2many.h" #include "irregular.h" #include "memory.h" diff --git a/examples/COUPLE/library/many2one.cpp b/examples/COUPLE/library/many2one.cpp index 5b5467aa61d325abf2afb324e35320a49b4718ad..ba227bf4719a162559350888ec0a548f53f79b4e 100644 --- a/examples/COUPLE/library/many2one.cpp +++ b/examples/COUPLE/library/many2one.cpp @@ -1,6 +1,6 @@ -#include "mpi.h" -#include "stdio.h" -#include "stdlib.h" +#include +#include +#include #include "many2one.h" #include "memory.h" diff --git a/examples/COUPLE/library/memory.cpp b/examples/COUPLE/library/memory.cpp index 9d299a8376e27c7126d9a62d881cd3eae73584e1..98ef8bafc02cbad582fb9b97dcc703a0bcdcb84b 100644 --- a/examples/COUPLE/library/memory.cpp +++ b/examples/COUPLE/library/memory.cpp @@ -1,6 +1,6 @@ #include -#include -#include +#include +#include #include "memory.h" #include "error.h" diff --git a/examples/COUPLE/library/one2many.cpp b/examples/COUPLE/library/one2many.cpp index 5c4a1799ba8ac3ee78271bcef27ed921755d5462..aa4a03720a54729c2937abf089642317b1285f34 100644 --- a/examples/COUPLE/library/one2many.cpp +++ b/examples/COUPLE/library/one2many.cpp @@ -1,5 +1,5 @@ #include -#include +#include #include "one2many.h" #include "memory.h" diff --git a/examples/COUPLE/library/send2one.cpp b/examples/COUPLE/library/send2one.cpp index d969b4678d3563413d8d0011197c2aed121d66bb..d35cf19a4ecee245b740ae1959ae1c2c0a3b06c8 100644 --- a/examples/COUPLE/library/send2one.cpp +++ b/examples/COUPLE/library/send2one.cpp @@ -1,6 +1,6 @@ -#include "mpi.h" -#include "stdlib.h" -#include "stdio.h" +#include +#include +#include #include "send2one.h" #include "memory.h" #include "error.h" diff --git a/examples/COUPLE/multiple/multiple.cpp b/examples/COUPLE/multiple/multiple.cpp index f2de959bac43c37cdc8472f3d6b02e221a1ec6cd..c58c3c78a97624b8eb0ff9237eec4d134549da8d 100644 --- a/examples/COUPLE/multiple/multiple.cpp +++ b/examples/COUPLE/multiple/multiple.cpp @@ -23,10 +23,10 @@ // Tdelta = incremental temperature for each of N runs // See README for compilation instructions -#include "stdio.h" -#include "stdlib.h" -#include "string.h" -#include "mpi.h" +#include +#include +#include +#include #include "lammps.h" // these are LAMMPS include files #include "input.h" diff --git a/examples/COUPLE/simple/simple.cpp b/examples/COUPLE/simple/simple.cpp index 912f4b868954e913e92010354bc6b3a296068297..a76ed8a6e9f4785ee19305279a1eb614d33c4621 100644 --- a/examples/COUPLE/simple/simple.cpp +++ b/examples/COUPLE/simple/simple.cpp @@ -19,15 +19,16 @@ // in.lammps = LAMMPS input script // See README for compilation instructions -#include "stdio.h" -#include "stdlib.h" -#include "string.h" -#include "mpi.h" - -#include "lammps.h" // these are LAMMPS include files -#include "input.h" -#include "atom.h" -#include "library.h" +#include +#include +#include +#include + +// these are LAMMPS include files +#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/examples/SPIN/README b/examples/SPIN/README new file mode 100644 index 0000000000000000000000000000000000000000..5ad252e7f2c71ee1d0232ec1f67f4ee39a91f612 --- /dev/null +++ b/examples/SPIN/README @@ -0,0 +1,20 @@ +This directory contains examples and applications of the SPIN package +===================================================================== + +- the iron, cobalt_hcp, cobalt_fcc and nickel directories provide +examples of spin-lattice calculations. + +- the bfo repository provides an example of spin dynamics calculation +performed on a fixed lattice, and applied to the multiferroic +material bismuth-oxide. + +- the read_restart directory provides examples allowing to write or +read data files, and restart magneto-mechanical simulations. + +- vizualization of the dump files can be achieved using Ovito or +VMD. See the vmd repository for help vizualizing results with VMD. + +** Note, the aim of this repository is mainly to provide users with +examples. Better values and tuning of the magnetic and mechanical +interactions can be achieved for more accurate materials +simulations. ** diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo new file mode 100644 index 0000000000000000000000000000000000000000..de23ba87ba2b825c129b88fd55fcfcb33703eb01 --- /dev/null +++ b/examples/SPIN/bfo/in.spin.bfo @@ -0,0 +1,56 @@ +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + +#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 +pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +#thermo_style custom step time v_magnorm v_emag temp etotal +thermo_style custom step time v_magnorm pe ke v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..8e9eb82d1fe23962eb6110ea22c17319f406792e --- /dev/null +++ b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 @@ -0,0 +1,212 @@ +LAMMPS (11 May 2018) +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +Lattice spacing in x,y,z = 3.96 3.96 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (134.64 134.64 19.8) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 5780 atoms + Time spent = 0.0013566 secs + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + 5780 settings made for spin/random + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 5000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 45 45 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair spin/magelec, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.010071723 -0.13298298 0 -0.12034311 + 50 0.01 0.0098643821 -1.3898985 0 -1.3772103 + 100 0.02 0.0096526211 -2.6381677 0 -2.6254222 + 150 0.03 0.0094342235 -3.8784006 0 -3.8656019 + 200 0.04 0.0092074832 -5.111441 0 -5.0986001 + 250 0.05 0.0089713115 -6.3380611 0 -6.3251904 + 300 0.06 0.0087256081 -7.5587787 0 -7.5458894 + 350 0.07 0.0084715548 -8.7738491 0 -8.7609521 + 400 0.08 0.008211486 -9.9833855 0 -9.9704932 + 450 0.09 0.0079483243 -11.18751 0 -11.174637 + 500 0.1 0.0076849713 -12.386462 0 -12.37362 + 550 0.11 0.007424064 -13.580633 0 -13.567832 + 600 0.12 0.0071680699 -14.770519 0 -14.757759 + 650 0.13 0.0069192726 -15.956579 0 -15.943853 + 700 0.14 0.0066793495 -17.139049 0 -17.126343 + 750 0.15 0.0064488038 -18.317803 0 -18.305099 + 800 0.16 0.0062267571 -19.492336 0 -19.479616 + 850 0.17 0.0060112235 -20.661925 0 -20.649176 + 900 0.18 0.0057995251 -21.825931 0 -21.813141 + 950 0.19 0.0055886511 -22.98413 0 -22.971297 + 1000 0.2 0.0053757923 -24.136967 0 -24.124095 + 1050 0.21 0.0051592263 -25.285621 0 -25.272717 + 1100 0.22 0.0049391661 -26.431928 0 -26.419004 + 1150 0.23 0.0047179149 -27.578212 0 -27.565281 + 1200 0.24 0.0044991004 -28.727051 0 -28.714128 + 1250 0.25 0.0042864034 -29.880967 0 -29.868062 + 1300 0.26 0.0040824475 -31.042054 0 -31.029173 + 1350 0.27 0.0038883007 -32.21165 0 -32.198795 + 1400 0.28 0.0037036595 -33.390159 0 -33.377326 + 1450 0.29 0.0035274815 -34.577121 0 -34.564302 + 1500 0.3 0.0033587207 -35.771483 0 -35.758672 + 1550 0.31 0.0031969501 -36.971996 0 -36.95919 + 1600 0.32 0.0030429081 -38.177601 0 -38.164801 + 1650 0.33 0.0028989804 -39.387757 0 -39.374962 + 1700 0.34 0.0027692024 -40.602665 0 -40.589873 + 1750 0.35 0.0026581403 -41.823341 0 -41.81054 + 1800 0.36 0.0025686991 -43.05145 0 -43.038628 + 1850 0.37 0.002500124 -44.288966 0 -44.276111 + 1900 0.38 0.0024477804 -45.537752 0 -45.52486 + 1950 0.39 0.0024050049 -46.799255 0 -46.786336 + 2000 0.4 0.0023657031 -48.074388 0 -48.061466 + 2050 0.41 0.0023260844 -49.363587 0 -49.350695 + 2100 0.42 0.0022848329 -50.666866 0 -50.654039 + 2150 0.43 0.0022419759 -51.983781 0 -51.971055 + 2200 0.44 0.0021972506 -53.31336 0 -53.300764 + 2250 0.45 0.0021488322 -54.654121 0 -54.641676 + 2300 0.46 0.0020929483 -56.004207 0 -55.991918 + 2350 0.47 0.0020244601 -57.361586 0 -57.349442 + 2400 0.48 0.001938225 -58.72428 0 -58.712247 + 2450 0.49 0.0018309419 -60.09064 0 -60.078671 + 2500 0.5 0.0017030436 -61.459658 0 -61.447705 + 2550 0.51 0.0015599449 -62.831213 0 -62.819237 + 2600 0.52 0.0014117554 -64.206088 0 -64.194074 + 2650 0.53 0.0012709942 -65.585701 0 -65.573657 + 2700 0.54 0.0011490452 -66.971565 0 -66.959515 + 2750 0.55 0.001053009 -68.364663 0 -68.352635 + 2800 0.56 0.00098415327 -69.765002 0 -69.753017 + 2850 0.57 0.00093809306 -71.171532 0 -71.159598 + 2900 0.58 0.00090656933 -72.58234 0 -72.570459 + 2950 0.59 0.00088069677 -73.994931 0 -73.983099 + 3000 0.6 0.00085472643 -75.406507 0 -75.39472 + 3050 0.61 0.00082842902 -76.814319 0 -76.802575 + 3100 0.62 0.00080642618 -78.216074 0 -78.204373 + 3150 0.63 0.00079463972 -79.610246 0 -79.598589 + 3200 0.64 0.0007962304 -80.996103 0 -80.984494 + 3250 0.65 0.00080980411 -82.37346 0 -82.361903 + 3300 0.66 0.00083070982 -83.742356 0 -83.730855 + 3350 0.67 0.00085389185 -85.102808 0 -85.091374 + 3400 0.68 0.00087624091 -86.454619 0 -86.443259 + 3450 0.69 0.00089741986 -87.797089 0 -87.785814 + 3500 0.7 0.00091910796 -89.12875 0 -89.117567 + 3550 0.71 0.00094318459 -90.447312 0 -90.436232 + 3600 0.72 0.00096989367 -91.750008 0 -91.739046 + 3650 0.73 0.00099713096 -93.034224 0 -93.023402 + 3700 0.74 0.0010212995 -94.298186 0 -94.287529 + 3750 0.75 0.0010391164 -95.5414 0 -95.530926 + 3800 0.76 0.0010491462 -96.764626 0 -96.754338 + 3850 0.77 0.0010521238 -97.969346 0 -97.95923 + 3900 0.78 0.0010500324 -99.156875 0 -99.146899 + 3950 0.79 0.0010447043 -100.32743 0 -100.31756 + 4000 0.8 0.0010368986 -101.4796 0 -101.46978 + 4050 0.81 0.0010263632 -102.61044 0 -102.60064 + 4100 0.82 0.0010126933 -103.71619 0 -103.70639 + 4150 0.83 0.00099631895 -104.79338 0 -104.78358 + 4200 0.84 0.0009789075 -105.8398 0 -105.82998 + 4250 0.85 0.00096287608 -106.85496 0 -106.84515 + 4300 0.86 0.00095034023 -107.84011 0 -107.83029 + 4350 0.87 0.00094219078 -108.7976 0 -108.78778 + 4400 0.88 0.00093779428 -109.73016 0 -109.72031 + 4450 0.89 0.0009354459 -110.63996 0 -110.63008 + 4500 0.9 0.00093342614 -111.52805 0 -111.51812 + 4550 0.91 0.0009311077 -112.39417 0 -112.38416 + 4600 0.92 0.00092926689 -113.23706 0 -113.22697 + 4650 0.93 0.00092921566 -114.05512 0 -114.04495 + 4700 0.94 0.00093142598 -114.84701 0 -114.83675 + 4750 0.95 0.00093479851 -115.61197 0 -115.60164 + 4800 0.96 0.0009369799 -116.3499 0 -116.33951 + 4850 0.97 0.00093516768 -117.06128 0 -117.05084 + 4900 0.98 0.00092684411 -117.74695 0 -117.73645 + 4950 0.99 0.00091046222 -118.40798 0 -118.39742 + 5000 1 0.00088619957 -119.04554 0 -119.03492 +Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms + +Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.227 | 24.227 | 24.227 | 0.0 | 18.88 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.081048 | 0.081048 | 0.081048 | 0.0 | 0.06 +Output | 39.796 | 39.796 | 39.796 | 0.0 | 31.02 +Modify | 64.112 | 64.112 | 64.112 | 0.0 | 49.97 +Other | | 0.08788 | | | 0.07 + +Nlocal: 5780 ave 5780 max 5780 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1065 ave 1065 max 1065 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 92480 ave 92480 max 92480 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 92480 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:08 diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..c0f96b81954d032ece3935718bf95099e22c643e --- /dev/null +++ b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 @@ -0,0 +1,212 @@ +LAMMPS (11 May 2018) +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +Lattice spacing in x,y,z = 3.96 3.96 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (134.64 134.64 19.8) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 5780 atoms + Time spent = 0.000355959 secs + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + 5780 settings made for spin/random + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 5000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 45 45 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair spin/magelec, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.010071723 -0.13298298 0 -0.12034311 + 50 0.01 0.0098643821 -1.3898985 0 -1.3772103 + 100 0.02 0.009652621 -2.6381677 0 -2.6254222 + 150 0.03 0.0094342234 -3.8784007 0 -3.8656019 + 200 0.04 0.009207483 -5.1114411 0 -5.0986001 + 250 0.05 0.0089713114 -6.3380611 0 -6.3251904 + 300 0.06 0.0087256079 -7.5587787 0 -7.5458894 + 350 0.07 0.0084715546 -8.7738491 0 -8.7609521 + 400 0.08 0.0082114858 -9.9833855 0 -9.9704932 + 450 0.09 0.0079483242 -11.18751 0 -11.174637 + 500 0.1 0.0076849711 -12.386462 0 -12.37362 + 550 0.11 0.0074240638 -13.580633 0 -13.567832 + 600 0.12 0.0071680697 -14.770519 0 -14.757759 + 650 0.13 0.0069192724 -15.956579 0 -15.943853 + 700 0.14 0.0066793493 -17.139049 0 -17.126343 + 750 0.15 0.0064488035 -18.317803 0 -18.305099 + 800 0.16 0.0062267569 -19.492336 0 -19.479616 + 850 0.17 0.0060112233 -20.661925 0 -20.649176 + 900 0.18 0.005799525 -21.825931 0 -21.813141 + 950 0.19 0.0055886511 -22.98413 0 -22.971297 + 1000 0.2 0.0053757923 -24.136967 0 -24.124095 + 1050 0.21 0.0051592265 -25.285621 0 -25.272717 + 1100 0.22 0.0049391664 -26.431928 0 -26.419004 + 1150 0.23 0.0047179153 -27.578212 0 -27.565281 + 1200 0.24 0.0044991009 -28.727051 0 -28.714128 + 1250 0.25 0.0042864039 -29.880967 0 -29.868062 + 1300 0.26 0.004082448 -31.042054 0 -31.029174 + 1350 0.27 0.0038883012 -32.21165 0 -32.198795 + 1400 0.28 0.0037036599 -33.390159 0 -33.377326 + 1450 0.29 0.0035274817 -34.577121 0 -34.564302 + 1500 0.3 0.0033587208 -35.771483 0 -35.758672 + 1550 0.31 0.0031969501 -36.971996 0 -36.95919 + 1600 0.32 0.0030429079 -38.177601 0 -38.164801 + 1650 0.33 0.0028989801 -39.387757 0 -39.374962 + 1700 0.34 0.0027692022 -40.602666 0 -40.589873 + 1750 0.35 0.0026581401 -41.823341 0 -41.81054 + 1800 0.36 0.002568699 -43.05145 0 -43.038628 + 1850 0.37 0.0025001242 -44.288966 0 -44.276111 + 1900 0.38 0.0024477808 -45.537752 0 -45.52486 + 1950 0.39 0.0024050056 -46.799255 0 -46.786336 + 2000 0.4 0.002365704 -48.074388 0 -48.061466 + 2050 0.41 0.0023260854 -49.363587 0 -49.350695 + 2100 0.42 0.002284834 -50.666866 0 -50.654039 + 2150 0.43 0.0022419771 -51.983781 0 -51.971055 + 2200 0.44 0.0021972518 -53.31336 0 -53.300764 + 2250 0.45 0.0021488333 -54.654121 0 -54.641676 + 2300 0.46 0.0020929494 -56.004207 0 -55.991918 + 2350 0.47 0.0020244612 -57.361586 0 -57.349441 + 2400 0.48 0.0019382262 -58.72428 0 -58.712247 + 2450 0.49 0.001830943 -60.090639 0 -60.078671 + 2500 0.5 0.0017030446 -61.459658 0 -61.447704 + 2550 0.51 0.0015599459 -62.831213 0 -62.819237 + 2600 0.52 0.0014117562 -64.206088 0 -64.194074 + 2650 0.53 0.001270995 -65.5857 0 -65.573657 + 2700 0.54 0.001149046 -66.971565 0 -66.959515 + 2750 0.55 0.0010530098 -68.364663 0 -68.352635 + 2800 0.56 0.00098415418 -69.765002 0 -69.753017 + 2850 0.57 0.00093809402 -71.171532 0 -71.159598 + 2900 0.58 0.00090657031 -72.58234 0 -72.570459 + 2950 0.59 0.00088069773 -73.994931 0 -73.983099 + 3000 0.6 0.00085472731 -75.406507 0 -75.39472 + 3050 0.61 0.00082842975 -76.814319 0 -76.802575 + 3100 0.62 0.00080642669 -78.216074 0 -78.204373 + 3150 0.63 0.00079464 -79.610246 0 -79.59859 + 3200 0.64 0.00079623049 -80.996103 0 -80.984494 + 3250 0.65 0.00080980416 -82.373461 0 -82.361903 + 3300 0.66 0.00083070997 -83.742356 0 -83.730856 + 3350 0.67 0.00085389223 -85.102809 0 -85.091374 + 3400 0.68 0.00087624159 -86.454619 0 -86.44326 + 3450 0.69 0.00089742086 -87.79709 0 -87.785815 + 3500 0.7 0.00091910931 -89.12875 0 -89.117568 + 3550 0.71 0.00094318635 -90.447312 0 -90.436233 + 3600 0.72 0.00096989594 -91.750008 0 -91.739047 + 3650 0.73 0.00099713386 -93.034224 0 -93.023403 + 3700 0.74 0.0010213031 -94.298186 0 -94.287529 + 3750 0.75 0.0010391209 -95.541401 0 -95.530926 + 3800 0.76 0.0010491514 -96.764626 0 -96.754339 + 3850 0.77 0.0010521296 -97.969347 0 -97.959231 + 3900 0.78 0.0010500386 -99.156876 0 -99.146899 + 3950 0.79 0.0010447106 -100.32743 0 -100.31756 + 4000 0.8 0.0010369046 -101.4796 0 -101.46978 + 4050 0.81 0.0010263688 -102.61044 0 -102.60064 + 4100 0.82 0.0010126985 -103.71619 0 -103.70639 + 4150 0.83 0.00099632366 -104.79338 0 -104.78358 + 4200 0.84 0.00097891183 -105.8398 0 -105.82998 + 4250 0.85 0.00096288003 -106.85496 0 -106.84515 + 4300 0.86 0.00095034371 -107.84011 0 -107.83029 + 4350 0.87 0.00094219371 -108.7976 0 -108.78778 + 4400 0.88 0.00093779663 -109.73016 0 -109.72031 + 4450 0.89 0.00093544766 -110.63996 0 -110.63008 + 4500 0.9 0.00093342739 -111.52805 0 -111.51812 + 4550 0.91 0.00093110855 -112.39417 0 -112.38416 + 4600 0.92 0.00092926746 -113.23706 0 -113.22697 + 4650 0.93 0.00092921608 -114.05512 0 -114.04495 + 4700 0.94 0.0009314263 -114.84701 0 -114.83675 + 4750 0.95 0.0009347987 -115.61197 0 -115.60164 + 4800 0.96 0.00093697985 -116.3499 0 -116.33951 + 4850 0.97 0.00093516726 -117.06128 0 -117.05084 + 4900 0.98 0.00092684316 -117.74695 0 -117.73645 + 4950 0.99 0.00091046061 -118.40798 0 -118.39742 + 5000 1 0.00088619727 -119.04554 0 -119.03492 +Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms + +Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s +98.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.2804 | 6.3487 | 6.4569 | 2.7 | 17.09 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.15385 | 0.27957 | 0.36215 | 14.6 | 0.75 +Output | 10.573 | 10.784 | 10.994 | 4.8 | 29.03 +Modify | 19.48 | 19.707 | 19.925 | 3.7 | 53.06 +Other | | 0.02255 | | | 0.06 + +Nlocal: 1445 ave 1445 max 1445 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 555 ave 555 max 555 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 23120 ave 23120 max 23120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 92480 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:37 diff --git a/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy new file mode 100644 index 0000000000000000000000000000000000000000..3af058baf721c59a57e61971e1211bee9a8e9305 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1,6006 @@ +Cobalt EAM potential: G. P. Purja Pun and Y. Mishin, Phys. Rev. B xx, 004100 (2012) (in press) +Data below r = 1.5 A is extrapolated. F(Rho) data not extrapolated. +Created on Wed Sep 26 17:29:54 2012 +1 Co +10000 4.788742913000000e-04 10000 6.499539000000001e-04 6.499539000000000e+00 +27 5.893320000000000e+01 2.507000000000000e+00 hcp + -1.680303080000000e-02 -1.879913964471138e-02 -2.091739081044659e-02 -2.303564197615629e-02 -2.503175082079116e-02 + -2.681996612041136e-02 -2.846010103933253e-02 -3.003179469400266e-02 -3.154842562124295e-02 -3.300931506782415e-02 + -3.442381570000001e-02 -3.580233366714632e-02 -3.714945763166951e-02 -3.846832763111274e-02 -3.976210669053554e-02 + -4.103374908125148e-02 -4.228535107207521e-02 -4.351872320172212e-02 -4.473539109100971e-02 -4.593674531110434e-02 + -4.712392115246503e-02 -4.829795108118731e-02 -4.945971154662068e-02 -5.061001094949964e-02 -5.174954151284258e-02 + -5.287894548568519e-02 -5.399878139884967e-02 -5.510957102742049e-02 -5.621177284174523e-02 -5.730581735016625e-02 + -5.839208651773948e-02 -5.947094067448531e-02 -6.054270215356945e-02 -6.160767623453070e-02 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1.364901589086205e-09 + 1.054599065845252e-09 8.004535320102697e-10 5.952414597054672e-10 4.322622496028902e-10 3.052766304104823e-10 + 2.085502003918036e-10 1.368642901349301e-10 8.546164059834664e-11 5.010215808832263e-11 2.705311520847365e-11 + 1.304599438344934e-11 5.339090781311160e-12 1.692041320615927e-12 3.321208355096226e-13 6.781366937015517e-15 diff --git a/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat new file mode 100644 index 0000000000000000000000000000000000000000..dce45c090dfb92ea3d9dd2c31fe925df9dc1bc01 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat @@ -0,0 +1,5 @@ +2.503 0.01476 +3.54 0.001497 +4.33 0.001578 +5.01 -0.001224 +5.597 0.000354 diff --git a/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..09be6db3e4de0ed5b564fdcc460c0ba3d9efbdb2 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_fcc_cobalt.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc new file mode 100644 index 0000000000000000000000000000000000000000..fd6833727bebf8b13f795cfdec73100f8fc8a6f2 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc @@ -0,0 +1,63 @@ +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..d832b0001a894877a2e512db25db55f4676ac61a --- /dev/null +++ b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +Lattice spacing in x,y,z = 3.54 3.54 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.7 17.7 17.7) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000651121 secs + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes +Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng + 0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636 + 50 0.005 0.049785486 0 0 1 -187.94112 95.094679 -2372.4636 + 100 0.01 0.049785486 0 0 1 -187.94071 81.578321 -2372.4636 + 150 0.015 0.049785486 0 0 1 -187.93912 62.802727 -2372.4636 + 200 0.02 0.049785486 0 0 1 -187.93551 43.35108 -2372.4636 + 250 0.025 0.049785486 0 0 1 -187.92942 27.749821 -2372.4636 + 300 0.03 0.049785486 0 0 1 -187.92118 19.149389 -2372.4636 + 350 0.035 0.049785486 0 0 1 -187.91199 18.453387 -2372.4636 + 400 0.04 0.049785486 0 0 1 -187.90364 24.249423 -2372.4636 + 450 0.045 0.049785486 0 0 1 -187.89806 33.548008 -2372.4636 + 500 0.05 0.049785486 0 0 1 -187.89668 42.973172 -2372.4636 + 550 0.055 0.049785486 0 0 1 -187.9 49.902539 -2372.4636 + 600 0.06 0.049785486 0 0 1 -187.90735 53.166772 -2372.4636 + 650 0.065 0.049785486 0 0 1 -187.91706 53.153416 -2372.4636 + 700 0.07 0.049785486 0 0 1 -187.92692 51.377187 -2372.4636 + 750 0.075 0.049785486 0 0 1 -187.9348 49.725449 -2372.4636 + 800 0.08 0.049785486 0 0 1 -187.93921 49.663576 -2372.4636 + 850 0.085 0.049785486 0 0 1 -187.93974 51.681567 -2372.4636 + 900 0.09 0.049785486 0 0 1 -187.937 55.166554 -2372.4636 + 950 0.095 0.049785486 0 0 1 -187.93239 58.718232 -2372.4636 + 1000 0.1 0.049785486 0 0 1 -187.92755 60.75567 -2372.4636 +Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms + +Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.142 | 2.142 | 2.142 | 0.0 | 51.86 +Neigh | 0.0094573 | 0.0094573 | 0.0094573 | 0.0 | 0.23 +Comm | 0.023293 | 0.023293 | 0.023293 | 0.0 | 0.56 +Output | 0.00031972 | 0.00031972 | 0.00031972 | 0.0 | 0.01 +Modify | 1.9488 | 1.9488 | 1.9488 | 0.0 | 47.18 +Other | | 0.006488 | | | 0.16 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24065 ave 24065 max 24065 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 48130 ave 48130 max 48130 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 48130 +Ave neighs/atom = 96.26 +Neighbor list builds = 6 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..358d7cfc7ab3c195d3056dc21fcbc358b18ac48e --- /dev/null +++ b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 @@ -0,0 +1,142 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +Lattice spacing in x,y,z = 3.54 3.54 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.7 17.7 17.7) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000240088 secs + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes +Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng + 0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636 + 50 0.005 0.049785486 0 0 1 -187.94101 95.174807 -2372.4636 + 100 0.01 0.049785486 0 0 1 -187.94029 81.854304 -2372.4636 + 150 0.015 0.049785486 0 0 1 -187.93834 63.270938 -2372.4636 + 200 0.02 0.049785486 0 0 1 -187.93446 43.867262 -2372.4636 + 250 0.025 0.049785486 0 0 1 -187.92831 28.075261 -2372.4636 + 300 0.03 0.049785486 0 0 1 -187.92031 19.046222 -2372.4636 + 350 0.035 0.049785486 0 0 1 -187.91161 17.79071 -2372.4636 + 400 0.04 0.049785486 0 0 1 -187.9039 23.079994 -2372.4636 + 450 0.045 0.049785486 0 0 1 -187.89895 32.127316 -2372.4636 + 500 0.05 0.049785486 0 0 1 -187.89801 41.709644 -2372.4636 + 550 0.055 0.049785486 0 0 1 -187.90146 49.246292 -2372.4636 + 600 0.06 0.049785486 0 0 1 -187.90859 53.465535 -2372.4636 + 650 0.065 0.049785486 0 0 1 -187.91778 54.522857 -2372.4636 + 700 0.07 0.049785486 0 0 1 -187.9269 53.635521 -2372.4636 + 750 0.075 0.049785486 0 0 1 -187.93396 52.419678 -2372.4636 + 800 0.08 0.049785486 0 0 1 -187.9376 52.176558 -2372.4636 + 850 0.085 0.049785486 0 0 1 -187.93744 53.380592 -2372.4636 + 900 0.09 0.049785486 0 0 1 -187.93412 55.551378 -2372.4636 + 950 0.095 0.049785486 0 0 1 -187.92902 57.540047 -2372.4636 + 1000 0.1 0.049785486 0 0 1 -187.92378 58.088674 -2372.4636 +Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms + +Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s +97.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.54717 | 0.57392 | 0.58784 | 2.1 | 33.48 +Neigh | 0.0023484 | 0.0025793 | 0.0026793 | 0.3 | 0.15 +Comm | 0.058548 | 0.073335 | 0.10006 | 5.9 | 4.28 +Output | 0.00042272 | 0.00079203 | 0.0018559 | 0.0 | 0.05 +Modify | 1.0577 | 1.0611 | 1.0625 | 0.2 | 61.90 +Other | | 0.00239 | | | 0.14 + +Nlocal: 125 ave 133 max 116 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1099 ave 1108 max 1091 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Neighs: 6032.5 ave 6417 max 5489 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +FullNghs: 12065 ave 13062 max 10970 min +Histogram: 1 0 0 0 0 2 0 0 0 1 + +Total # of neighbors = 48260 +Ave neighs/atom = 96.52 +Neighbor list builds = 6 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy new file mode 120000 index 0000000000000000000000000000000000000000..6a47c9eebef2dc333daa871fc882f2afc038bd4c --- /dev/null +++ b/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1 @@ +../cobalt_fcc/Co_PurjaPun_2012.eam.alloy \ No newline at end of file diff --git a/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..fa7dba417e94468ce01ea5225db9a00aed2205dd --- /dev/null +++ b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_hcp_co.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat new file mode 100644 index 0000000000000000000000000000000000000000..0968fa3edb793657830c65c64e99656de20a8274 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat @@ -0,0 +1,9 @@ +2.25569176882662 73.37931034482759 +2.3817863397548162 47.99999999999999 +2.4518388791593697 34.39080459770115 +2.507880910683012 31.816091954022987 +2.5359019264448337 28.137931034482747 +2.5779334500875657 25.011494252873554 +2.6339754816112086 19.126436781609186 +2.760070052539404 13.241379310344826 +3.5446584938704033 6.068965517241367 diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp new file mode 100644 index 0000000000000000000000000000000000000000..35aa1df86c4a2c2bdfff40f3e35f032939311b90 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp @@ -0,0 +1,59 @@ +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 +#set group all spin 1.72 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 20000 diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..4bb513de18886c91f1a4ef0fb3909e188d998489 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 @@ -0,0 +1,318 @@ +LAMMPS (11 May 2018) +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000801802 secs + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 4 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 1 -187.29499 100.00543 -2375.8943 + 10 0.001 1 -187.29714 99.845593 -2375.8943 + 20 0.002 1 -187.30356 99.367234 -2375.8943 + 30 0.003 1 -187.31419 98.573996 -2375.8943 + 40 0.004 1 -187.32896 97.472027 -2375.8943 + 50 0.005 1 -187.34772 96.069944 -2375.8943 + 60 0.006 1 -187.37032 94.378764 -2375.8943 + 70 0.007 1 -187.39656 92.411827 -2375.8943 + 80 0.008 1 -187.4262 90.184697 -2375.8943 + 90 0.009 1 -187.459 87.715037 -2375.8943 + 100 0.01 1 -187.49466 85.022479 -2375.8943 + 110 0.011 1 -187.53289 82.128462 -2375.8943 + 120 0.012 1 -187.57334 79.05606 -2375.8943 + 130 0.013 1 -187.61568 75.82979 -2375.8943 + 140 0.014 1 -187.65953 72.475403 -2375.8943 + 150 0.015 1 -187.70453 69.019658 -2375.8943 + 160 0.016 1 -187.75028 65.490086 -2375.8943 + 170 0.017 1 -187.79642 61.914735 -2375.8943 + 180 0.018 1 -187.84254 58.321911 -2375.8943 + 190 0.019 1 -187.88828 54.739907 -2375.8943 + 200 0.02 1 -187.93324 51.196728 -2375.8943 + 210 0.021 1 -187.97708 47.719812 -2375.8943 + 220 0.022 1 -188.01947 44.335762 -2375.8943 + 230 0.023 1 -188.06003 41.07007 -2375.8943 + 240 0.024 1 -188.09853 37.946852 -2375.8944 + 250 0.025 1 -188.13457 34.988599 -2375.8944 + 260 0.026 1 -188.16795 32.215943 -2375.8944 + 270 0.027 1 -188.19851 29.647465 -2375.8944 + 280 0.028 1 -188.22593 27.299481 -2375.8944 + 290 0.029 1 -188.25011 25.185896 -2375.8944 + 300 0.03 1 -188.27095 23.318075 -2375.8945 + 310 0.031 1 -188.2883 21.70475 -2375.8945 + 320 0.032 1 -188.30213 20.35194 -2375.8945 + 330 0.033 1 -188.31251 19.262946 -2375.8945 + 340 0.034 1 -188.31928 18.438347 -2375.8945 + 350 0.035 1 -188.32258 17.876036 -2375.8945 + 360 0.036 1 -188.32249 17.571322 -2375.8945 + 370 0.037 1 -188.31913 17.517032 -2375.8945 + 380 0.038 1 -188.31264 17.703653 -2375.8945 + 390 0.039 1 -188.30321 18.119513 -2375.8945 + 400 0.04 1 -188.29102 18.750969 -2375.8945 + 410 0.041 1 -188.2763 19.582631 -2375.8945 + 420 0.042 1 -188.25929 20.597597 -2375.8945 + 430 0.043 1 -188.24025 21.777699 -2375.8945 + 440 0.044 1 -188.21945 23.103765 -2375.8945 + 450 0.045 1 -188.19719 24.555878 -2375.8946 + 460 0.046 1 -188.17368 26.113643 -2375.8946 + 470 0.047 1 -188.1493 27.756439 -2375.8946 + 480 0.048 1 -188.12429 29.463677 -2375.8946 + 490 0.049 1 -188.09895 31.21504 -2375.8946 + 500 0.05 1 -188.07354 32.990713 -2375.8946 + 510 0.051 1 -188.04832 34.771601 -2375.8945 + 520 0.052 1 -188.02358 36.539517 -2375.8945 + 530 0.053 1 -187.99951 38.27736 -2375.8945 + 540 0.054 1 -187.97636 39.969275 -2375.8945 + 550 0.055 1 -187.95437 41.600775 -2375.8945 + 560 0.056 1 -187.93364 43.158863 -2375.8944 + 570 0.057 1 -187.9144 44.632119 -2375.8944 + 580 0.058 1 -187.89669 46.010765 -2375.8944 + 590 0.059 1 -187.88074 47.286714 -2375.8944 + 600 0.06 1 -187.86658 48.453573 -2375.8944 + 610 0.061 1 -187.85422 49.506668 -2375.8943 + 620 0.062 1 -187.84377 50.443021 -2375.8943 + 630 0.063 1 -187.8352 51.261297 -2375.8943 + 640 0.064 1 -187.8285 51.961764 -2375.8943 + 650 0.065 1 -187.8236 52.54622 -2375.8943 + 660 0.066 1 -187.8205 53.017899 -2375.8943 + 670 0.067 1 -187.81909 53.381374 -2375.8943 + 680 0.068 1 -187.81926 53.64244 -2375.8943 + 690 0.069 1 -187.82092 53.807997 -2375.8943 + 700 0.07 1 -187.82391 53.885909 -2375.8943 + 710 0.071 1 -187.82814 53.884865 -2375.8943 + 720 0.072 1 -187.83339 53.814238 -2375.8943 + 730 0.073 1 -187.83952 53.68392 -2375.8943 + 740 0.074 1 -187.84635 53.504185 -2375.8943 + 750 0.075 1 -187.85375 53.285525 -2375.8943 + 760 0.076 1 -187.86153 53.038494 -2375.8943 + 770 0.077 1 -187.86952 52.773567 -2375.8943 + 780 0.078 1 -187.87758 52.500994 -2375.8943 + 790 0.079 1 -187.88549 52.230655 -2375.8943 + 800 0.08 1 -187.89313 51.971933 -2375.8943 + 810 0.081 1 -187.90035 51.733593 -2375.8943 + 820 0.082 1 -187.90702 51.523671 -2375.8943 + 830 0.083 1 -187.91302 51.349376 -2375.8943 + 840 0.084 1 -187.91824 51.217006 -2375.8943 + 850 0.085 1 -187.9226 51.131875 -2375.8943 + 860 0.086 1 -187.92602 51.098259 -2375.8943 + 870 0.087 1 -187.92844 51.119356 -2375.8943 + 880 0.088 1 -187.92979 51.197261 -2375.8943 + 890 0.089 1 -187.93011 51.332955 -2375.8943 + 900 0.09 1 -187.92937 51.526314 -2375.8943 + 910 0.091 1 -187.92757 51.77613 -2375.8943 + 920 0.092 1 -187.92475 52.080145 -2375.8943 + 930 0.093 1 -187.92096 52.435106 -2375.8943 + 940 0.094 1 -187.91624 52.836825 -2375.8943 + 950 0.095 1 -187.91068 53.280251 -2375.8943 + 960 0.096 1 -187.90435 53.759559 -2375.8943 + 970 0.097 1 -187.89734 54.268246 -2375.8943 + 980 0.098 1 -187.88981 54.799223 -2375.8943 + 990 0.099 1 -187.88185 55.344928 -2375.8943 + 1000 0.1 1 -187.87357 55.897438 -2375.8943 + 1010 0.101 1 -187.86511 56.448585 -2375.8943 + 1020 0.102 1 -187.8566 56.990069 -2375.8943 + 1030 0.103 1 -187.84817 57.513575 -2375.8943 + 1040 0.104 1 -187.83995 58.010887 -2375.8943 + 1050 0.105 1 -187.83208 58.474004 -2375.8943 + 1060 0.106 1 -187.8247 58.89524 -2375.8943 + 1070 0.107 1 -187.81789 59.267328 -2375.8943 + 1080 0.108 1 -187.81177 59.583518 -2375.8943 + 1090 0.109 1 -187.80646 59.837665 -2375.8943 + 1100 0.11 1 -187.80204 60.024306 -2375.8943 + 1110 0.111 1 -187.79861 60.138734 -2375.8943 + 1120 0.112 1 -187.79625 60.177056 -2375.8943 + 1130 0.113 1 -187.79497 60.136244 -2375.8943 + 1140 0.114 1 -187.79485 60.014176 -2375.8943 + 1150 0.115 1 -187.7959 59.809665 -2375.8943 + 1160 0.116 1 -187.79811 59.52248 -2375.8943 + 1170 0.117 1 -187.80157 59.153353 -2375.8943 + 1180 0.118 1 -187.80618 58.703971 -2375.8943 + 1190 0.119 1 -187.81193 58.176956 -2375.8943 + 1200 0.12 1 -187.81879 57.575849 -2375.8943 + 1210 0.121 1 -187.82668 56.905072 -2375.8943 + 1220 0.122 1 -187.83554 56.169878 -2375.8943 + 1230 0.123 1 -187.84528 55.376297 -2375.8943 + 1240 0.124 1 -187.85581 54.53107 -2375.8943 + 1250 0.125 1 -187.86702 53.641573 -2375.8943 + 1260 0.126 1 -187.8788 52.715739 -2375.8943 + 1270 0.127 1 -187.89103 51.761969 -2375.8943 + 1280 0.128 1 -187.90358 50.789036 -2375.8943 + 1290 0.129 1 -187.91632 49.805988 -2375.8943 + 1300 0.13 1 -187.92911 48.822045 -2375.8943 + 1310 0.131 1 -187.94182 47.846491 -2375.8943 + 1320 0.132 1 -187.95428 46.888574 -2375.8943 + 1330 0.133 1 -187.96643 45.957394 -2375.8943 + 1340 0.134 1 -187.9781 45.061794 -2375.8943 + 1350 0.135 1 -187.9892 44.210263 -2375.8943 + 1360 0.136 1 -187.99955 43.410832 -2375.8943 + 1370 0.137 1 -188.00907 42.670979 -2375.8943 + 1380 0.138 1 -188.01767 41.997547 -2375.8943 + 1390 0.139 1 -188.02525 41.396655 -2375.8943 + 1400 0.14 1 -188.03177 40.873631 -2375.8944 + 1410 0.141 1 -188.03711 40.432952 -2375.8944 + 1420 0.142 1 -188.04124 40.078172 -2375.8944 + 1430 0.143 1 -188.04413 39.811902 -2375.8944 + 1440 0.144 1 -188.04575 39.635775 -2375.8944 + 1450 0.145 1 -188.04607 39.550435 -2375.8943 + 1460 0.146 1 -188.04515 39.555512 -2375.8943 + 1470 0.147 1 -188.04298 39.649651 -2375.8943 + 1480 0.148 1 -188.03961 39.830523 -2375.8943 + 1490 0.149 1 -188.03508 40.094865 -2375.8943 + 1500 0.15 1 -188.02944 40.438519 -2375.8943 + 1510 0.151 1 -188.02275 40.856491 -2375.8943 + 1520 0.152 1 -188.01515 41.343019 -2375.8943 + 1530 0.153 1 -188.00671 41.891643 -2375.8943 + 1540 0.154 1 -187.99753 42.495295 -2375.8943 + 1550 0.155 1 -187.98772 43.14639 -2375.8943 + 1560 0.156 1 -187.9774 43.836918 -2375.8943 + 1570 0.157 1 -187.9667 44.558553 -2375.8943 + 1580 0.158 1 -187.95576 45.302751 -2375.8943 + 1590 0.159 1 -187.94466 46.060862 -2375.8943 + 1600 0.16 1 -187.93356 46.824226 -2375.8943 + 1610 0.161 1 -187.92257 47.584289 -2375.8943 + 1620 0.162 1 -187.91183 48.332703 -2375.8943 + 1630 0.163 1 -187.90145 49.061422 -2375.8943 + 1640 0.164 1 -187.89155 49.762798 -2375.8943 + 1650 0.165 1 -187.88222 50.429671 -2375.8943 + 1660 0.166 1 -187.87357 51.055445 -2375.8943 + 1670 0.167 1 -187.86569 51.634167 -2375.8943 + 1680 0.168 1 -187.85864 52.160588 -2375.8943 + 1690 0.169 1 -187.85249 52.630219 -2375.8943 + 1700 0.17 1 -187.8473 53.039377 -2375.8943 + 1710 0.171 1 -187.84311 53.385221 -2375.8943 + 1720 0.172 1 -187.83994 53.665778 -2375.8943 + 1730 0.173 1 -187.83781 53.879954 -2375.8943 + 1740 0.174 1 -187.83671 54.027539 -2375.8943 + 1750 0.175 1 -187.83663 54.109201 -2375.8943 + 1760 0.176 1 -187.83753 54.126472 -2375.8943 + 1770 0.177 1 -187.83941 54.081708 -2375.8943 + 1780 0.178 1 -187.8422 53.97806 -2375.8943 + 1790 0.179 1 -187.84584 53.819424 -2375.8943 + 1800 0.18 1 -187.85025 53.610389 -2375.8943 + 1810 0.181 1 -187.85535 53.356163 -2375.8943 + 1820 0.182 1 -187.86105 53.06251 -2375.8943 + 1830 0.183 1 -187.86723 52.735671 -2375.8943 + 1840 0.184 1 -187.87384 52.382262 -2375.8943 + 1850 0.185 1 -187.88075 52.009201 -2375.8943 + 1860 0.186 1 -187.88784 51.623613 -2375.8943 + 1870 0.187 1 -187.89501 51.232726 -2375.8943 + 1880 0.188 1 -187.90214 50.843782 -2375.8943 + 1890 0.189 1 -187.90912 50.463929 -2375.8943 + 1900 0.19 1 -187.91585 50.100133 -2375.8943 + 1910 0.191 1 -187.92222 49.759075 -2375.8943 + 1920 0.192 1 -187.92814 49.447064 -2375.8943 + 1930 0.193 1 -187.93351 49.169949 -2375.8943 + 1940 0.194 1 -187.93826 48.933036 -2375.8943 + 1950 0.195 1 -187.94232 48.741013 -2375.8943 + 1960 0.196 1 -187.94561 48.597888 -2375.8943 + 1970 0.197 1 -187.94809 48.506926 -2375.8943 + 1980 0.198 1 -187.94972 48.470605 -2375.8943 + 1990 0.199 1 -187.95047 48.490576 -2375.8943 + 2000 0.2 1 -187.95033 48.567643 -2375.8943 +Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms + +Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.9958 | 4.9958 | 4.9958 | 0.0 | 47.40 +Neigh | 0.020741 | 0.020741 | 0.020741 | 0.0 | 0.20 +Comm | 0.05899 | 0.05899 | 0.05899 | 0.0 | 0.56 +Output | 1.1598 | 1.1598 | 1.1598 | 0.0 | 11.00 +Modify | 4.2885 | 4.2885 | 4.2885 | 0.0 | 40.69 +Other | | 0.01522 | | | 0.14 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2444 ave 2444 max 2444 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 27041 ave 27041 max 27041 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 54082 ave 54082 max 54082 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 54082 +Ave neighs/atom = 108.164 +Neighbor list builds = 12 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..4e7e6b1b976dbccb98b136c39daa3ebc0689e3b6 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 @@ -0,0 +1,318 @@ +LAMMPS (11 May 2018) +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000241518 secs + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 4 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 1 -187.29499 100.00543 -2375.8943 + 10 0.001 1 -187.29721 99.841045 -2375.8943 + 20 0.002 1 -187.30385 99.349208 -2375.8943 + 30 0.003 1 -187.31485 98.533905 -2375.8943 + 40 0.004 1 -187.33011 97.401749 -2375.8943 + 50 0.005 1 -187.34949 95.961938 -2375.8943 + 60 0.006 1 -187.37283 94.22618 -2375.8943 + 70 0.007 1 -187.39992 92.208606 -2375.8943 + 80 0.008 1 -187.43051 89.92566 -2375.8943 + 90 0.009 1 -187.46434 87.39597 -2375.8943 + 100 0.01 1 -187.5011 84.640195 -2375.8943 + 110 0.011 1 -187.54047 81.680862 -2375.8943 + 120 0.012 1 -187.5821 78.542172 -2375.8943 + 130 0.013 1 -187.62564 75.249797 -2375.8943 + 140 0.014 1 -187.67069 71.830656 -2375.8943 + 150 0.015 1 -187.71686 68.312673 -2375.8943 + 160 0.016 1 -187.76377 64.724523 -2375.8943 + 170 0.017 1 -187.81099 61.095365 -2375.8943 + 180 0.018 1 -187.85814 57.454566 -2375.8943 + 190 0.019 1 -187.90481 53.831412 -2375.8943 + 200 0.02 1 -187.95061 50.254822 -2375.8943 + 210 0.021 1 -187.99517 46.753056 -2375.8943 + 220 0.022 1 -188.03812 43.353428 -2375.8943 + 230 0.023 1 -188.07913 40.082023 -2375.8943 + 240 0.024 1 -188.11787 36.963429 -2375.8943 + 250 0.025 1 -188.15409 34.020481 -2375.8943 + 260 0.026 1 -188.1875 31.27403 -2375.8943 + 270 0.027 1 -188.21782 28.74271 -2375.8943 + 280 0.028 1 -188.2449 26.44276 -2375.8943 + 290 0.029 1 -188.26857 24.387875 -2375.8943 + 300 0.03 1 -188.28877 22.589076 -2375.8944 + 310 0.031 1 -188.30529 21.054615 -2375.8944 + 320 0.032 1 -188.31814 19.789913 -2375.8944 + 330 0.033 1 -188.3273 18.797563 -2375.8944 + 340 0.034 1 -188.33284 18.077336 -2375.8944 + 350 0.035 1 -188.33478 17.626237 -2375.8945 + 360 0.036 1 -188.33319 17.438611 -2375.8945 + 370 0.037 1 -188.32824 17.506247 -2375.8945 + 380 0.038 1 -188.32007 17.818564 -2375.8945 + 390 0.039 1 -188.30888 18.362769 -2375.8945 + 400 0.04 1 -188.2949 19.124086 -2375.8945 + 410 0.041 1 -188.27837 20.085983 -2375.8945 + 420 0.042 1 -188.25957 21.230423 -2375.8945 + 430 0.043 1 -188.23868 22.538112 -2375.8945 + 440 0.044 1 -188.21604 23.988778 -2375.8945 + 450 0.045 1 -188.19195 25.561447 -2375.8945 + 460 0.046 1 -188.16672 27.234703 -2375.8945 + 470 0.047 1 -188.14064 28.986964 -2375.8946 + 480 0.048 1 -188.11402 30.796738 -2375.8946 + 490 0.049 1 -188.08713 32.642869 -2375.8945 + 500 0.05 1 -188.06032 34.504776 -2375.8945 + 510 0.051 1 -188.03383 36.362662 -2375.8945 + 520 0.052 1 -188.00793 38.197721 -2375.8945 + 530 0.053 1 -187.98284 39.992314 -2375.8945 + 540 0.054 1 -187.95884 41.730127 -2375.8945 + 550 0.055 1 -187.93612 43.396298 -2375.8945 + 560 0.056 1 -187.91489 44.97754 -2375.8945 + 570 0.057 1 -187.89524 46.462224 -2375.8945 + 580 0.058 1 -187.87735 47.840443 -2375.8945 + 590 0.059 1 -187.8613 49.104064 -2375.8945 + 600 0.06 1 -187.84719 50.246744 -2375.8945 + 610 0.061 1 -187.83509 51.26393 -2375.8944 + 620 0.062 1 -187.82506 52.152839 -2375.8944 + 630 0.063 1 -187.81706 52.912413 -2375.8944 + 640 0.064 1 -187.81109 53.543272 -2375.8944 + 650 0.065 1 -187.80708 54.047636 -2375.8944 + 660 0.066 1 -187.80499 54.429234 -2375.8944 + 670 0.067 1 -187.8047 54.693202 -2375.8944 + 680 0.068 1 -187.80613 54.845965 -2375.8944 + 690 0.069 1 -187.80914 54.895106 -2375.8944 + 700 0.07 1 -187.81356 54.849238 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-2375.8943 + 2000 0.2 1 -187.96171 47.851079 -2375.8943 +Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms + +Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s +96.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2934 | 1.3683 | 1.432 | 4.2 | 31.09 +Neigh | 0.005039 | 0.0053418 | 0.0054908 | 0.2 | 0.12 +Comm | 0.12642 | 0.1922 | 0.26891 | 11.6 | 4.37 +Output | 0.39256 | 0.40875 | 0.43431 | 2.5 | 9.29 +Modify | 2.395 | 2.4202 | 2.4352 | 1.0 | 54.99 +Other | | 0.006007 | | | 0.14 + +Nlocal: 125 ave 130 max 122 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 1324 ave 1330 max 1316 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 6747 ave 6959 max 6652 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +FullNghs: 13494 ave 14060 max 13186 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 53976 +Ave neighs/atom = 107.952 +Neighbor list builds = 12 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/iron/Fe_Mishin2006.eam.alloy b/examples/SPIN/iron/Fe_Mishin2006.eam.alloy new file mode 100644 index 0000000000000000000000000000000000000000..69231bb7eeed5677009482896fe520f4445413dd --- /dev/null +++ b/examples/SPIN/iron/Fe_Mishin2006.eam.alloy @@ -0,0 +1,15009 @@ +comment 1 +comment 2 +Converted by Ganga P Purja Pun using C++ code on Mon Nov 3 10:48:17 2014 +1 Fe +5001 2.400000000000000e-03 5001 1.134673400048920e-03 5.673367000244601e+00 +26 5.584700000000000e+01 2.855300000000000e+00 BCC + 0.000000000000000e+00 + -2.338738741480766e-02 + -4.628214468925276e-02 + -6.912258036387915e-02 + -9.175603963501618e-02 + -1.141497214000000e-01 + -1.363388222824136e-01 + -1.583226111166723e-01 + -1.800965752913192e-01 + -2.016645989796093e-01 + -2.230289901000000e-01 + -2.441907391820846e-01 + 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-2.316338735426513e-07 + -1.843129441850586e-07 + -1.446395043479685e-07 + -1.117434618507405e-07 + -8.480406305106530e-08 + -6.305553831873507e-08 + -4.578544870958251e-08 + -3.233089380928512e-08 + -2.208448022054805e-08 + -1.449165750478591e-08 + -9.047683233008124e-09 + -5.303766739728543e-09 + -2.863504097386866e-09 + -1.380623394721897e-09 + -5.650641971230870e-10 + -1.790372475752245e-10 + -3.511990521548007e-11 + -8.192061809269277e-13 + 0.000000000000000e+00 diff --git a/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat new file mode 100644 index 0000000000000000000000000000000000000000..58134f244466c5a60bb103b73e6f8ba61414e14b --- /dev/null +++ b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat @@ -0,0 +1,5 @@ +2.4824 0.01948336 +2.8665 0.01109 +4.0538 -0.0002176 +4.753 -0.001714 +4.965 -0.001986 diff --git a/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..ccf84fc233bbc4a29bcc01ab4d6336e00ba2ab6d --- /dev/null +++ b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_bcc_iron.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/iron/fe_dd.dat b/examples/SPIN/iron/fe_dd.dat new file mode 100644 index 0000000000000000000000000000000000000000..a4b4c9a0d7c06a14f1a42cd33846405299e368a9 --- /dev/null +++ b/examples/SPIN/iron/fe_dd.dat @@ -0,0 +1,19 @@ + 6 8 + Optimal parameter set + 1 4.100199340884814 F + 2 1.565647547483517 F + 1 0.9332056681088162 T 3.000000000000000 + 2 -1.162558782567700 T 2.866666666666670 + 3 -0.3502026949249225 T 2.733333333333330 + 4 0.4287820835430028 T 2.600000000000000 + 5 4.907925057809273 T 2.400000000000000 + 6 -5.307049068415304 T 2.300000000000000 + 1 -0.1960674387419232 F 4.100000000000000 + 2 0.3687525935422963 F 3.800000000000000 + 3 -1.505333614924853 F 3.500000000000000 + 4 4.948907078156191 T 3.200000000000000 + 5 -4.894613262753399 T 2.900000000000000 + 6 3.468897724782442 T 2.600000000000000 + 7 -1.792218099820337 T 2.400000000000000 + 8 80.22069592246987 T 2.300000000000000 + diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron new file mode 100644 index 0000000000000000000000000000000000000000..c2d5082cb6a27751627d72d850ed11ad8feade66 --- /dev/null +++ b/examples/SPIN/iron/in.spin.iron @@ -0,0 +1,56 @@ +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.1 b/examples/SPIN/iron/log.11May18.spin.iron.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..1b27478002833f74c99fc56572e8bc786c9f3b01 --- /dev/null +++ b/examples/SPIN/iron/log.11May18.spin.iron.g++.1 @@ -0,0 +1,1115 @@ +LAMMPS (11 May 2018) +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 250 atoms + Time spent = 0.000727415 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456974 9316.7659 96.663685 -0.86504718 3.1111957 -1070.7504 -1067.6392 + 100 0.01 0.076456983 9488.3743 86.965803 -0.88035771 2.7990619 -1070.4383 -1067.6392 + 150 0.015 0.076456973 9589.0566 72.421197 -0.8996913 2.3309324 -1069.9702 -1067.6392 + 200 0.02 0.076456944 9415.3095 55.633188 -0.921682 1.7905973 -1069.4298 -1067.6392 + 250 0.025 0.076456953 8878.9394 39.802206 -0.94649004 1.2810649 -1068.9203 -1067.6392 + 300 0.03 0.076457027 8203.3388 27.882295 -0.97253854 0.8974133 -1068.5366 -1067.6392 + 350 0.035 0.076457103 7720.309 21.776538 -0.99708692 0.70089477 -1068.3401 -1067.6392 + 400 0.04 0.076457117 7531.0683 21.857102 -1.0190244 0.70348778 -1068.3427 -1067.6392 + 450 0.045 0.076457072 7479.8073 26.959407 -1.0389343 0.86770942 -1068.5069 -1067.6392 + 500 0.05 0.076457001 7461.6683 34.92521 -1.0582008 1.124095 -1068.7633 -1067.6392 + 550 0.055 0.076456962 7396.1112 43.405912 -1.0785156 1.397053 -1069.0363 -1067.6392 + 600 0.06 0.076456997 7121.894 50.544844 -1.102048 1.626825 -1069.2661 -1067.6392 + 650 0.065 0.076457079 6683.4805 55.261218 -1.1296588 1.7786252 -1069.4179 -1067.6392 + 700 0.07 0.076457136 6313.6896 57.25083 -1.1595102 1.8426624 -1069.4819 -1067.6392 + 750 0.075 0.076457132 6199.0363 56.934336 -1.1893875 1.8324758 -1069.4717 -1067.6392 + 800 0.08 0.076457116 6265.997 55.266343 -1.2181223 1.7787901 -1069.418 -1067.6392 + 850 0.085 0.076457116 6326.5886 53.376453 -1.2443326 1.7179626 -1069.3572 -1067.6392 + 900 0.09 0.076457121 6336.1261 52.279557 -1.2676425 1.6826581 -1069.3219 -1067.6392 + 950 0.095 0.076457122 6288.4204 52.667743 -1.2902335 1.6951522 -1069.3344 -1067.6392 + 1000 0.1 0.076457135 6122.1622 54.684094 -1.314147 1.76005 -1069.3993 -1067.6392 + 1050 0.105 0.076457155 5830.2219 57.880399 -1.3392396 1.8629256 -1069.5022 -1067.6392 + 1100 0.11 0.076457162 5477.4214 61.505616 -1.3662331 1.979606 -1069.6188 -1067.6392 + 1150 0.115 0.076457195 5194.1423 64.810972 -1.3984474 2.0859914 -1069.7252 -1067.6392 + 1200 0.12 0.076457219 5096.2484 67.147472 -1.438326 2.1611935 -1069.8004 -1067.6392 + 1250 0.125 0.076457214 5180.7444 67.957533 -1.4822383 2.1872659 -1069.8265 -1067.6392 + 1300 0.13 0.076457208 5332.4483 66.96652 -1.5226303 2.1553694 -1069.7946 -1067.6392 + 1350 0.135 0.076457225 5441.1287 64.471602 -1.5553539 2.0750686 -1069.7143 -1067.6392 + 1400 0.14 0.076457244 5466.8622 61.292592 -1.5804721 1.9727496 -1069.612 -1067.6392 + 1450 0.145 0.07645724 5403.309 58.518161 -1.6006864 1.8834524 -1069.5227 -1067.6392 + 1500 0.15 0.076457224 5275.2171 57.1713 -1.6196756 1.8401027 -1069.4793 -1067.6392 + 1550 0.155 0.076457217 5122.7481 57.878063 -1.6407322 1.8628504 -1069.5021 -1067.6392 + 1600 0.16 0.076457217 4968.5049 60.639452 -1.6657935 1.9517278 -1069.591 -1067.6392 + 1650 0.165 0.076457208 4850.1861 64.668839 -1.690847 2.0814168 -1069.7206 -1067.6392 + 1700 0.17 0.076457217 4809.0194 68.693586 -1.7087416 2.2109564 -1069.8502 -1067.6392 + 1750 0.175 0.076457274 4835.8611 71.611033 -1.7188587 2.3048567 -1069.9441 -1067.6392 + 1800 0.18 0.076457318 4929.7428 72.815077 -1.7280248 2.3436098 -1069.9828 -1067.6392 + 1850 0.185 0.076457279 5036.6365 72.102335 -1.7426092 2.3206696 -1069.9599 -1067.6392 + 1900 0.19 0.076457222 5116.2436 69.579977 -1.7638235 2.2394856 -1069.8787 -1067.6392 + 1950 0.195 0.076457228 5207.2334 65.715745 -1.7895824 2.1151122 -1069.7543 -1067.6392 + 2000 0.2 0.076457288 5216.0413 61.340972 -1.8174915 1.9743068 -1069.6135 -1067.6392 + 2050 0.205 0.076457267 5023.1601 57.468628 -1.8456914 1.8496724 -1069.4889 -1067.6392 + 2100 0.21 0.076457198 4748.7818 55.033266 -1.8742291 1.7712884 -1069.4105 -1067.6392 + 2150 0.215 0.076457199 4558.1302 54.573806 -1.9035225 1.7565003 -1069.3957 -1067.6392 + 2200 0.22 0.076457185 4483.1644 56.074241 -1.9322669 1.804793 -1069.444 -1067.6392 + 2250 0.225 0.076457114 4430.1583 59.0552 -1.9577399 1.9007374 -1069.54 -1067.6392 + 2300 0.23 0.076457092 4353.7973 62.874849 -1.9801275 2.0236758 -1069.6629 -1067.6392 + 2350 0.235 0.076457145 4303.5275 66.892738 -2.0022129 2.1529947 -1069.7922 -1067.6392 + 2400 0.24 0.076457171 4258.6889 70.426826 -2.0233072 2.2667421 -1069.906 -1067.6392 + 2450 0.245 0.076457169 4178.5775 72.910422 -2.0405304 2.3466785 -1069.9859 -1067.6392 + 2500 0.25 0.07645717 4114.786 74.106367 -2.0531755 2.3851709 -1070.0244 -1067.6392 + 2550 0.255 0.076457136 4067.5017 74.169349 -2.0634674 2.3871981 -1070.0264 -1067.6392 + 2600 0.26 0.076457099 4045.3324 73.586199 -2.0755814 2.3684289 -1070.0077 -1067.6392 + 2650 0.265 0.076457099 4137.898 72.914235 -2.0913646 2.3468012 -1069.986 -1067.6392 + 2700 0.27 0.076457106 4332.063 72.583192 -2.1091075 2.3361464 -1069.9754 -1067.6392 + 2750 0.275 0.07645709 4465.1953 72.814559 -2.125099 2.3435931 -1069.9828 -1067.6392 + 2800 0.28 0.076457051 4516.5192 73.652154 -2.1371914 2.3705517 -1070.0098 -1067.6392 + 2850 0.285 0.076457019 4555.5962 75.060211 -2.1489378 2.4158711 -1070.0551 -1067.6392 + 2900 0.29 0.076457069 4544.2734 76.844795 -2.1667679 2.4733094 -1070.1125 -1067.6392 + 2950 0.295 0.076457172 4460.2109 78.48171 -2.1924421 2.5259948 -1070.1652 -1067.6392 + 3000 0.3 0.076457219 4323.2746 79.20682 -2.2209955 2.549333 -1070.1886 -1067.6392 + 3050 0.305 0.076457213 4155.688 78.543529 -2.2505299 2.5279844 -1070.1672 -1067.6392 + 3100 0.31 0.076457203 3969.6188 76.554785 -2.2858382 2.4639752 -1070.1032 -1067.6392 + 3150 0.315 0.076457187 3761.432 73.396149 -2.3245055 2.362312 -1070.0015 -1067.6392 + 3200 0.32 0.076457142 3602.8035 69.313196 -2.3577056 2.230899 -1069.8701 -1067.6392 + 3250 0.325 0.076457116 3505.707 65.032482 -2.3836874 2.0931209 -1069.7324 -1067.6392 + 3300 0.33 0.07645716 3424.8795 61.551539 -2.4057167 1.9810841 -1069.6203 -1067.6392 + 3350 0.335 0.076457236 3335.9672 59.709703 -2.4251844 1.9218031 -1069.561 -1067.6392 + 3400 0.34 0.076457298 3238.0186 60.026953 -2.4425501 1.9320141 -1069.5712 -1067.6392 + 3450 0.345 0.076457297 3185.0674 62.613739 -2.4593531 2.0152718 -1069.6545 -1067.6392 + 3500 0.35 0.07645723 3197.4087 67.011871 -2.4756907 2.1568291 -1069.7961 -1067.6392 + 3550 0.355 0.076457177 3216.1428 72.316209 -2.4911379 2.3275533 -1069.9668 -1067.6392 + 3600 0.36 0.076457165 3241.0326 77.550071 -2.5083858 2.4960092 -1070.1352 -1067.6392 + 3650 0.365 0.076457168 3309.6874 81.877688 -2.5306273 2.6352969 -1070.2745 -1067.6392 + 3700 0.37 0.07645718 3350.748 84.764646 -2.5595247 2.7282159 -1070.3674 -1067.6392 + 3750 0.375 0.07645721 3368.085 86.031781 -2.5938559 2.7689996 -1070.4082 -1067.6392 + 3800 0.38 0.076457208 3425.3173 85.733048 -2.6266899 2.7593847 -1070.3986 -1067.6392 + 3850 0.385 0.076457165 3420.4429 84.240647 -2.6514805 2.7113506 -1070.3506 -1067.6392 + 3900 0.39 0.076457146 3323.0403 82.320886 -2.6700966 2.6495616 -1070.2888 -1067.6392 + 3950 0.395 0.076457179 3273.2625 80.780607 -2.6892405 2.5999865 -1070.2392 -1067.6392 + 4000 0.4 0.076457229 3313.2671 79.92769 -2.709641 2.5725347 -1070.2118 -1067.6392 + 4050 0.405 0.076457272 3381.1117 79.663389 -2.7291493 2.564028 -1070.2033 -1067.6392 + 4100 0.41 0.07645731 3373.3005 79.895158 -2.7514856 2.5714877 -1070.2107 -1067.6392 + 4150 0.415 0.076457296 3279.6989 80.402828 -2.7788004 2.5878274 -1070.2271 -1067.6392 + 4200 0.42 0.076457251 3197.0478 80.770336 -2.8064773 2.599656 -1070.2389 -1067.6392 + 4250 0.425 0.076457243 3160.9065 80.756747 -2.8307967 2.5992186 -1070.2385 -1067.6392 + 4300 0.43 0.076457282 3173.9599 80.446488 -2.852192 2.5892326 -1070.2285 -1067.6392 + 4350 0.435 0.076457289 3185.8003 80.110494 -2.8726607 2.5784184 -1070.2177 -1067.6392 + 4400 0.44 0.076457262 3166.3054 80.045036 -2.8936787 2.5763116 -1070.2155 -1067.6392 + 4450 0.445 0.076457226 3177.4332 80.500194 -2.9171408 2.5909612 -1070.2302 -1067.6392 + 4500 0.45 0.076457174 3238.8362 81.573722 -2.9447352 2.6255135 -1070.2647 -1067.6392 + 4550 0.455 0.07645714 3277.7104 83.104228 -2.975052 2.6747741 -1070.314 -1067.6392 + 4600 0.46 0.076457157 3224.8571 84.845473 -3.0065552 2.7308174 -1070.37 -1067.6392 + 4650 0.465 0.076457215 3112.9952 86.608217 -3.03972 2.7875527 -1070.4268 -1067.6392 + 4700 0.47 0.076457254 3001.141 88.18732 -3.074928 2.8383773 -1070.4776 -1067.6392 + 4750 0.475 0.076457235 2904.0735 89.204263 -3.1082127 2.8711084 -1070.5103 -1067.6392 + 4800 0.48 0.076457195 2832.0276 89.24571 -3.134302 2.8724424 -1070.5117 -1067.6392 + 4850 0.485 0.076457172 2833.7453 88.206351 -3.1541802 2.8389899 -1070.4782 -1067.6392 + 4900 0.49 0.076457184 2941.993 86.310712 -3.1725372 2.7779773 -1070.4172 -1067.6392 + 4950 0.495 0.076457228 3082.4825 84.029047 -3.1931038 2.7045401 -1070.3438 -1067.6392 + 5000 0.5 0.07645727 3155.7095 81.99875 -3.2175967 2.6391934 -1070.2784 -1067.6392 + 5050 0.505 0.076457297 3162.1875 80.72053 -3.2420203 2.5980529 -1070.2373 -1067.6392 + 5100 0.51 0.076457279 3133.3889 80.483768 -3.2606472 2.5904325 -1070.2297 -1067.6392 + 5150 0.515 0.076457223 3144.6361 81.566513 -3.2759117 2.6252815 -1070.2645 -1067.6392 + 5200 0.52 0.076457166 3156.8183 84.062018 -3.2944729 2.7056013 -1070.3448 -1067.6392 + 5250 0.525 0.076457128 3059.9886 87.694328 -3.3209415 2.82251 -1070.4617 -1067.6392 + 5300 0.53 0.076457126 2891.6506 91.782947 -3.3547324 2.9541054 -1070.5933 -1067.6392 + 5350 0.535 0.076457151 2751.9451 95.417928 -3.3914125 3.0711001 -1070.7103 -1067.6392 + 5400 0.54 0.07645725 2681.0265 97.845096 -3.4276651 3.1492204 -1070.7885 -1067.6392 + 5450 0.545 0.076457325 2657.0871 98.736021 -3.4632111 3.1778955 -1070.8171 -1067.6392 + 5500 0.55 0.076457263 2653.1919 98.075727 -3.4957627 3.1566434 -1070.7959 -1067.6392 + 5550 0.555 0.076457185 2644.2053 96.114963 -3.5208827 3.0935347 -1070.7328 -1067.6392 + 5600 0.56 0.076457195 2622.4174 93.525807 -3.5389264 3.0102007 -1070.6494 -1067.6392 + 5650 0.565 0.07645725 2616.3851 91.264369 -3.5558733 2.9374145 -1070.5766 -1067.6392 + 5700 0.57 0.076457256 2608.2454 90.135397 -3.5771374 2.9010777 -1070.5403 -1067.6392 + 5750 0.575 0.076457193 2573.217 90.456889 -3.6030061 2.9114252 -1070.5507 -1067.6392 + 5800 0.58 0.076457145 2565.3325 92.099499 -3.6318265 2.9642939 -1070.6035 -1067.6392 + 5850 0.585 0.076457161 2566.2763 94.62532 -3.6627041 3.0455894 -1070.6848 -1067.6392 + 5900 0.59 0.076457186 2564.6814 97.321391 -3.6927592 3.1323645 -1070.7716 -1067.6392 + 5950 0.595 0.076457195 2570.6317 99.384979 -3.7170023 3.1987827 -1070.838 -1067.6392 + 6000 0.6 0.076457206 2556.8466 100.3814 -3.7363622 3.2308533 -1070.8701 -1067.6392 + 6050 0.605 0.076457195 2521.7989 100.35237 -3.7587516 3.2299188 -1070.8692 -1067.6392 + 6100 0.61 0.076457175 2476.1857 99.370382 -3.7869326 3.1983129 -1070.8375 -1067.6392 + 6150 0.615 0.076457178 2397.2805 97.465979 -3.8168635 3.1370182 -1070.7763 -1067.6392 + 6200 0.62 0.07645713 2286.8528 94.931714 -3.8450242 3.0554509 -1070.6947 -1067.6392 + 6250 0.625 0.076457116 2250.5238 92.438461 -3.8722441 2.9752036 -1070.6144 -1067.6392 + 6300 0.63 0.076457156 2338.521 90.714356 -3.9006124 2.9197119 -1070.5589 -1067.6392 + 6350 0.635 0.07645717 2433.0115 90.142291 -3.9291158 2.9012996 -1070.5405 -1067.6392 + 6400 0.64 0.076457159 2467.5348 90.771111 -3.9562691 2.9215387 -1070.5608 -1067.6392 + 6450 0.645 0.076457107 2475.8592 92.488016 -3.9828131 2.9767986 -1070.616 -1067.6392 + 6500 0.65 0.0764571 2489.7418 95.127451 -4.0122141 3.0617508 -1070.701 -1067.6392 + 6550 0.655 0.076457169 2500.4747 98.171693 -4.0419177 3.1597321 -1070.799 -1067.6392 + 6600 0.66 0.076457208 2530.7924 100.74938 -4.0631997 3.242697 -1070.8819 -1067.6392 + 6650 0.665 0.076457205 2539.1274 102.26227 -4.0743158 3.2913904 -1070.9306 -1067.6392 + 6700 0.67 0.076457193 2456.6296 102.74328 -4.083416 3.3068723 -1070.9461 -1067.6392 + 6750 0.675 0.076457138 2387.5795 102.56259 -4.0973623 3.3010567 -1070.9403 -1067.6392 + 6800 0.68 0.076457109 2401.1036 102.04306 -4.113996 3.284335 -1070.9236 -1067.6392 + 6850 0.685 0.076457149 2426.9334 101.49407 -4.1282015 3.2666654 -1070.9059 -1067.6392 + 6900 0.69 0.076457185 2389.4808 101.35428 -4.1401792 3.2621662 -1070.9014 -1067.6392 + 6950 0.695 0.076457175 2323.8732 101.97431 -4.1517617 3.2821222 -1070.9214 -1067.6392 + 7000 0.7 0.076457145 2273.8742 103.4638 -4.1630859 3.3300628 -1070.9693 -1067.6392 + 7050 0.705 0.076457126 2231.6619 105.80757 -4.1770066 3.4054989 -1071.0447 -1067.6392 + 7100 0.71 0.076457114 2185.0913 108.81901 -4.1989399 3.5024243 -1071.1417 -1067.6392 + 7150 0.715 0.076457137 2139.1488 111.85718 -4.2283649 3.60021 -1071.2394 -1067.6392 + 7200 0.72 0.076457149 2101.4843 113.84985 -4.2560033 3.6643459 -1071.3036 -1067.6392 + 7250 0.725 0.07645712 2118.2459 113.9441 -4.2761251 3.6673792 -1071.3066 -1067.6392 + 7300 0.73 0.076457121 2191.8612 111.95162 -4.2925363 3.6032496 -1071.2425 -1067.6392 + 7350 0.735 0.076457137 2227.2133 108.21226 -4.3103732 3.4828957 -1071.1221 -1067.6392 + 7400 0.74 0.076457111 2182.8818 103.43153 -4.3300151 3.329024 -1070.9683 -1067.6392 + 7450 0.745 0.076457109 2101.9195 98.839733 -4.354205 3.1812335 -1070.8205 -1067.6392 + 7500 0.75 0.076457149 2036.6331 95.828658 -4.3866968 3.0843197 -1070.7235 -1067.6392 + 7550 0.755 0.076457161 1994.7766 95.143411 -4.4221882 3.0622645 -1070.7015 -1067.6392 + 7600 0.76 0.076457127 1970.8688 96.749372 -4.4522754 3.1139536 -1070.7532 -1067.6392 + 7650 0.765 0.076457086 1994.0036 100.15642 -4.4763519 3.223612 -1070.8628 -1067.6392 + 7700 0.77 0.076457048 2073.628 104.50472 -4.498005 3.3635656 -1071.0028 -1067.6392 + 7750 0.775 0.076457027 2167.9613 108.65949 -4.5168957 3.49729 -1071.1365 -1067.6392 + 7800 0.78 0.07645702 2217.2571 111.71851 -4.5326316 3.5957471 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0.076457184 2101.9996 122.34334 -4.9126837 3.9377155 -1071.5769 -1067.6392 + 8450 0.845 0.076457201 2057.1092 121.73484 -4.921619 3.9181301 -1071.5574 -1067.6392 + 8500 0.85 0.076457149 2005.1132 119.2385 -4.9251343 3.8377838 -1071.477 -1067.6392 + 8550 0.855 0.076457098 1942.6247 115.64537 -4.9291799 3.722136 -1071.3614 -1067.6392 + 8600 0.86 0.076457115 1910.1502 111.98317 -4.9396222 3.6042654 -1071.2435 -1067.6392 + 8650 0.865 0.076457185 1943.3663 109.19353 -4.9603011 3.5144784 -1071.1537 -1067.6392 + 8700 0.87 0.076457254 2019.4182 107.80177 -4.9898541 3.4696837 -1071.1089 -1067.6392 + 8750 0.875 0.076457249 2073.1225 107.76716 -5.0205034 3.4685697 -1071.1078 -1067.6392 + 8800 0.88 0.076457175 2088.6545 108.72646 -5.0437829 3.4994455 -1071.1387 -1067.6392 + 8850 0.885 0.076457093 2077.5406 110.36499 -5.0572565 3.5521827 -1071.1914 -1067.6392 + 8900 0.89 0.076457088 2039.5392 112.51291 -5.0650529 3.6213154 -1071.2605 -1067.6392 + 8950 0.895 0.076457167 2016.6853 114.99374 -5.0744542 3.7011627 -1071.3404 -1067.6392 + 9000 0.9 0.076457241 2000.3012 117.47475 -5.0917242 3.781016 -1071.4202 -1067.6392 + 9050 0.905 0.076457226 1957.0091 119.35854 -5.1139655 3.8416472 -1071.4809 -1067.6392 + 9100 0.91 0.076457166 1923.1545 120.23087 -5.1350957 3.869724 -1071.509 -1067.6392 + 9150 0.915 0.076457128 1933.618 120.11319 -5.1511544 3.8659364 -1071.5052 -1067.6392 + 9200 0.92 0.076457114 1961.4473 119.3017 -5.1596749 3.8398178 -1071.4791 -1067.6392 + 9250 0.925 0.076457136 1962.1 118.34889 -5.1642618 3.8091509 -1071.4484 -1067.6392 + 9300 0.93 0.076457156 1942.9357 117.84262 -5.1720815 3.7928561 -1071.4321 -1067.6392 + 9350 0.935 0.076457138 1911.4886 118.10075 -5.1877615 3.8011641 -1071.4404 -1067.6392 + 9400 0.94 0.076457123 1890.6033 118.99959 -5.2079977 3.830094 -1071.4693 -1067.6392 + 9450 0.945 0.076457145 1911.9879 120.23989 -5.2265042 3.8700141 -1071.5092 -1067.6392 + 9500 0.95 0.076457172 1944.8053 121.67513 -5.2423826 3.9162086 -1071.5554 -1067.6392 + 9550 0.955 0.076457175 1950.6137 123.16708 -5.2566963 3.9642282 -1071.6035 -1067.6392 + 9600 0.96 0.076457174 1953.467 124.46943 -5.2686278 4.0061451 -1071.6454 -1067.6392 + 9650 0.965 0.076457174 1991.321 125.52237 -5.2816008 4.0400348 -1071.6793 -1067.6392 + 9700 0.97 0.076457153 2064.4494 126.48746 -5.3037304 4.0710971 -1071.7103 -1067.6392 + 9750 0.975 0.076457119 2117.0576 127.38593 -5.3401962 4.100015 -1071.7392 -1067.6392 + 9800 0.98 0.076457147 2129.8396 127.90735 -5.38872 4.1167973 -1071.756 -1067.6392 + 9850 0.985 0.076457201 2114.5902 127.47883 -5.4369444 4.103005 -1071.7422 -1067.6392 + 9900 0.99 0.076457216 2054.2807 125.71916 -5.4695662 4.0463688 -1071.6856 -1067.6392 + 9950 0.995 0.076457168 1984.2158 123.01154 -5.4834672 3.9592219 -1071.5985 -1067.6392 + 10000 1 0.076457131 1962.6658 120.32305 -5.4872199 3.8726906 -1071.5119 -1067.6392 + 10050 1.005 0.076457159 1973.2973 118.61523 -5.4922129 3.8177233 -1071.457 -1067.6392 + 10100 1.01 0.076457216 1957.9424 118.36973 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0.076457078 986.81013 328.40773 -18.100384 10.570058 -1078.2093 -1067.6392 + 47650 4.765 0.076457236 980.12421 319.46388 -18.120191 10.282193 -1077.9214 -1067.6392 + 47700 4.77 0.076457087 973.75413 310.20532 -18.133538 9.984199 -1077.6234 -1067.6392 + 47750 4.775 0.076456955 944.49227 304.05996 -18.150575 9.7864056 -1077.4256 -1067.6392 + 47800 4.78 0.076457043 934.26558 302.74055 -18.16342 9.7439395 -1077.3832 -1067.6392 + 47850 4.785 0.076457163 946.5867 306.50326 -18.158739 9.8650453 -1077.5043 -1067.6392 + 47900 4.79 0.076457207 956.86274 314.93949 -18.15119 10.136572 -1077.7758 -1067.6392 + 47950 4.795 0.07645715 958.82327 326.06488 -18.164425 10.494651 -1078.1339 -1067.6392 + 48000 4.8 0.076457039 947.13341 336.0645 -18.196245 10.816497 -1078.4557 -1067.6392 + 48050 4.805 0.076457079 939.87276 341.25341 -18.222449 10.983506 -1078.6227 -1067.6392 + 48100 4.81 0.076457027 941.59608 340.87478 -18.232947 10.971319 -1078.6106 -1067.6392 + 48150 4.815 0.076456851 947.69448 337.06143 -18.235444 10.848584 -1078.4878 -1067.6392 + 48200 4.82 0.076456923 945.0083 331.93845 -18.226235 10.683697 -1078.3229 -1067.6392 + 48250 4.825 0.076457065 955.23353 326.88598 -18.206503 10.521079 -1078.1603 -1067.6392 + 48300 4.83 0.076457035 976.25082 323.10993 -18.198786 10.399544 -1078.0388 -1067.6392 + 48350 4.835 0.076456918 980.22652 320.95231 -18.21424 10.330099 -1077.9693 -1067.6392 + 48400 4.84 0.07645681 991.61794 319.56431 -18.236887 10.285425 -1077.9247 -1067.6392 + 48450 4.845 0.076456811 1004.3973 319.00657 -18.259638 10.267474 -1077.9067 -1067.6392 + 48500 4.85 0.076456872 1011.2382 320.78368 -18.281738 10.324672 -1077.9639 -1067.6392 + 48550 4.855 0.076456865 1011.4359 325.48338 -18.293785 10.475935 -1078.1152 -1067.6392 + 48600 4.86 0.076456844 1005.7488 332.46822 -18.305193 10.700748 -1078.34 -1067.6392 + 48650 4.865 0.076456876 989.87609 340.85827 -18.332595 10.970788 -1078.61 -1067.6392 + 48700 4.87 0.07645693 968.07155 348.89288 -18.372402 11.229388 -1078.8686 -1067.6392 + 48750 4.875 0.076456873 954.48433 354.07093 -18.412323 11.396048 -1079.0353 -1067.6392 + 48800 4.88 0.076456838 951.82821 354.8518 -18.445418 11.421181 -1079.0604 -1067.6392 + 48850 4.885 0.076456946 955.18291 351.65785 -18.473652 11.318381 -1078.9576 -1067.6392 + 48900 4.89 0.076457014 961.21122 345.9779 -18.498732 11.135567 -1078.7748 -1067.6392 + 48950 4.895 0.076456863 971.60448 338.99359 -18.517002 10.910772 -1078.55 -1067.6392 + 49000 4.9 0.076456715 983.55102 331.29604 -18.525123 10.66302 -1078.3022 -1067.6392 + 49050 4.905 0.076456793 965.60848 324.24302 -18.535514 10.436013 -1078.0752 -1067.6392 + 49100 4.91 0.076456864 944.53951 319.79955 -18.557009 10.292997 -1077.9322 -1067.6392 + 49150 4.915 0.076456768 947.20225 319.09103 -18.582911 10.270192 -1077.9094 -1067.6392 + 49200 4.92 0.076456734 944.86084 321.47471 -18.607567 10.346913 -1077.9861 -1067.6392 + 49250 4.925 0.076456851 940.6342 324.66116 -18.626242 10.449471 -1078.0887 -1067.6392 + 49300 4.93 0.076456872 950.6162 326.9518 -18.64032 10.523198 -1078.1624 -1067.6392 + 49350 4.935 0.076456643 952.42705 328.08816 -18.649274 10.559772 -1078.199 -1067.6392 + 49400 4.94 0.076456451 940.33548 329.05106 -18.66058 10.590764 -1078.23 -1067.6392 + 49450 4.945 0.076456558 946.93554 331.05799 -18.683544 10.655358 -1078.2946 -1067.6392 + 49500 4.95 0.076456719 968.13429 334.1178 -18.710726 10.753841 -1078.3931 -1067.6392 + 49550 4.955 0.076456712 989.14725 337.02333 -18.733226 10.847357 -1078.4866 -1067.6392 + 49600 4.96 0.076456681 986.97561 338.47429 -18.752155 10.894058 -1078.5333 -1067.6392 + 49650 4.965 0.076456692 980.18259 338.36307 -18.779369 10.890478 -1078.5297 -1067.6392 + 49700 4.97 0.076456776 962.29895 337.41689 -18.815353 10.860024 -1078.4993 -1067.6392 + 49750 4.975 0.076456852 943.47442 335.97999 -18.836611 10.813777 -1078.453 -1067.6392 + 49800 4.98 0.076456829 951.10385 334.29845 -18.839995 10.759655 -1078.3989 -1067.6392 + 49850 4.985 0.076456797 968.57767 333.00568 -18.84792 10.718046 -1078.3573 -1067.6392 + 49900 4.99 0.076456886 973.40031 332.98155 -18.860429 10.71727 -1078.3565 -1067.6392 + 49950 4.995 0.076456914 964.32242 335.13156 -18.853933 10.786469 -1078.4257 -1067.6392 + 50000 5 0.076456921 972.52311 340.63067 -18.841947 10.963463 -1078.6027 -1067.6392 +Loop time of 90.4316 on 1 procs for 50000 steps with 250 atoms + +Performance: 4.777 ns/day, 5.024 hours/ns, 552.904 timesteps/s +99.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 37.302 | 37.302 | 37.302 | 0.0 | 41.25 +Neigh | 0.386 | 0.386 | 0.386 | 0.0 | 0.43 +Comm | 0.7718 | 0.7718 | 0.7718 | 0.0 | 0.85 +Output | 15.35 | 15.35 | 15.35 | 0.0 | 16.97 +Modify | 36.465 | 36.465 | 36.465 | 0.0 | 40.32 +Other | | 0.1579 | | | 0.17 + +Nlocal: 250 ave 250 max 250 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1327 ave 1327 max 1327 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7747 ave 7747 max 7747 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15494 ave 15494 max 15494 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15494 +Ave neighs/atom = 61.976 +Neighbor list builds = 614 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:30 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.4 b/examples/SPIN/iron/log.11May18.spin.iron.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..1467f8e2c58a451299cb375773ef76f43a1bb8bc --- /dev/null +++ b/examples/SPIN/iron/log.11May18.spin.iron.g++.4 @@ -0,0 +1,1115 @@ +LAMMPS (11 May 2018) +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 250 atoms + Time spent = 0.00023818 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456995 9402.4007 96.298333 -0.85659448 3.0994366 -1070.7387 -1067.6392 + 100 0.01 0.076457028 9589.1846 86.330828 -0.87003341 2.7786247 -1070.4179 -1067.6392 + 150 0.015 0.076457074 9673.9268 71.603402 -0.89006992 2.3046111 -1069.9438 -1067.6392 + 200 0.02 0.076457106 9509.1148 54.648817 -0.91124541 1.7589146 -1069.3981 -1067.6392 + 250 0.025 0.076457128 9004.27 38.599515 -0.93187522 1.2423553 -1068.8816 -1067.6392 + 300 0.03 0.076457157 8353.4371 26.383018 -0.95082226 0.8491579 -1068.4884 -1067.6392 + 350 0.035 0.076457207 7911.1316 20.01039 -0.96826468 0.64404992 -1068.2833 -1067.6392 + 400 0.04 0.076457243 7775.9492 20.097682 -0.98706373 0.64685949 -1068.2861 -1067.6392 + 450 0.045 0.076457231 7737.1225 25.687511 -1.0095684 0.82677249 -1068.466 -1067.6392 + 500 0.05 0.076457204 7676.9809 34.604697 -1.0349855 1.113779 -1068.753 -1067.6392 + 550 0.055 0.076457196 7550.2809 44.251809 -1.0609123 1.4242788 -1069.0635 -1067.6392 + 600 0.06 0.076457188 7209.7657 52.475202 -1.0880854 1.6889551 -1069.3282 -1067.6392 + 650 0.065 0.07645718 6691.1787 57.926479 -1.1179657 1.8644087 -1069.5036 -1067.6392 + 700 0.07 0.076457185 6276.4003 60.030548 -1.1469999 1.9321298 -1069.5714 -1067.6392 + 750 0.075 0.07645719 6149.9253 59.122504 -1.1721939 1.9029037 -1069.5421 -1067.6392 + 800 0.08 0.076457195 6207.0587 56.349146 -1.1949365 1.813641 -1069.4529 -1067.6392 + 850 0.085 0.076457199 6328.4635 53.154464 -1.2164642 1.7108177 -1069.35 -1067.6392 + 900 0.09 0.076457199 6456.2716 50.837416 -1.2366018 1.6362417 -1069.2755 -1067.6392 + 950 0.095 0.076457222 6495.1064 50.234549 -1.2539657 1.6168379 -1069.2561 -1067.6392 + 1000 0.1 0.076457266 6416.775 51.592727 -1.2671834 1.6605519 -1069.2998 -1067.6392 + 1050 0.105 0.076457256 6305.9015 54.719414 -1.2794824 1.7611868 -1069.4004 -1067.6392 + 1100 0.11 0.076457222 6165.987 59.01343 -1.2960617 1.8993931 -1069.5386 -1067.6392 + 1150 0.115 0.076457194 5941.7807 63.475298 -1.317859 2.0430017 -1069.6822 -1067.6392 + 1200 0.12 0.076457182 5692.0982 67.036713 -1.3432854 2.1576286 -1069.7969 -1067.6392 + 1250 0.125 0.076457217 5543.1736 68.917405 -1.3719994 2.2181602 -1069.8574 -1067.6392 + 1300 0.13 0.076457263 5507.9968 68.753418 -1.4042339 2.2128821 -1069.8521 -1067.6392 + 1350 0.135 0.076457286 5500.7848 66.608286 -1.4385667 2.1438394 -1069.7831 -1067.6392 + 1400 0.14 0.076457254 5523.456 62.967429 -1.4712143 2.0266556 -1069.6659 -1067.6392 + 1450 0.145 0.076457188 5501.5777 58.75732 -1.4990458 1.89115 -1069.5304 -1067.6392 + 1500 0.15 0.076457175 5324.4931 55.246308 -1.5236774 1.7781453 -1069.4174 -1067.6392 + 1550 0.155 0.076457234 5025.5908 53.607297 -1.5492947 1.7253925 -1069.3646 -1067.6392 + 1600 0.16 0.076457297 4742.9546 54.443418 -1.5785798 1.7523036 -1069.3915 -1067.6392 + 1650 0.165 0.076457321 4558.083 57.572305 -1.6113848 1.8530093 -1069.4922 -1067.6392 + 1700 0.17 0.076457304 4479.4352 62.073307 -1.6443595 1.9978776 -1069.6371 -1067.6392 + 1750 0.175 0.076457272 4520.5577 66.677964 -1.6742729 2.146082 -1069.7853 -1067.6392 + 1800 0.18 0.076457253 4659.9114 70.277293 -1.7021557 2.2619292 -1069.9012 -1067.6392 + 1850 0.185 0.076457257 4734.1597 72.135028 -1.7307798 2.3217219 -1069.961 -1067.6392 + 1900 0.19 0.076457279 4632.2637 71.873382 -1.7598165 2.3133006 -1069.9525 -1067.6392 + 1950 0.195 0.076457276 4496.6621 69.52131 -1.7866398 2.2375973 -1069.8768 -1067.6392 + 2000 0.2 0.076457276 4507.4594 65.61098 -1.8106776 2.1117403 -1069.751 -1067.6392 + 2050 0.205 0.076457288 4652.9279 61.016261 -1.8317479 1.9638557 -1069.6031 -1067.6392 + 2100 0.21 0.076457307 4738.4188 56.745795 -1.8489776 1.8264074 -1069.4656 -1067.6392 + 2150 0.215 0.076457279 4643.423 53.837376 -1.8647516 1.7327977 -1069.372 -1067.6392 + 2200 0.22 0.076457215 4517.9871 53.044053 -1.8828305 1.707264 -1069.3465 -1067.6392 + 2250 0.225 0.07645717 4436.4399 54.521839 -1.9038753 1.7548277 -1069.3941 -1067.6392 + 2300 0.23 0.076457132 4318.8261 57.895634 -1.9276454 1.8634159 -1069.5026 -1067.6392 + 2350 0.235 0.076457114 4148.8616 62.484473 -1.9559372 2.0111113 -1069.6503 -1067.6392 + 2400 0.24 0.076457144 4014.8498 67.404243 -1.9902034 2.1694579 -1069.8087 -1067.6392 + 2450 0.245 0.076457189 4004.017 71.654167 -2.0278558 2.306245 -1069.9455 -1067.6392 + 2500 0.25 0.076457202 4109.5497 74.379393 -2.0629968 2.3939585 -1070.0332 -1067.6392 + 2550 0.255 0.076457205 4251.6933 75.255112 -2.0918484 2.4221442 -1070.0614 -1067.6392 + 2600 0.26 0.076457208 4320.6876 74.700611 -2.1169691 2.4042972 -1070.0435 -1067.6392 + 2650 0.265 0.076457197 4297.5527 73.627823 -2.143 2.3697686 -1070.009 -1067.6392 + 2700 0.27 0.076457213 4198.4852 72.957211 -2.1702374 2.3481845 -1069.9874 -1067.6392 + 2750 0.275 0.076457256 4019.2384 73.353574 -2.1967187 2.3609417 -1070.0002 -1067.6392 + 2800 0.28 0.076457288 3867.2492 75.083781 -2.2227117 2.4166298 -1070.0559 -1067.6392 + 2850 0.285 0.076457302 3879.8471 77.82546 -2.2488766 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1.035 0.076457432 1759.9766 128.82223 -5.8669372 4.1462436 -1071.7855 -1067.6392 + 10400 1.04 0.076457457 1756.0701 125.3228 -5.8723914 4.0336114 -1071.6728 -1067.6392 + 10450 1.045 0.076457431 1796.2676 122.12283 -5.8711897 3.930618 -1071.5698 -1067.6392 + 10500 1.05 0.076457363 1832.5849 120.24945 -5.8728862 3.870322 -1071.5096 -1067.6392 + 10550 1.055 0.076457315 1825.9591 120.26647 -5.8808515 3.8708698 -1071.5101 -1067.6392 + 10600 1.06 0.076457322 1783.5912 121.98369 -5.8879416 3.9261399 -1071.5654 -1067.6392 + 10650 1.065 0.07645737 1765.4445 124.88567 -5.8906657 4.0195423 -1071.6588 -1067.6392 + 10700 1.07 0.076457449 1789.2376 128.29349 -5.8943984 4.1292256 -1071.7685 -1067.6392 + 10750 1.075 0.076457481 1818.6141 131.12076 -5.9023895 4.2202233 -1071.8595 -1067.6392 + 10800 1.08 0.076457417 1821.6989 132.13157 -5.9106221 4.2527572 -1071.892 -1067.6392 + 10850 1.085 0.076457331 1835.7675 130.83646 -5.9174483 4.2110729 -1071.8503 -1067.6392 + 10900 1.09 0.076457313 1863.9325 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4.955 0.076457651 985.5222 322.69351 -18.765732 10.386141 -1078.0254 -1067.6392 + 49600 4.96 0.076457607 966.22788 316.25074 -18.798665 10.178775 -1077.818 -1067.6392 + 49650 4.965 0.076457494 961.04675 313.18195 -18.839015 10.080004 -1077.7192 -1067.6392 + 49700 4.97 0.076457431 960.65868 314.4735 -18.863274 10.121574 -1077.7608 -1067.6392 + 49750 4.975 0.076457515 966.54445 320.68235 -18.880959 10.32141 -1077.9606 -1067.6392 + 49800 4.98 0.076457498 965.47876 331.30789 -18.90627 10.663401 -1078.3026 -1067.6392 + 49850 4.985 0.076457382 964.05595 343.93887 -18.938996 11.069939 -1078.7092 -1067.6392 + 49900 4.99 0.076457357 944.93024 354.89734 -18.970612 11.422646 -1079.0619 -1067.6392 + 49950 4.995 0.076457532 918.77322 361.48317 -18.987516 11.634616 -1079.2739 -1067.6392 + 50000 5 0.07645762 900.51128 363.08297 -18.994661 11.686107 -1079.3253 -1067.6392 +Loop time of 52.5523 on 4 procs for 50000 steps with 250 atoms + +Performance: 8.220 ns/day, 2.920 hours/ns, 951.434 timesteps/s +94.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.242 | 10.478 | 10.799 | 6.3 | 19.94 +Neigh | 0.10368 | 0.10776 | 0.11329 | 1.1 | 0.21 +Comm | 2.4492 | 2.7097 | 2.8852 | 11.0 | 5.16 +Output | 5.5737 | 5.9107 | 6.2742 | 11.8 | 11.25 +Modify | 32.833 | 33.256 | 33.661 | 5.2 | 63.28 +Other | | 0.09063 | | | 0.17 + +Nlocal: 62.5 ave 66 max 57 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 772 ave 785 max 755 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 1931 ave 2025 max 1751 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +FullNghs: 3862 ave 4082 max 3518 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 15448 +Ave neighs/atom = 61.792 +Neighbor list builds = 614 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:52 diff --git a/examples/SPIN/nickel/Ni99.eam.alloy b/examples/SPIN/nickel/Ni99.eam.alloy new file mode 100644 index 0000000000000000000000000000000000000000..458f550462147985aebc64bee947ca587bcb2200 --- /dev/null +++ b/examples/SPIN/nickel/Ni99.eam.alloy @@ -0,0 +1,30006 @@ + Ni EAM from Phys. Rev. B 59, 3393 (1999) in the LAMMPS setfl format. + Conversion by C. A. Becker from Y. 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0.1753659819102016E-05 + 0.1535011699446480E-05 + 0.1335308706819185E-05 + 0.1153698121804797E-05 + 0.9893265964069983E-06 + 0.8413397937480116E-06 + 0.7088819770183164E-06 + 0.5910969229666829E-06 + 0.4871272699961916E-06 + 0.3961146220277366E-06 + 0.3172001065531827E-06 + 0.2495236941769535E-06 + 0.1922246407671419E-06 + 0.1444416614955101E-06 + 0.1053124328882129E-06 + 0.7397412700923994E-07 + 0.4956332050161572E-07 + 0.3121579423557010E-07 + 0.1806692087863425E-07 + 0.9251422554216926E-08 + 0.3903384615269487E-08 + 0.1156542889210542E-08 + 0.1443625144722101E-09 diff --git a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat new file mode 100644 index 0000000000000000000000000000000000000000..376f6fd16242f4255bd4ba277efb0cfd1e5b4ddc --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat @@ -0,0 +1,5 @@ +2.492 0.0028027 +3.524 0.0000816 +4.316 0.0003537 +4.984 0.0001632 +5.572 0.0000408 diff --git a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat new file mode 100644 index 0000000000000000000000000000000000000000..4e5aa4765957bd9d196f7543751fb5ce174634b4 --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat @@ -0,0 +1,5 @@ +2.495 8.3 +3.524 -3.99 +4.31 0.998 +4.99 -0.955 +5.56 0.213 diff --git a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..4046fa45f7c9dde935e492daf7fdf9453daea82a --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py @@ -0,0 +1,33 @@ +# program fitting the exchange interaction +# model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +# definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +# exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_fcc_ni.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +# perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=([0.0,-1.0,0.0], [100.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +# print the fitted parameters +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +# ploting the result +plt.xlabel('r_ij') +pylab.xlim([0.0,6.5]) +#pylab.ylim([-2.0,10.0]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel new file mode 100644 index 0000000000000000000000000000000000000000..ba447b077f24c4ee1213aca34325d370657b1f4e --- /dev/null +++ b/examples/SPIN/nickel/in.spin.nickel @@ -0,0 +1,58 @@ +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 + diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..82f54f4e6b208c946edb445c6ec57b5780912802 --- /dev/null +++ b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 @@ -0,0 +1,157 @@ +LAMMPS (11 May 2018) +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000804186 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018 + 50 0.005 0.028733807 0.070491717 101.47879 -56307.038 -2218.1018 + 100 0.01 0.028733815 -0.70937134 101.7311 5851.6355 -2218.1018 + 150 0.015 0.028733823 -1.853981 99.63039 2395.8677 -2218.1018 + 200 0.02 0.028733828 -3.2679239 94.850105 1482.3486 -2218.1018 + 250 0.025 0.028733824 -4.863967 88.444584 1100.7396 -2218.1018 + 300 0.03 0.028733807 -6.5763457 82.689581 899.56642 -2218.1018 + 350 0.035 0.028733783 -8.3489158 80.108798 768.64457 -2218.1018 + 400 0.04 0.028733763 -10.120216 82.374947 670.03091 -2218.1018 + 450 0.045 0.028733755 -11.828932 89.814597 593.77931 -2218.1018 + 500 0.05 0.028733762 -13.423712 101.39613 535.03371 -2218.1018 + 550 0.055 0.028733783 -14.866724 115.07399 489.92024 -2218.1018 + 600 0.06 0.028733801 -16.135279 128.57849 458.66654 -2218.1018 + 650 0.065 0.028733804 -17.222838 140.22402 440.11437 -2218.1018 + 700 0.07 0.028733795 -18.154813 149.61295 425.91356 -2218.1018 + 750 0.075 0.028733781 -18.996903 157.5814 412.82654 -2218.1018 + 800 0.08 0.028733768 -19.804249 164.92075 407.77954 -2218.1018 + 850 0.085 0.028733752 -20.579151 171.67278 406.84726 -2218.1018 + 900 0.09 0.028733728 -21.294277 177.67238 399.69633 -2218.1018 + 950 0.095 0.028733715 -21.943945 183.2621 389.92281 -2218.1018 + 1000 0.1 0.02873374 -22.551277 188.99284 383.19592 -2218.1018 + 1050 0.105 0.028733783 -23.120147 194.51391 375.87245 -2218.1018 + 1100 0.11 0.028733792 -23.602325 198.18631 365.37753 -2218.1018 + 1150 0.115 0.028733774 -23.976048 199.04022 354.04863 -2218.1018 + 1200 0.12 0.02873376 -24.31575 198.41999 346.40397 -2218.1018 + 1250 0.125 0.028733759 -24.718347 198.3669 343.1701 -2218.1018 + 1300 0.13 0.028733765 -25.189073 199.57949 336.90052 -2218.1018 + 1350 0.135 0.028733774 -25.650252 201.45897 329.07023 -2218.1018 + 1400 0.14 0.028733785 -26.042702 203.6926 327.97373 -2218.1018 + 1450 0.145 0.028733791 -26.373965 206.80469 327.38747 -2218.1018 + 1500 0.15 0.028733791 -26.691802 211.43923 322.75885 -2218.1018 + 1550 0.155 0.028733794 -27.021573 217.10969 315.55781 -2218.1018 + 1600 0.16 0.028733792 -27.344066 222.16052 310.6743 -2218.1018 + 1650 0.165 0.028733788 -27.640017 225.28449 310.49671 -2218.1018 + 1700 0.17 0.028733803 -27.907241 226.37676 310.9389 -2218.1018 + 1750 0.175 0.028733828 -28.143477 226.31095 313.28034 -2218.1018 + 1800 0.18 0.028733833 -28.363397 226.43633 317.31668 -2218.1018 + 1850 0.185 0.028733811 -28.58153 227.36287 318.98645 -2218.1018 + 1900 0.19 0.028733796 -28.785208 228.39889 316.9972 -2218.1018 + 1950 0.195 0.028733826 -28.9724 228.84666 309.8027 -2218.1018 + 2000 0.2 0.02873386 -29.175039 228.918 297.88519 -2218.1018 +Loop time of 10.033 on 1 procs for 2000 steps with 500 atoms + +Performance: 1.722 ns/day, 13.935 hours/ns, 199.342 timesteps/s +99.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.909 | 3.909 | 3.909 | 0.0 | 38.96 +Neigh | 0.031031 | 0.031031 | 0.031031 | 0.0 | 0.31 +Comm | 0.046559 | 0.046559 | 0.046559 | 0.0 | 0.46 +Output | 2.4087 | 2.4087 | 2.4087 | 0.0 | 24.01 +Modify | 3.625 | 3.625 | 3.625 | 0.0 | 36.13 +Other | | 0.01268 | | | 0.13 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19508 ave 19508 max 19508 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 39016 ave 39016 max 39016 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39016 +Ave neighs/atom = 78.032 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..373271459f2e68ede27cbd9b7fa635bc089c917f --- /dev/null +++ b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 @@ -0,0 +1,157 @@ +LAMMPS (11 May 2018) +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000523567 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018 + 50 0.005 0.028733805 0.25324083 98.741633 -15727.749 -2218.1018 + 100 0.01 0.028733812 -0.37320751 97.073875 11244.373 -2218.1018 + 150 0.015 0.028733819 -1.3971549 94.073447 3250.0517 -2218.1018 + 200 0.02 0.028733825 -2.7238372 89.419944 1838.752 -2218.1018 + 250 0.025 0.028733829 -4.2684428 84.07494 1304.3675 -2218.1018 + 300 0.03 0.028733824 -5.9636712 80.06368 1025.7815 -2218.1018 + 350 0.035 0.02873381 -7.7386326 79.366702 844.49729 -2218.1018 + 400 0.04 0.028733802 -9.5148059 83.052751 715.20758 -2218.1018 + 450 0.045 0.028733806 -11.234935 91.282747 621.75552 -2218.1018 + 500 0.05 0.02873381 -12.875184 103.49836 550.04479 -2218.1018 + 550 0.055 0.028733808 -14.413473 118.16526 495.70417 -2218.1018 + 600 0.06 0.028733803 -15.812466 132.83837 461.35805 -2218.1018 + 650 0.065 0.028733808 -17.061311 145.41049 444.38951 -2218.1018 + 700 0.07 0.028733818 -18.181903 154.83414 438.85866 -2218.1018 + 750 0.075 0.028733823 -19.176259 160.58645 436.90462 -2218.1018 + 800 0.08 0.028733825 -20.035157 163.02829 429.73193 -2218.1018 + 850 0.085 0.028733825 -20.806548 164.4197 419.73763 -2218.1018 + 900 0.09 0.028733829 -21.571419 167.8571 411.59699 -2218.1018 + 950 0.095 0.028733825 -22.365879 175.00875 402.66175 -2218.1018 + 1000 0.1 0.028733821 -23.133464 184.68305 391.05824 -2218.1018 + 1050 0.105 0.028733833 -23.770507 193.83795 379.23354 -2218.1018 + 1100 0.11 0.02873385 -24.249882 200.5039 372.08521 -2218.1018 + 1150 0.115 0.028733864 -24.630489 204.46984 367.92135 -2218.1018 + 1200 0.12 0.028733877 -24.956281 205.96624 363.72367 -2218.1018 + 1250 0.125 0.028733884 -25.227332 205.18503 361.09236 -2218.1018 + 1300 0.13 0.028733877 -25.43568 202.76969 359.10924 -2218.1018 + 1350 0.135 0.028733868 -25.588748 199.85462 358.69556 -2218.1018 + 1400 0.14 0.028733866 -25.723582 197.99165 360.27856 -2218.1018 + 1450 0.145 0.028733851 -25.866283 198.30283 360.46623 -2218.1018 + 1500 0.15 0.028733812 -26.014569 200.95517 354.66722 -2218.1018 + 1550 0.155 0.02873379 -26.192673 205.95485 348.37935 -2218.1018 + 1600 0.16 0.028733795 -26.444059 212.87557 345.53576 -2218.1018 + 1650 0.165 0.028733838 -26.75551 219.86449 338.9224 -2218.1018 + 1700 0.17 0.028733868 -27.068513 224.47868 327.81241 -2218.1018 + 1750 0.175 0.028733862 -27.344118 225.62318 319.85486 -2218.1018 + 1800 0.18 0.028733849 -27.57563 224.07463 320.07064 -2218.1018 + 1850 0.185 0.028733852 -27.774274 221.70618 323.12599 -2218.1018 + 1900 0.19 0.028733864 -27.967999 220.53947 322.9504 -2218.1018 + 1950 0.195 0.028733863 -28.173041 221.61407 318.63401 -2218.1018 + 2000 0.2 0.028733853 -28.362177 224.22281 310.55185 -2218.1018 +Loop time of 3.95094 on 4 procs for 2000 steps with 500 atoms + +Performance: 4.374 ns/day, 5.487 hours/ns, 506.208 timesteps/s +98.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0289 | 1.0467 | 1.0811 | 2.0 | 26.49 +Neigh | 0.0079527 | 0.0081946 | 0.0084369 | 0.2 | 0.21 +Comm | 0.094456 | 0.13311 | 0.15138 | 6.2 | 3.37 +Output | 0.69702 | 0.71998 | 0.74483 | 2.1 | 18.22 +Modify | 2.0107 | 2.0383 | 2.0598 | 1.3 | 51.59 +Other | | 0.004668 | | | 0.12 + +Nlocal: 125 ave 132 max 120 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 1099 ave 1104 max 1092 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 4876.5 ave 5100 max 4721 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +FullNghs: 9753 ave 10296 max 9362 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 39012 +Ave neighs/atom = 78.024 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy new file mode 120000 index 0000000000000000000000000000000000000000..6a47c9eebef2dc333daa871fc882f2afc038bd4c --- /dev/null +++ b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1 @@ +../cobalt_fcc/Co_PurjaPun_2012.eam.alloy \ No newline at end of file diff --git a/examples/SPIN/read_restart/Norm_randXY_8x8x32.data b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data new file mode 100644 index 0000000000000000000000000000000000000000..d239bb6ca07359deb45bf37e6fbbb7447fa8458a --- /dev/null +++ b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data @@ -0,0 +1,8207 @@ +LAMMPS data file via write_data, version 4 May 2017, timestep = 0 + +8192 atoms +1 atom types + +0.0000000000000000e+00 2.8320000000000000e+01 xlo xhi +0.0000000000000000e+00 2.8320000000000000e+01 ylo yhi +0.0000000000000000e+00 1.1328000000000000e+02 zlo zhi + +Masses + +1 58.93 + +Atoms # spin + +1 1 1.72 0.0 0.0 0.0 0.52887 -0.848703 1.0 +2 1 1.72 1.77 1.77 0.0 -0.745115 -0.666936 1.0 +3 1 1.72 1.77 0.0 1.77 -0.989437 -0.144964 1.0 +4 1 1.72 0.0 1.77 1.77 0.999926 -0.0121449 1.0 +5 1 1.72 3.54 0.0 0.0 0.377063 -0.926188 1.0 +6 1 1.72 5.31 1.77 0.0 0.412944 0.910756 1.0 +7 1 1.72 5.31 0.0 1.77 -0.999979 0.00650985 1.0 +8 1 1.72 3.54 1.77 1.77 0.535453 -0.844565 1.0 +9 1 1.72 7.0799999 0.0 0.0 -0.986135 0.165942 1.0 +10 1 1.72 8.8500004 1.77 0.0 -0.37352 -0.927622 1.0 +11 1 1.72 8.8500004 0.0 1.77 -0.926878 0.375363 1.0 +12 1 1.72 7.0799999 1.77 1.77 -0.690063 -0.72375 1.0 +13 1 1.72 10.6199999 0.0 0.0 -0.7204 -0.693559 1.0 +14 1 1.72 12.3900004 1.77 0.0 -0.832046 -0.554707 1.0 +15 1 1.72 12.3900004 0.0 1.77 0.23719 0.971463 1.0 +16 1 1.72 10.6199999 1.77 1.77 0.456617 -0.889663 1.0 +17 1 1.72 14.1599999 0.0 0.0 -0.661715 0.749755 1.0 +18 1 1.72 15.9300004 1.77 0.0 -0.847309 -0.531099 1.0 +19 1 1.72 15.9300004 0.0 1.77 -0.956536 0.291614 1.0 +20 1 1.72 14.1599999 1.77 1.77 -0.770778 -0.637104 1.0 +21 1 1.72 17.7000008 0.0 0.0 -0.896558 -0.442927 1.0 +22 1 1.72 19.4699993 1.77 0.0 0.557673 0.830061 1.0 +23 1 1.72 19.4699993 0.0 1.77 0.983224 0.182403 1.0 +24 1 1.72 17.7000008 1.77 1.77 -0.939201 0.343368 1.0 +25 1 1.72 21.2399998 0.0 0.0 0.894393 0.447281 1.0 +26 1 1.72 23.0100002 1.77 0.0 0.484661 0.874702 1.0 +27 1 1.72 23.0100002 0.0 1.77 0.525609 -0.850726 1.0 +28 1 1.72 21.2399998 1.77 1.77 0.551899 0.833911 1.0 +29 1 1.72 24.7800007 0.0 0.0 -0.307979 0.951393 1.0 +30 1 1.72 26.5499993 1.77 0.0 -0.993353 -0.115107 1.0 +31 1 1.72 26.5499993 0.0 1.77 0.786777 -0.617237 1.0 +32 1 1.72 24.7800007 1.77 1.77 -0.646691 0.762752 1.0 +33 1 1.72 0.0 3.54 0.0 0.119106 -0.992881 1.0 +34 1 1.72 1.77 5.31 0.0 0.719383 0.694614 1.0 +35 1 1.72 1.77 3.54 1.77 -0.704699 0.709506 1.0 +36 1 1.72 0.0 5.31 1.77 0.795511 -0.605939 1.0 +37 1 1.72 3.54 3.54 0.0 -0.97 -0.243107 1.0 +38 1 1.72 5.31 5.31 0.0 0.976076 0.217428 1.0 +39 1 1.72 5.31 3.54 1.77 0.735471 -0.677556 1.0 +40 1 1.72 3.54 5.31 1.77 -0.319137 -0.947708 1.0 +41 1 1.72 7.0799999 3.54 0.0 -0.610942 0.791675 1.0 +42 1 1.72 8.8500004 5.31 0.0 -0.679543 0.733635 1.0 +43 1 1.72 8.8500004 3.54 1.77 0.983607 -0.180324 1.0 +44 1 1.72 7.0799999 5.31 1.77 -0.217118 -0.976145 1.0 +45 1 1.72 10.6199999 3.54 0.0 -0.997762 0.0668716 1.0 +46 1 1.72 12.3900004 5.31 0.0 0.275194 -0.961389 1.0 +47 1 1.72 12.3900004 3.54 1.77 -0.828419 -0.560108 1.0 +48 1 1.72 10.6199999 5.31 1.77 0.118246 -0.992984 1.0 +49 1 1.72 14.1599999 3.54 0.0 0.737418 0.675437 1.0 +50 1 1.72 15.9300004 5.31 0.0 0.723539 -0.690283 1.0 +51 1 1.72 15.9300004 3.54 1.77 0.445177 0.895443 1.0 +52 1 1.72 14.1599999 5.31 1.77 -0.0224847 -0.999747 1.0 +53 1 1.72 17.7000008 3.54 0.0 -0.0340097 0.999422 1.0 +54 1 1.72 19.4699993 5.31 0.0 -0.842076 -0.539358 1.0 +55 1 1.72 19.4699993 3.54 1.77 0.628732 -0.777622 1.0 +56 1 1.72 17.7000008 5.31 1.77 -0.710873 -0.70332 1.0 +57 1 1.72 21.2399998 3.54 0.0 -0.997492 0.0707798 1.0 +58 1 1.72 23.0100002 5.31 0.0 -0.643338 -0.765582 1.0 +59 1 1.72 23.0100002 3.54 1.77 -0.891542 0.452938 1.0 +60 1 1.72 21.2399998 5.31 1.77 -0.576343 -0.817208 1.0 +61 1 1.72 24.7800007 3.54 0.0 0.915658 -0.401959 1.0 +62 1 1.72 26.5499993 5.31 0.0 -0.674018 -0.738715 1.0 +63 1 1.72 26.5499993 3.54 1.77 -0.92775 -0.373203 1.0 +64 1 1.72 24.7800007 5.31 1.77 -0.336441 0.941705 1.0 +65 1 1.72 0.0 7.0799999 0.0 0.499974 0.86604 1.0 +66 1 1.72 1.77 8.8500004 0.0 -0.582403 0.8129 1.0 +67 1 1.72 1.77 7.0799999 1.77 0.46326 -0.886222 1.0 +68 1 1.72 0.0 8.8500004 1.77 0.812676 -0.582716 1.0 +69 1 1.72 3.54 7.0799999 0.0 0.572515 0.819894 1.0 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109.7399979 0.945592 -0.325356 1.0 +8087 1 1.72 19.4699993 14.1599999 111.5100022 0.237079 -0.97149 1.0 +8088 1 1.72 17.7000008 15.9300004 111.5100022 0.541095 -0.840961 1.0 +8089 1 1.72 21.2399998 14.1599999 109.7399979 0.547786 0.836619 1.0 +8090 1 1.72 23.0100002 15.9300004 109.7399979 -0.810246 0.58609 1.0 +8091 1 1.72 23.0100002 14.1599999 111.5100022 -0.0396045 -0.999215 1.0 +8092 1 1.72 21.2399998 15.9300004 111.5100022 0.999244 0.0388725 1.0 +8093 1 1.72 24.7800007 14.1599999 109.7399979 -0.995393 -0.0958841 1.0 +8094 1 1.72 26.5499993 15.9300004 109.7399979 0.707666 -0.706547 1.0 +8095 1 1.72 26.5499993 14.1599999 111.5100022 -0.857797 0.513989 1.0 +8096 1 1.72 24.7800007 15.9300004 111.5100022 0.688346 0.725383 1.0 +8097 1 1.72 0.0 17.7000008 109.7399979 0.453695 0.891157 1.0 +8098 1 1.72 1.77 19.4699993 109.7399979 -0.869991 0.493068 1.0 +8099 1 1.72 1.77 17.7000008 111.5100022 -0.828945 0.55933 1.0 +8100 1 1.72 0.0 19.4699993 111.5100022 -0.578312 -0.815815 1.0 +8101 1 1.72 3.54 17.7000008 109.7399979 -0.474111 -0.880465 1.0 +8102 1 1.72 5.31 19.4699993 109.7399979 -0.953145 0.302515 1.0 +8103 1 1.72 5.31 17.7000008 111.5100022 -0.662482 0.749078 1.0 +8104 1 1.72 3.54 19.4699993 111.5100022 -0.673709 0.738997 1.0 +8105 1 1.72 7.0799999 17.7000008 109.7399979 0.703708 0.71049 1.0 +8106 1 1.72 8.8500004 19.4699993 109.7399979 -0.962777 0.270298 1.0 +8107 1 1.72 8.8500004 17.7000008 111.5100022 -0.409325 0.912389 1.0 +8108 1 1.72 7.0799999 19.4699993 111.5100022 0.992278 0.12403 1.0 +8109 1 1.72 10.6199999 17.7000008 109.7399979 -0.256869 -0.966446 1.0 +8110 1 1.72 12.3900004 19.4699993 109.7399979 -0.81811 0.575062 1.0 +8111 1 1.72 12.3900004 17.7000008 111.5100022 0.944442 -0.328678 1.0 +8112 1 1.72 10.6199999 19.4699993 111.5100022 -0.790776 0.612106 1.0 +8113 1 1.72 14.1599999 17.7000008 109.7399979 0.99885 0.047945 1.0 +8114 1 1.72 15.9300004 19.4699993 109.7399979 -0.75767 0.652638 1.0 +8115 1 1.72 15.9300004 17.7000008 111.5100022 0.104479 -0.994527 1.0 +8116 1 1.72 14.1599999 19.4699993 111.5100022 -0.366155 -0.930554 1.0 +8117 1 1.72 17.7000008 17.7000008 109.7399979 -0.100712 0.994916 1.0 +8118 1 1.72 19.4699993 19.4699993 109.7399979 0.20119 -0.979552 1.0 +8119 1 1.72 19.4699993 17.7000008 111.5100022 0.7043 -0.709902 1.0 +8120 1 1.72 17.7000008 19.4699993 111.5100022 0.995221 -0.0976515 1.0 +8121 1 1.72 21.2399998 17.7000008 109.7399979 0.0913868 0.995815 1.0 +8122 1 1.72 23.0100002 19.4699993 109.7399979 -0.783334 0.6216 1.0 +8123 1 1.72 23.0100002 17.7000008 111.5100022 0.762993 0.646407 1.0 +8124 1 1.72 21.2399998 19.4699993 111.5100022 0.969106 -0.246644 1.0 +8125 1 1.72 24.7800007 17.7000008 109.7399979 -0.99318 -0.116594 1.0 +8126 1 1.72 26.5499993 19.4699993 109.7399979 0.751321 -0.659937 1.0 +8127 1 1.72 26.5499993 17.7000008 111.5100022 -0.41311 -0.910681 1.0 +8128 1 1.72 24.7800007 19.4699993 111.5100022 -0.231533 0.972827 1.0 +8129 1 1.72 0.0 21.2399998 109.7399979 -0.638342 -0.769753 1.0 +8130 1 1.72 1.77 23.0100002 109.7399979 -0.358386 -0.933574 1.0 +8131 1 1.72 1.77 21.2399998 111.5100022 0.0433983 -0.999058 1.0 +8132 1 1.72 0.0 23.0100002 111.5100022 -0.986115 -0.166067 1.0 +8133 1 1.72 3.54 21.2399998 109.7399979 0.996583 0.082601 1.0 +8134 1 1.72 5.31 23.0100002 109.7399979 -0.865815 0.500364 1.0 +8135 1 1.72 5.31 21.2399998 111.5100022 0.446465 0.894801 1.0 +8136 1 1.72 3.54 23.0100002 111.5100022 0.701589 -0.712582 1.0 +8137 1 1.72 7.0799999 21.2399998 109.7399979 0.994388 0.105798 1.0 +8138 1 1.72 8.8500004 23.0100002 109.7399979 0.779675 0.626184 1.0 +8139 1 1.72 8.8500004 21.2399998 111.5100022 -0.913378 0.407112 1.0 +8140 1 1.72 7.0799999 23.0100002 111.5100022 -0.974435 0.22467 1.0 +8141 1 1.72 10.6199999 21.2399998 109.7399979 0.0180628 0.999837 1.0 +8142 1 1.72 12.3900004 23.0100002 109.7399979 -0.393018 0.919531 1.0 +8143 1 1.72 12.3900004 21.2399998 111.5100022 0.171283 -0.985222 1.0 +8144 1 1.72 10.6199999 23.0100002 111.5100022 0.853928 0.520391 1.0 +8145 1 1.72 14.1599999 21.2399998 109.7399979 -0.893534 -0.448996 1.0 +8146 1 1.72 15.9300004 23.0100002 109.7399979 0.783901 0.620886 1.0 +8147 1 1.72 15.9300004 21.2399998 111.5100022 -0.636441 0.771326 1.0 +8148 1 1.72 14.1599999 23.0100002 111.5100022 -0.62653 0.779398 1.0 +8149 1 1.72 17.7000008 21.2399998 109.7399979 -0.426717 -0.904385 1.0 +8150 1 1.72 19.4699993 23.0100002 109.7399979 0.150477 -0.988614 1.0 +8151 1 1.72 19.4699993 21.2399998 111.5100022 0.993032 -0.117843 1.0 +8152 1 1.72 17.7000008 23.0100002 111.5100022 -0.858474 -0.512857 1.0 +8153 1 1.72 21.2399998 21.2399998 109.7399979 0.671527 -0.74098 1.0 +8154 1 1.72 23.0100002 23.0100002 109.7399979 0.724398 -0.689382 1.0 +8155 1 1.72 23.0100002 21.2399998 111.5100022 -0.533734 -0.845652 1.0 +8156 1 1.72 21.2399998 23.0100002 111.5100022 0.446337 0.894865 1.0 +8157 1 1.72 24.7800007 21.2399998 109.7399979 0.100506 -0.994936 1.0 +8158 1 1.72 26.5499993 23.0100002 109.7399979 0.663547 -0.748135 1.0 +8159 1 1.72 26.5499993 21.2399998 111.5100022 -0.838999 0.544134 1.0 +8160 1 1.72 24.7800007 23.0100002 111.5100022 -0.412355 -0.911023 1.0 +8161 1 1.72 0.0 24.7800007 109.7399979 -0.768577 -0.639757 1.0 +8162 1 1.72 1.77 26.5499993 109.7399979 0.876973 -0.480539 1.0 +8163 1 1.72 1.77 24.7800007 111.5100022 0.940988 0.33844 1.0 +8164 1 1.72 0.0 26.5499993 111.5100022 -0.739484 -0.673174 1.0 +8165 1 1.72 3.54 24.7800007 109.7399979 0.463964 0.885854 1.0 +8166 1 1.72 5.31 26.5499993 109.7399979 0.834599 0.550857 1.0 +8167 1 1.72 5.31 24.7800007 111.5100022 -0.414423 -0.910084 1.0 +8168 1 1.72 3.54 26.5499993 111.5100022 0.209991 0.977703 1.0 +8169 1 1.72 7.0799999 24.7800007 109.7399979 -0.200071 -0.979781 1.0 +8170 1 1.72 8.8500004 26.5499993 109.7399979 -0.593916 0.804527 1.0 +8171 1 1.72 8.8500004 24.7800007 111.5100022 -0.976341 -0.216238 1.0 +8172 1 1.72 7.0799999 26.5499993 111.5100022 0.892014 -0.452008 1.0 +8173 1 1.72 10.6199999 24.7800007 109.7399979 0.262541 0.964921 1.0 +8174 1 1.72 12.3900004 26.5499993 109.7399979 -0.541535 -0.840678 1.0 +8175 1 1.72 12.3900004 24.7800007 111.5100022 0.789328 0.613972 1.0 +8176 1 1.72 10.6199999 26.5499993 111.5100022 0.500046 0.865999 1.0 +8177 1 1.72 14.1599999 24.7800007 109.7399979 0.353277 0.935519 1.0 +8178 1 1.72 15.9300004 26.5499993 109.7399979 0.604788 0.796387 1.0 +8179 1 1.72 15.9300004 24.7800007 111.5100022 0.840508 -0.541799 1.0 +8180 1 1.72 14.1599999 26.5499993 111.5100022 0.296351 -0.955079 1.0 +8181 1 1.72 17.7000008 24.7800007 109.7399979 -0.957237 0.289304 1.0 +8182 1 1.72 19.4699993 26.5499993 109.7399979 0.344119 -0.938926 1.0 +8183 1 1.72 19.4699993 24.7800007 111.5100022 -0.989355 -0.145521 1.0 +8184 1 1.72 17.7000008 26.5499993 111.5100022 0.787109 0.616813 1.0 +8185 1 1.72 21.2399998 24.7800007 109.7399979 -0.321766 0.946819 1.0 +8186 1 1.72 23.0100002 26.5499993 109.7399979 -0.647284 -0.762249 1.0 +8187 1 1.72 23.0100002 24.7800007 111.5100022 -0.999094 0.0425548 1.0 +8188 1 1.72 21.2399998 26.5499993 111.5100022 -0.33438 0.942438 1.0 +8189 1 1.72 24.7800007 24.7800007 109.7399979 0.960667 -0.277704 1.0 +8190 1 1.72 26.5499993 26.5499993 109.7399979 0.822147 -0.569276 1.0 +8191 1 1.72 26.5499993 24.7800007 111.5100022 0.915832 -0.401561 1.0 +8192 1 1.72 24.7800007 26.5499993 111.5100022 -0.746316 -0.665592 1.0 diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data new file mode 100644 index 0000000000000000000000000000000000000000..80de0366616956ab9b505be148d19fadf3a0bdae --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -0,0 +1,45 @@ +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart new file mode 100644 index 0000000000000000000000000000000000000000..a1198ccf9351e07e8ae6784a49edece5dcbeab39 --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.restart @@ -0,0 +1,49 @@ +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart new file mode 100644 index 0000000000000000000000000000000000000000..84fea24611540156a0fdd9d1863d1b745aae67ef --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.write_restart @@ -0,0 +1,55 @@ +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +write_restart restart_hcp_cobalt.equil + diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..405be50bd987b18e6353ae8bd00bc6788c208247 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 @@ -0,0 +1,112 @@ +LAMMPS (11 May 2018) +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + orthogonal box = (0 0 0) to (28.32 28.32 113.28) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8192 atoms + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 8 8 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 0 0 0.980832325249102 -2984.9466433509 51.7121203365409 0 -38881.8459242429 + 10 0.001 0.980832325038224 -2984.94800197308 52.2550760237226 0.00128259392155095 -38881.8459243688 + 20 0.002 0.980832322622779 -2984.95196908579 53.4253029071033 0.0050206854169363 -38881.8459246487 + 30 0.003 0.980832317889283 -2984.95826684048 55.1488791221993 0.0109316238061975 -38881.8459250502 + 40 0.004 0.980832310888481 -2984.96649810512 57.3217709603901 0.0186091353316915 -38881.8459255204 + 50 0.005 0.980832301939686 -2984.97619813381 59.8271487572311 0.0275752699737783 -38881.8459260027 + 60 0.006 0.980832291654664 -2984.98688847988 62.5518654049861 0.0373348857300743 -38881.8459264498 + 70 0.007 0.980832280861627 -2984.99812400566 65.3978892661935 0.0474235455824994 -38881.845926824 + 80 0.008 0.980832270462785 -2985.00952679611 68.286219599829 0.0574425858114516 -38881.8459271072 + 90 0.009 0.980832261284587 -2985.02080458573 71.1539714621652 0.0670788260497413 -38881.8459272915 + 100 0.01 0.980832253960703 -2985.03175506188 73.9486358176052 0.0761100787140068 -38881.8459273845 +Loop time of 12.4286 on 1 procs for 100 steps with 8192 atoms + +Performance: 0.070 ns/day, 345.239 hours/ns, 8.046 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.0123 | 4.0123 | 4.0123 | 0.0 | 32.28 +Neigh | 3.005 | 3.005 | 3.005 | 0.0 | 24.18 +Comm | 0.041798 | 0.041798 | 0.041798 | 0.0 | 0.34 +Output | 1.8465 | 1.8465 | 1.8465 | 0.0 | 14.86 +Modify | 3.5157 | 3.5157 | 3.5157 | 0.0 | 28.29 +Other | | 0.007261 | | | 0.06 + +Nlocal: 8192 ave 8192 max 8192 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 14621 ave 14621 max 14621 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 573440 ave 573440 max 573440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1146880 +Ave neighs/atom = 140 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:12 diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..56fed3530760762fa2131929f31cb8343daac0e0 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 @@ -0,0 +1,112 @@ +LAMMPS (11 May 2018) +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + orthogonal box = (0 0 0) to (28.32 28.32 113.28) + 1 by 1 by 4 MPI processor grid + reading atoms ... + 8192 atoms + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 8 8 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.994 | 8.25 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 0 0 0.980832325249103 -2984.9466433509 51.7121203365411 0 -38881.8459242507 + 10 0.001 0.980832325329477 -2984.94800197307 52.2550778515409 0.00128259391683994 -38881.8459243698 + 20 0.002 0.980832324654401 -2984.95196908569 53.4253110612179 0.00502068532291255 -38881.8459246487 + 30 0.003 0.98083232312993 -2984.95826683995 55.148898005011 0.0109316232931419 -38881.84592505 + 40 0.004 0.980832320808156 -2984.9664981035 57.3218040934977 0.0186091337978305 -38881.8459255198 + 50 0.005 0.980832317596783 -2984.97619813016 59.827198436387 0.0275752665472358 -38881.8459260035 + 60 0.006 0.980832313514709 -2984.98688847322 62.5519331668858 0.037334879488755 -38881.84592645 + 70 0.007 0.980832309220414 -2984.99812399537 65.3979760533737 0.0474235360022736 -38881.8459268243 + 80 0.008 0.980832304490479 -2985.00952678209 68.2863250613635 0.0574425728014485 -38881.8459271068 + 90 0.009 0.980832299379824 -2985.02080456789 71.1540940309591 0.0670788096168283 -38881.8459272917 + 100 0.01 0.980832294622694 -2985.03175503971 73.9487734241296 0.0761100584457276 -38881.8459273851 +Loop time of 3.6612 on 4 procs for 100 steps with 8192 atoms + +Performance: 0.236 ns/day, 101.700 hours/ns, 27.313 timesteps/s +98.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0622 | 1.076 | 1.0936 | 1.1 | 29.39 +Neigh | 0.77462 | 0.79542 | 0.81798 | 1.9 | 21.73 +Comm | 0.024701 | 0.066122 | 0.10261 | 11.1 | 1.81 +Output | 0.50304 | 0.51253 | 0.52111 | 0.9 | 14.00 +Modify | 1.2006 | 1.2082 | 1.2205 | 0.7 | 33.00 +Other | | 0.002962 | | | 0.08 + +Nlocal: 2048 ave 2095 max 1981 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 5765 ave 5832 max 5718 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 143360 ave 146361 max 139058 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +FullNghs: 286720 ave 293300 max 277340 min +Histogram: 1 0 0 0 0 0 2 0 0 1 + +Total # of neighbors = 1146880 +Ave neighs/atom = 140 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..16eb7c3f5e9ccf9d72f69b6ac90a2a43cfe6d33b --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 @@ -0,0 +1,117 @@ +LAMMPS (11 May 2018) +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.315 | 6.315 | 6.315 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 1000 0 0.106120063678768 -11.8110267448938 5244.87332482316 0 -2206.81097898043 + 1010 0.001 0.106120047478105 -11.8198467887534 5263.87502105137 0.136650312456579 -2206.81097929055 + 1020 0.002 0.106120026430373 -11.8460960518731 5267.29822866382 0.542282409605327 -2206.81098022997 + 1030 0.003 0.106120005015917 -11.8891434078861 5252.95323564256 1.204018338139 -2206.81098172551 + 1040 0.004 0.106119988532653 -11.9479778701641 5220.88508622311 2.10120884995911 -2206.81098371047 + 1050 0.005 0.10611998133687 -12.021242685853 5172.58549378915 3.20622445795757 -2206.81098610701 + 1060 0.006 0.10611998489458 -12.107271344148 5110.57395203849 4.48535975411235 -2206.81098879725 + 1070 0.007 0.106119996964771 -12.204156761765 5038.48903231346 5.9003121044977 -2206.81099161183 + 1080 0.008 0.106120013042521 -12.3098695046152 4961.0327167967 7.4104497466856 -2206.81099434653 + 1090 0.009 0.106120029236234 -12.4224157835754 4883.3210922213 8.97568980540163 -2206.81099680117 + 1100 0.01 0.106120044071404 -12.5400036896932 4809.88136080052 10.559459821976 -2206.81099883104 +Loop time of 0.833234 on 1 procs for 100 steps with 500 atoms + +Performance: 1.037 ns/day, 23.145 hours/ns, 120.014 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.26558 | 0.26558 | 0.26558 | 0.0 | 31.87 +Neigh | 0.21352 | 0.21352 | 0.21352 | 0.0 | 25.62 +Comm | 0.0057988 | 0.0057988 | 0.0057988 | 0.0 | 0.70 +Output | 0.12463 | 0.12463 | 0.12463 | 0.0 | 14.96 +Modify | 0.22275 | 0.22275 | 0.22275 | 0.0 | 26.73 +Other | | 0.0009537 | | | 0.11 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2534 ave 2534 max 2534 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36500 ave 36500 max 36500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 73000 ave 73000 max 73000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..f93605a10a2e28eb923241d1fc629eea81ecf31f --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 @@ -0,0 +1,118 @@ +LAMMPS (11 May 2018) +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil +WARNING: Restart file used different # of processors (../read_restart.cpp:723) + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 1000 0 0.106120063678768 -11.8110267448939 5244.87332482316 0 -2206.81097898003 + 1010 0.001 0.106120030254187 -11.8198467883806 5263.87550015043 0.136650306637598 -2206.81097929055 + 1020 0.002 0.106119996655714 -11.8460960476455 5267.299198699 0.542282344092749 -2206.81098022997 + 1030 0.003 0.106119967407682 -11.8891433919665 5252.95473019843 1.20401809237154 -2206.81098172552 + 1040 0.004 0.106119960016585 -11.9479778326021 5220.88686874944 2.10120827278397 -2206.81098371049 + 1050 0.005 0.106119961252471 -12.0212426191481 5172.58712301374 3.20622343988728 -2206.81098610703 + 1060 0.006 0.106119967598995 -12.1072712483404 5110.57504803718 4.48535830705751 -2206.81098879724 + 1070 0.007 0.106119967669058 -12.2041566468564 5038.48927079832 5.90031039867811 -2206.81099161179 + 1080 0.008 0.106119969263395 -12.3098693905406 4961.03212459716 7.41044810751949 -2206.8109943465 + 1090 0.009 0.106119960964075 -12.4224156966204 4883.31968289062 8.97568865379831 -2206.81099680112 + 1100 0.01 0.106119945605273 -12.5400036591612 4809.87930844463 10.5594596175303 -2206.81099883101 +Loop time of 0.304678 on 4 procs for 100 steps with 500 atoms + +Performance: 2.836 ns/day, 8.463 hours/ns, 328.215 timesteps/s +98.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.071445 | 0.073018 | 0.074151 | 0.4 | 23.97 +Neigh | 0.054448 | 0.055709 | 0.057528 | 0.5 | 18.28 +Comm | 0.0061178 | 0.0074609 | 0.0090766 | 1.2 | 2.45 +Output | 0.037489 | 0.038586 | 0.039952 | 0.5 | 12.66 +Modify | 0.12826 | 0.12954 | 0.13065 | 0.3 | 42.52 +Other | | 0.0003686 | | | 0.12 + +Nlocal: 125 ave 129 max 120 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 1387 ave 1392 max 1383 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 9125 ave 9428 max 8740 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 18250 ave 18834 max 17520 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c3be90cb505bace4db678ff8fb4f94d5dce948d2 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 @@ -0,0 +1,119 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.00027585 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + 500 settings made for spin/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.446 | 6.446 | 6.446 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.076558814 1.7982359 0 1.7982359 + 100 0.01 0.079107243 0.56368447 0 0.56368447 + 200 0.02 0.08225862 -0.42421042 0 -0.42421042 + 300 0.03 0.08397714 -1.4964948 0 -1.4964948 + 400 0.04 0.084704989 -2.6740652 0 -2.6740652 + 500 0.05 0.087486342 -4.2043382 0 -4.2043382 + 600 0.06 0.09187261 -5.6687169 0 -5.6687169 + 700 0.07 0.096925249 -6.937499 0 -6.937499 + 800 0.08 0.098988236 -8.2456715 0 -8.2456715 + 900 0.09 0.10434092 -10.111953 0 -10.111953 + 1000 0.1 0.10612006 -11.811027 0 -11.811027 +Loop time of 2.60215 on 1 procs for 1000 steps with 500 atoms + +Performance: 3.320 ns/day, 7.228 hours/ns, 384.297 timesteps/s +99.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.35178 | 0.35178 | 0.35178 | 0.0 | 13.52 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014421 | 0.014421 | 0.014421 | 0.0 | 0.55 +Output | 1.2046 | 1.2046 | 1.2046 | 0.0 | 46.29 +Modify | 1.0274 | 1.0274 | 1.0274 | 0.0 | 39.48 +Other | | 0.004006 | | | 0.15 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1221 ave 1221 max 1221 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 10000 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..e54299b9ddbef2d6328c7d4cc1b62c212ddcc019 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 @@ -0,0 +1,119 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000257969 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + 500 settings made for spin/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.367 | 6.367 | 6.367 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.076558814 1.7982359 0 1.7982359 + 100 0.01 0.081414414 0.70545723 0 0.70545723 + 200 0.02 0.084519539 -0.33171078 0 -0.33171078 + 300 0.03 0.089334139 -1.3988283 0 -1.3988283 + 400 0.04 0.092873722 -2.8519371 0 -2.8519371 + 500 0.05 0.0970839 -4.1531164 0 -4.1531164 + 600 0.06 0.099626132 -5.7993765 0 -5.7993765 + 700 0.07 0.10467169 -7.3011333 0 -7.3011333 + 800 0.08 0.10893493 -8.6918141 0 -8.6918141 + 900 0.09 0.11389657 -10.236174 0 -10.236174 + 1000 0.1 0.1180057 -11.896933 0 -11.896933 +Loop time of 1.05012 on 4 procs for 1000 steps with 500 atoms + +Performance: 8.228 ns/day, 2.917 hours/ns, 952.272 timesteps/s +98.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.08972 | 0.090456 | 0.091872 | 0.3 | 8.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.016958 | 0.018047 | 0.019791 | 0.8 | 1.72 +Output | 0.36286 | 0.37483 | 0.38975 | 1.6 | 35.69 +Modify | 0.55131 | 0.56541 | 0.57702 | 1.3 | 53.84 +Other | | 0.001374 | | | 0.13 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 597.5 ave 600 max 595 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2500 ave 2500 max 2500 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/SPIN/vmd/prepare_vmd.sh b/examples/SPIN/vmd/prepare_vmd.sh new file mode 100755 index 0000000000000000000000000000000000000000..fa62c6e109d75315abbd26bb4467d7c5d02c9cb3 --- /dev/null +++ b/examples/SPIN/vmd/prepare_vmd.sh @@ -0,0 +1,91 @@ +#!/bin/bash +# example prepare_vmd.sh /home/jtranch/Documents/lammps/src/dump_VSRSV.lammpstrj +# you will get a return file + +echo "vmd script for file $1 is preparing..." + +timestamp(){ + date +%s +} + +TS=$(timestamp) +FILE=view_${TS}.vmd + +cat >${FILE} <] [resolution ] [radius ] [filled ]"} + # defaults + set scale 2.0 + set res 50 + set radius 0.1 + set filled yes + + if {[llength \$args] < 3} { + error "wrong # args: should be \$usage" + } + set mol [lindex \$args 0] + set center [lindex \$args 1] + set vector [lindex \$args 2] + if {[llength \$center] != 3 || [llength \$vector] != 3} { + error "wrong type of args: should be \$usage" + } + + foreach {flag value} [lrange \$args 3 end] { + switch -glob \$flag { + scale {set scale \$value} + res* {set res \$value} + rad* {set radius \$value} + fill* {set filled \$value} + default {error "unknown option '\$flag': should be \$usage" } + } + } + + set vechalf [vecscale [expr \$scale * 0.5] \$vector] + return [list \\ + [graphics \$mol color yellow]\\ + [graphics \$mol cylinder [vecsub \$center \$vechalf]\\ + [vecadd \$center [vecscale 0.7 \$vechalf]] \\ + radius \$radius resolution \$res filled \$filled] \\ + [graphics \$mol color orange]\\ + [graphics \$mol cone [vecadd \$center [vecscale 0.6 \$vechalf]] \\ + [vecadd \$center \$vechalf] radius [expr \$radius * 2.5] \\ + resolution \$res]] +} + +proc vmd_draw_spin {args} { + global molid + graphics \$molid delete all + set frame [molinfo \$molid get frame] + set natoms [molinfo \$molid get numatoms] + for {set i 0} {\$i < \$natoms} {incr i} { + set sel [atomselect top "index \$i"] + set coords [lindex [\$sel get {x y z}] \$molid] + set velocities [lindex [\$sel get {vx vy vz}] \$molid] + draw vector \$coords \$velocities + set uvx [lindex [\$sel get {vx}] \$molid] + set uvy [lindex [\$sel get {vy}] \$molid] + set uvz [lindex [\$sel get {vz}] \$molid] + \$sel set user [vecadd [vecadd [vecscale \$uvy \$uvy] [vecscale \$uvz \$uvz] ] [vecscale \$uvx \$uvx]] + \$sel set user \$uvy + #draw vector \$coords {0.0 uvy 0.0} + } + #pbc box -color 3 +} + +proc enable_trace {} { + global vmd_frame + trace variable vmd_frame([molinfo top]) w vmd_draw_spin +} + +set molid [mol addfile {$1} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all] +scale by 0.5 +animate style Loop +enable_trace +EOF +echo "$FILE is ready..." diff --git a/examples/SPIN/vmd/vmd_nano.vmd b/examples/SPIN/vmd/vmd_nano.vmd new file mode 100644 index 0000000000000000000000000000000000000000..f9e345427076250c5c98e96a9f9b625c6354947d --- /dev/null +++ b/examples/SPIN/vmd/vmd_nano.vmd @@ -0,0 +1,79 @@ +proc vmd_draw_arrow {mol start end} { + set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]] + graphics $mol cylinder $start $middle radius 0.05 + graphics $mol cone $middle $end radius 0.01 color 3 +} + +proc vmd_draw_vector {args} { + set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale ] [resolution ] [radius ] [filled ]"} + # defaults + set scale 2.0 + set res 50 + set radius 0.1 + set filled yes + + if {[llength $args] < 3} { + error "wrong # args: should be $usage" + } + set mol [lindex $args 0] + set center [lindex $args 1] + set vector [lindex $args 2] + if {[llength $center] != 3 || [llength $vector] != 3} { + error "wrong type of args: should be $usage" + } + + foreach {flag value} [lrange $args 3 end] { + switch -glob $flag { + scale {set scale $value} + res* {set res $value} + rad* {set radius $value} + fill* {set filled $value} + default {error "unknown option '$flag': should be $usage" } + } + } + + set vechalf [vecscale [expr $scale * 0.5] $vector] + return [list \ + [graphics $mol color yellow]\ + [graphics $mol cylinder [vecsub $center $vechalf]\ + [vecadd $center [vecscale 0.7 $vechalf]] \ + radius $radius resolution $res filled $filled] \ + [graphics $mol color orange]\ + [graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \ + [vecadd $center $vechalf] radius [expr $radius * 2.5] \ + resolution $res]] +} + +proc vmd_draw_spin {args} { + global molid + graphics $molid delete all + set frame [molinfo $molid get frame] + set natoms [molinfo $molid get numatoms] + for {set i 0} {$i < $natoms} {incr i} { + set sel [atomselect top "index $i"] +# set sel [atomselect top "index 1200"] + set coords [lindex [$sel get {x y z}] $molid] + set velocities [lindex [$sel get {vx vy vz}] $molid] + draw vector $coords $velocities + set uvx [lindex [$sel get {vx}] $molid] + set uvy [lindex [$sel get {vy}] $molid] + set uvz [lindex [$sel get {vz}] $molid] + $sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]] + $sel set user $uvy + #draw vector $coords {0.0 uvy 0.0} + } + #pbc box -color 3 +} + +proc enable_trace {} { + global vmd_frame + trace variable vmd_frame([molinfo top]) w vmd_draw_spin + } + +set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all] +scale by 0.5 +animate style Loop +enable_trace + + + diff --git a/examples/USER/bocs/README b/examples/USER/bocs/README new file mode 100644 index 0000000000000000000000000000000000000000..ae1739f8c0378256a7232290ecdd6a3a238bc7e9 --- /dev/null +++ b/examples/USER/bocs/README @@ -0,0 +1,6 @@ +This folder contains the files to run a NPT simulation of 1 site CG methanol +while employing a correction to the barostat. +The pair force was computed via the Multi-Scale Coarse-Graining method. +The resulting model was then iteratively pressure matched. +The model accurately reproduces both structural (RDF) and thermodynamic +(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol. diff --git a/examples/USER/bocs/in.methanol b/examples/USER/bocs/in.methanol new file mode 100644 index 0000000000000000000000000000000000000000..e7c80e014d04de182615de67dd142c54034beccf --- /dev/null +++ b/examples/USER/bocs/in.methanol @@ -0,0 +1,69 @@ +units real +dimension 3 +boundary p p p +atom_style atomic + +newton on +timestep 1.0 + +read_data methanol.data + +velocity all create 300.0 16802 dist gaussian + +pair_style table spline 15000 + +pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 + +neigh_modify delay 0 every 1 check yes one 10000 +neighbor 12.0 bin + +thermo 500 +thermo_style custom step temp pe etotal press vol + +variable STEP equal step +variable TEMP equal temp +## volume from cubic angstroms to cubic nm +variable VOL equal vol/1000.0 +## pressure from atm to bar +variable PRESS equal press*1.01325 +variable PXX equal pxx*1.01325 +variable PYY equal pyy*1.01325 +variable PZZ equal pzz*1.01325 +variable PXY equal pxy*1.01325 +variable PXZ equal pxz*1.01325 +variable PYZ equal pyz*1.01325 +## energy from kcal/mol to kJ/mol +variable KE equal ke*4.184 +variable PE equal pe*4.184 +variable UVDW equal evdwl*4.184 + + +##### SPECIAL COMMANDS FOR FIX_BOCS ##### +# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2 +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 + +# Report the modified pressure +thermo_modify press 1_press + + + +## Uncomment to save some data from simulation to files +#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no +#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no +#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no +#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no +#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no +#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no +#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no +#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no + +## Prints a configuration to dump.txt every 500 steps +#dump 1 all custom 500 dump.txt id type x y z fx fy fz + +# Write restart files to continue simulations +#restart 10000 state1.restart state2.restart + +## Run for this many steps +run_style verlet +run 10000 + diff --git a/examples/USER/bocs/lammps_nb_MET-MET.table b/examples/USER/bocs/lammps_nb_MET-MET.table new file mode 100644 index 0000000000000000000000000000000000000000..c6d9fc6ca251cd012c78f50b1e86bc03c72cc6be --- /dev/null +++ b/examples/USER/bocs/lammps_nb_MET-MET.table @@ -0,0 +1,2505 @@ +#Converted from table.xvg + +nb_METMET +N 2500 + +1 0.010000 573.151769 380.122371 +2 0.020000 569.356836 378.855163 +3 0.030000 565.574570 377.588193 +4 0.040000 561.805210 376.320985 +5 0.050000 558.048279 375.053776 +6 0.060000 554.304015 373.786807 +7 0.070000 550.572419 372.519598 +8 0.080000 546.853728 371.252390 +9 0.090000 543.147467 369.985421 +10 0.100000 539.453872 368.718212 +11 0.110000 535.773184 367.451004 +12 0.120000 532.104924 366.184034 +13 0.130000 528.449331 364.916826 +14 0.140000 524.806644 363.649618 +15 0.150000 521.176386 362.382648 +16 0.160000 517.559034 361.115440 +17 0.170000 513.954111 359.848231 +18 0.180000 510.361855 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0.000000 0.000000 +2497 24.970000 0.000000 0.000000 +2498 24.980000 0.000000 0.000000 +2499 24.990000 0.000000 0.000000 +2500 25.000000 0.000000 0.000000 diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.1 b/examples/USER/bocs/log.20Apr18.methanol.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..a94bd959c816c3cb1faa1b03ee9dc176b5301950 --- /dev/null +++ b/examples/USER/bocs/log.20Apr18.methanol.g++.1 @@ -0,0 +1,143 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +units real +dimension 3 +boundary p p p +atom_style atomic + +newton on +timestep 1.0 + +read_data methanol.data + orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 968 atoms + +velocity all create 300.0 16802 dist gaussian + +pair_style table spline 15000 + +pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 +WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:481) + +neigh_modify delay 0 every 1 check yes one 10000 +neighbor 12.0 bin + +thermo 500 +thermo_style custom step temp pe etotal press vol + +variable STEP equal step +variable TEMP equal temp +## volume from cubic angstroms to cubic nm +variable VOL equal vol/1000.0 +## pressure from atm to bar +variable PRESS equal press*1.01325 +variable PXX equal pxx*1.01325 +variable PYY equal pyy*1.01325 +variable PZZ equal pzz*1.01325 +variable PXY equal pxy*1.01325 +variable PXZ equal pxz*1.01325 +variable PYZ equal pyz*1.01325 +## energy from kcal/mol to kJ/mol +variable KE equal ke*4.184 +variable PE equal pe*4.184 +variable UVDW equal evdwl*4.184 + + +##### SPECIAL COMMANDS FOR FIX_BOCS ##### +# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2 +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 + +# Report the modified pressure +thermo_modify press 1_press + + + +## Uncomment to save some data from simulation to files +#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no +#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no +#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no +#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no +#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no +#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no +#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no +#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no + +## Prints a configuration to dump.txt every 500 steps +#dump 1 all custom 500 dump.txt id type x y z fx fy fz + +# Write restart files to continue simulations +#restart 10000 state1.restart state2.restart + +## Run for this many steps +run_style verlet +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 10000, page size: 100000 + master list distance cutoff = 24 + ghost atom cutoff = 24 + binsize = 12, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes +Step Temp PotEng TotEng Press Volume + 0 300 1061.5961 1926.3291 107.006 66250.679 + 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 + 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 + 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 + 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 + 2500 301.18564 1033.9214 1902.0719 40.48255 66607.667 + 3000 301.06632 1022.0381 1889.8447 47.582344 66341.947 + 3500 297.98361 989.80983 1848.7307 -204.69879 67462.078 + 4000 299.03493 1034.6571 1896.6083 89.188888 66457.385 + 4500 306.03351 985.4121 1867.5363 -51.102407 67519.446 + 5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467 + 5500 292.23444 1029.5558 1871.905 20.764579 66683.876 + 6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031 + 6500 305.26461 960.08118 1839.9891 -352.42596 67612.317 + 7000 300.34449 1055.0664 1920.7923 22.04027 66187.27 + 7500 305.48612 1038.6651 1919.2115 17.807254 66324.168 + 8000 316.03232 1034.6809 1945.6262 27.482857 66502.198 + 8500 294.28636 1038.8213 1887.085 -72.840559 66851.661 + 9000 316.69029 1065.7481 1978.5899 245.61677 65678.385 + 9500 297.46127 1034.5547 1891.97 54.23428 66892.627 + 10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506 +Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms + +Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80 +Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35 +Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25 +Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00 +Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24 +Other | | 0.1252 | | | 0.36 + +Nlocal: 968 ave 968 max 968 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9112 ave 9112 max 9112 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 404392 ave 404392 max 404392 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 404392 +Ave neighs/atom = 417.76 +Neighbor list builds = 13 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:34 diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.4 b/examples/USER/bocs/log.20Apr18.methanol.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..cf5891f97cbf6fee1cc998fb40fb4e8e7cb04a24 --- /dev/null +++ b/examples/USER/bocs/log.20Apr18.methanol.g++.4 @@ -0,0 +1,143 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +units real +dimension 3 +boundary p p p +atom_style atomic + +newton on +timestep 1.0 + +read_data methanol.data + orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 968 atoms + +velocity all create 300.0 16802 dist gaussian + +pair_style table spline 15000 + +pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 +WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:481) + +neigh_modify delay 0 every 1 check yes one 10000 +neighbor 12.0 bin + +thermo 500 +thermo_style custom step temp pe etotal press vol + +variable STEP equal step +variable TEMP equal temp +## volume from cubic angstroms to cubic nm +variable VOL equal vol/1000.0 +## pressure from atm to bar +variable PRESS equal press*1.01325 +variable PXX equal pxx*1.01325 +variable PYY equal pyy*1.01325 +variable PZZ equal pzz*1.01325 +variable PXY equal pxy*1.01325 +variable PXZ equal pxz*1.01325 +variable PYZ equal pyz*1.01325 +## energy from kcal/mol to kJ/mol +variable KE equal ke*4.184 +variable PE equal pe*4.184 +variable UVDW equal evdwl*4.184 + + +##### SPECIAL COMMANDS FOR FIX_BOCS ##### +# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2 +fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 + +# Report the modified pressure +thermo_modify press 1_press + + + +## Uncomment to save some data from simulation to files +#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no +#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no +#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no +#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no +#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no +#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no +#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no +#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no + +## Prints a configuration to dump.txt every 500 steps +#dump 1 all custom 500 dump.txt id type x y z fx fy fz + +# Write restart files to continue simulations +#restart 10000 state1.restart state2.restart + +## Run for this many steps +run_style verlet +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 10000, page size: 100000 + master list distance cutoff = 24 + ghost atom cutoff = 24 + binsize = 12, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes +Step Temp PotEng TotEng Press Volume + 0 300 1061.5961 1926.3291 107.006 66250.679 + 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 + 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 + 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 + 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 + 2500 301.18564 1033.9214 1902.0719 40.482557 66607.667 + 3000 301.06631 1022.0381 1889.8447 47.582403 66341.947 + 3500 297.98353 989.81011 1848.7308 -204.69823 67462.076 + 4000 299.03465 1034.6603 1896.6108 89.196235 66457.338 + 4500 306.04532 985.37017 1867.5285 -51.094929 67519.735 + 5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517 + 5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551 + 6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611 + 6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898 + 7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674 + 7500 292.45089 1068.2863 1911.2595 103.23295 65778.08 + 8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038 + 8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305 + 9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344 + 9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361 + 10000 296.3083 1004.126 1858.2178 -28.293045 66862.576 +Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms + +Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s +95.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56 +Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25 +Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16 +Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01 +Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95 +Other | | 0.3112 | | | 1.08 + +Nlocal: 242 ave 244 max 239 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 5718.5 ave 5736 max 5702 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 100703 ave 108064 max 93454 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 402813 +Ave neighs/atom = 416.129 +Neighbor list builds = 14 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:28 diff --git a/examples/USER/bocs/methanol.data b/examples/USER/bocs/methanol.data new file mode 100644 index 0000000000000000000000000000000000000000..01f66de6f62294929f87497522ae541b567596a0 --- /dev/null +++ b/examples/USER/bocs/methanol.data @@ -0,0 +1,991 @@ +LAMMPS Description + + 968 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 impropers + + 1 atom types + 0 bond types + 0 angle types + 0 dihedral types + + 0 40.4635 xlo xhi + 0 40.4635 ylo yhi + 0 40.4635 zlo zhi + +Masses + + 1 32.0424 + +Atoms + +1 1 36.39 8.05 27.55 +2 1 18.38 15.72 26.03 +3 1 3.52 1.77 23.57 +4 1 31.09 11.38 12.17 +5 1 13.3 34.8 2.89 +6 1 1.72 38.55 10.36 +7 1 38.6 23.16 6.19 +8 1 0.74 33.21 0.17 +9 1 26.97 9.53 11.24 +10 1 31.68 12.19 17.04 +11 1 15.19 9.06 0.2 +12 1 34.39 20.63 35.71 +13 1 21.79 4.93 6.49 +14 1 28.08 33.01 24.51 +15 1 37.03 20.52 32.9 +16 1 32.69 20 30.11 +17 1 23.77 38.59 18.79 +18 1 16.01 2.31 20.15 +19 1 5.65 15.5 28.5 +20 1 8.35 17.35 20.48 +21 1 31.24 24.68 27.4 +22 1 29.41 16.64 19.79 +23 1 37.42 31.93 26.68 +24 1 18.76 39.06 30.68 +25 1 22.97 35 20.81 +26 1 39.47 18.28 29.6 +27 1 34.37 19.4 0.17 +28 1 5.94 9.53 10.95 +29 1 11.45 38.44 14.64 +30 1 39.57 11.04 1.57 +31 1 25.91 20.97 12.79 +32 1 36.3 22.1 1.68 +33 1 21.87 22.49 3.43 +34 1 5.77 18.66 3.97 +35 1 7 7.59 18.42 +36 1 39.76 27.63 17.98 +37 1 10.26 23.18 5.11 +38 1 23.23 21.37 17.38 +39 1 7.47 37.37 5.57 +40 1 0.73 21.6 14.78 +41 1 2.27 30.22 14.93 +42 1 7.39 28.22 14.88 +43 1 27.48 1.11 25.02 +44 1 8.37 13.19 14.64 +45 1 7.11 33.57 0.65 +46 1 34.19 35.11 3.17 +47 1 7.52 3.2 20.33 +48 1 1.02 17.69 37.85 +49 1 8.59 6.21 10.26 +50 1 2.89 16.81 30.02 +51 1 27.05 9.07 32.8 +52 1 12.32 14.79 21.11 +53 1 26.63 22.69 16.75 +54 1 31.6 2.79 20.45 +55 1 35.11 0.74 12.16 +56 1 29.71 31.23 37.63 +57 1 38.22 19.02 18.12 +58 1 10.95 17.4 0.39 +59 1 1.65 19.87 6.67 +60 1 5.15 1.94 14.61 +61 1 8.2 31.43 15.72 +62 1 0.55 20.85 2.45 +63 1 15.27 31.74 0.33 +64 1 17.9 9.84 23.87 +65 1 1.46 8.39 19.24 +66 1 37.79 25.11 12.24 +67 1 14.11 27.19 30.7 +68 1 29.39 24.12 38.92 +69 1 39.15 20.32 39.86 +70 1 11.79 11.38 30.6 +71 1 29.87 30.18 32.5 +72 1 11.06 37.8 30.18 +73 1 20.11 4.59 35.57 +74 1 37.19 27.23 1.44 +75 1 18.83 26.13 35.26 +76 1 29.27 7.86 36.75 +77 1 34.83 29.59 37.82 +78 1 22.16 34.68 25.27 +79 1 5.95 14.65 25.55 +80 1 -0.04 3.48 29.91 +81 1 14.69 6.75 38.06 +82 1 16.8 23.69 3.14 +83 1 14.52 38.72 21.61 +84 1 37.36 15.13 27.98 +85 1 29.79 17.03 27.55 +86 1 21.01 0.39 0.9 +87 1 35.3 6.45 14.41 +88 1 13.74 34.69 10.01 +89 1 13.83 7.92 31.88 +90 1 26.88 37.81 22.36 +91 1 31.76 7.34 10.03 +92 1 11.98 37.49 19.61 +93 1 29.19 31.74 20.69 +94 1 39.15 10.97 21.06 +95 1 1.47 5 22.21 +96 1 -0.1 1.33 16.26 +97 1 34.74 34.78 30.66 +98 1 22.09 26.78 2.27 +99 1 36.58 34.8 16.19 +100 1 19.09 24.88 15.75 +101 1 2.21 31.42 38.32 +102 1 28.02 8.18 29.77 +103 1 15.99 16.78 17.61 +104 1 32.43 12.2 35.3 +105 1 26.54 38.8 30.88 +106 1 35.58 22.23 18.31 +107 1 28.3 30.81 2.96 +108 1 8.95 32.9 9.02 +109 1 28.51 30.02 29.39 +110 1 13 5.35 34.26 +111 1 37.9 36.79 1.37 +112 1 12.78 1.99 40.66 +113 1 21.19 34.55 17.45 +114 1 10.5 20 5.07 +115 1 16.19 21.64 18.49 +116 1 14.62 26.41 19.88 +117 1 27.97 2.89 28.03 +118 1 29.44 14.35 39.04 +119 1 2.29 24.16 33.8 +120 1 39.22 15.81 32.02 +121 1 7.31 19.66 18.18 +122 1 27.67 7.98 15.53 +123 1 31.23 4.04 33 +124 1 29.52 39.44 28.71 +125 1 30.86 20.28 15.84 +126 1 32.25 7.44 19.79 +127 1 34.68 15.68 1.18 +128 1 16.58 27.98 27.97 +129 1 32.27 24.24 15.82 +130 1 3.86 6.57 39.8 +131 1 9.1 2.88 13.12 +132 1 17.84 27.8 11.79 +133 1 4.77 10.88 6.75 +134 1 16.58 24.21 24.5 +135 1 10.17 19.31 38.32 +136 1 6.27 7.81 36.44 +137 1 34.76 37.89 29.76 +138 1 40.99 38.22 35.21 +139 1 25.04 21.79 36.88 +140 1 4.78 15.35 16.44 +141 1 19.24 5.77 40.18 +142 1 13.59 11.27 37.14 +143 1 1.61 23.83 39.61 +144 1 6.02 33.07 3.77 +145 1 0.85 7.4 35.42 +146 1 6.47 40.34 4.65 +147 1 16.45 36.52 15.44 +148 1 19.58 9.5 1.64 +149 1 1.36 1.72 35.53 +150 1 11.74 5.48 4.98 +151 1 25.45 40.36 15.44 +152 1 19.09 0.74 36.18 +153 1 31.78 37.98 1.84 +154 1 23.26 18.47 38.56 +155 1 7.29 22.87 25.86 +156 1 2.36 7.83 8.78 +157 1 39.61 25.94 21.12 +158 1 7.78 18.97 25.29 +159 1 36.56 19.61 26.7 +160 1 4.64 12.06 19.9 +161 1 21.05 33.08 0.87 +162 1 33.93 22.87 39.71 +163 1 33.62 29.48 20.83 +164 1 0.64 18.79 9.52 +165 1 27.53 16.7 22.51 +166 1 17.66 9.84 14.61 +167 1 31.23 22.44 24.98 +168 1 39.3 34.88 11.03 +169 1 24.01 10.56 0.09 +170 1 15.81 33.44 18.52 +171 1 19.92 30.61 19.25 +172 1 16.49 3.95 38.28 +173 1 18.6 38.87 24.98 +174 1 33.04 25.55 8.57 +175 1 16.9 35.09 22.94 +176 1 15.18 6.74 2.33 +177 1 40.54 12.58 31.65 +178 1 21.21 37.62 14.35 +179 1 33.52 38.19 14.89 +180 1 22.06 12.49 29.81 +181 1 19.49 29.03 2.52 +182 1 26.97 18.55 38.45 +183 1 24.1 11.86 17.22 +184 1 12.02 0.55 10.39 +185 1 3.8 35.94 19.94 +186 1 8.31 14.31 37.4 +187 1 29.03 8.28 22.92 +188 1 18.92 0.22 27.87 +189 1 26.79 24.9 24.62 +190 1 36.59 18.86 21.13 +191 1 33.06 13.58 30.17 +192 1 32.37 2.02 39.69 +193 1 22.65 25.97 32.59 +194 1 21.81 38.04 33.85 +195 1 36.82 37.68 19.22 +196 1 32.48 31.43 33.66 +197 1 8.75 36.66 20.34 +198 1 14.88 15.11 28.76 +199 1 22.83 28.55 29.5 +200 1 2.98 12.06 2.88 +201 1 3.01 37 6.91 +202 1 14.79 16.69 3.66 +203 1 12.62 38.28 0.97 +204 1 40.07 21.27 25.25 +205 1 34.58 6.14 39.48 +206 1 11.51 30.52 33.53 +207 1 32.22 9.28 30.52 +208 1 0.7 4.01 38.87 +209 1 32.66 39.86 36.84 +210 1 27.34 34.57 21.76 +211 1 13.7 23.12 8.34 +212 1 28 9.71 6.29 +213 1 31.69 26.39 38.19 +214 1 2.04 20.93 36.95 +215 1 30.31 26.61 12.31 +216 1 25.37 20.63 9.4 +217 1 16.29 5.62 14.04 +218 1 1.36 1.95 4.97 +219 1 38.75 26.8 5.62 +220 1 40.28 29.89 12.27 +221 1 0.52 31.22 7.58 +222 1 15.64 21.64 14.71 +223 1 10.11 28.8 9.67 +224 1 19.03 37.3 38.87 +225 1 12.07 6.46 19.25 +226 1 36.22 21.11 15.02 +227 1 12.49 15.69 7.21 +228 1 25.2 30.8 19.71 +229 1 8.24 35.22 23.02 +230 1 9.94 4.1 1.86 +231 1 4.31 19.07 26.23 +232 1 22.03 19.99 14.19 +233 1 30.84 5.24 2.75 +234 1 35.51 30.52 32.3 +235 1 3.88 20.41 39.48 +236 1 30.86 0.39 31.56 +237 1 25.91 27.12 39.04 +238 1 33.39 5.37 4.51 +239 1 20.58 28.33 37.53 +240 1 11.83 21.81 39.11 +241 1 39.94 5.2 5.73 +242 1 29.89 33.21 15.44 +243 1 23.42 15.38 30.98 +244 1 28.66 11.56 16.13 +245 1 16.74 20.43 21.72 +246 1 9.31 0.26 22.42 +247 1 4.38 37.78 14.12 +248 1 13.86 4.65 16.99 +249 1 6.72 27.43 8.14 +250 1 33.45 18.74 19.98 +251 1 17.34 14.55 35.57 +252 1 14.21 37.39 28.76 +253 1 26.29 29.06 22.26 +254 1 36.52 26.18 15.62 +255 1 17.6 8.81 10.14 +256 1 21.95 25.19 17.69 +257 1 17.4 7.46 18.59 +258 1 6.15 29.7 35.99 +259 1 9.73 37.39 24.96 +260 1 28.58 28.21 36.19 +261 1 8.24 13.72 32.2 +262 1 13.25 34.6 22.71 +263 1 38.58 7.98 10.3 +264 1 18.29 29.75 23.51 +265 1 3.74 13.22 31.05 +266 1 30.78 0.7 24.57 +267 1 24.5 12.94 10.81 +268 1 33.88 26.44 1.96 +269 1 29.92 22.6 9.59 +270 1 15.87 21.94 33.44 +271 1 23.63 8.41 10.95 +272 1 26.53 0.01 7.58 +273 1 33.88 8.73 2.52 +274 1 39.74 31.46 36.87 +275 1 13.28 39.54 37 +276 1 24.74 35.41 32.14 +277 1 17.3 34.32 6.85 +278 1 24.43 13.36 5.63 +279 1 31.23 17.12 7.11 +280 1 15.58 37.85 34.06 +281 1 25.93 38.17 3.13 +282 1 31.84 34.34 39.67 +283 1 14.41 17.74 14.43 +284 1 9.4 1.78 29.53 +285 1 8.29 29.61 6.81 +286 1 7.13 17.36 -0.19 +287 1 38.04 19.52 11.25 +288 1 34.87 32.77 38.75 +289 1 27.18 22.49 5.69 +290 1 29.69 27.11 20.29 +291 1 25.23 2.22 39.75 +292 1 35.8 17.1 36.09 +293 1 20.53 17.67 35.47 +294 1 23.41 31.36 2.24 +295 1 25.17 20.09 29.2 +296 1 0.32 9.28 39.74 +297 1 22.49 18.77 29.89 +298 1 38.64 0.85 39.43 +299 1 18.55 5.87 9.15 +300 1 35.21 28.69 25.76 +301 1 39.24 15.68 6.36 +302 1 5.91 13.29 3.92 +303 1 0.5 21.25 21.62 +304 1 34.39 9.43 18.59 +305 1 22.7 1.03 8.79 +306 1 40.15 16.25 24.87 +307 1 16.52 13.69 10.25 +308 1 6.88 36.77 39.57 +309 1 11.95 37.1 7.59 +310 1 19.49 26.66 9.76 +311 1 36.34 29.89 29.31 +312 1 18.76 35.75 12.72 +313 1 23.15 38.68 4.96 +314 1 10.78 17.11 34.38 +315 1 13.58 14.89 0.34 +316 1 4.73 33.88 32.41 +317 1 12.68 29.51 17.07 +318 1 9.45 27 4.98 +319 1 29.02 19.27 6.45 +320 1 19.09 36.35 19.84 +321 1 23.13 6.75 19.78 +322 1 8.02 34.1 26.95 +323 1 26.03 14.18 1.57 +324 1 15.01 34.16 28.32 +325 1 28.71 36.53 15.08 +326 1 9.64 13.94 24.05 +327 1 1.24 36.96 30.41 +328 1 15.44 31.39 4.77 +329 1 25.72 14.42 38.01 +330 1 7.35 31.84 12.61 +331 1 32.33 16.79 3.07 +332 1 15.86 0.39 8.39 +333 1 27.69 7.32 25.74 +334 1 27.77 1.17 4.96 +335 1 29.38 26.68 23.48 +336 1 14.95 3.41 2.13 +337 1 2.45 38.8 17.54 +338 1 9.18 27.58 31.12 +339 1 36.62 15.23 23.66 +340 1 12.23 30.74 10.85 +341 1 12.87 0.23 24.05 +342 1 33.85 35.75 19.95 +343 1 36.36 30.35 13.94 +344 1 38.11 8.15 5.49 +345 1 15.58 1.29 29.89 +346 1 25.95 30.47 39.19 +347 1 27.69 15.5 13.37 +348 1 25.48 13.7 25.29 +349 1 0.72 39.53 4.41 +350 1 8.75 15.21 5.79 +351 1 10.49 26.46 27.25 +352 1 16.9 20.08 26.58 +353 1 3.95 4.33 20.25 +354 1 18.03 7.66 31.87 +355 1 21.35 2.88 17.26 +356 1 32.92 22.68 6.56 +357 1 21.72 4.62 12.02 +358 1 37.6 6.04 25.2 +359 1 22.22 23.78 7.36 +360 1 12.53 19.53 10.6 +361 1 17.87 26.05 19.32 +362 1 20.94 30.75 31.23 +363 1 22.33 11.87 35.79 +364 1 28.54 6.88 10.52 +365 1 29.58 26.13 8.56 +366 1 19.06 24.2 21.73 +367 1 25.05 38.41 26.91 +368 1 18.66 40.35 4.69 +369 1 11.87 6.75 12.72 +370 1 17.99 11.82 37.79 +371 1 8.97 24.7 0.61 +372 1 26.89 1.52 31.33 +373 1 6.88 22.51 14.06 +374 1 29.51 3.87 13.35 +375 1 0.95 14.53 10 +376 1 26.43 31.54 11.63 +377 1 6.1 35.16 11.28 +378 1 10.2 15.91 28.7 +379 1 13.24 25.67 24.3 +380 1 34.5 3.91 20.22 +381 1 22.48 2.17 5.2 +382 1 24.26 16.15 11.3 +383 1 20.63 32.57 27.3 +384 1 39.95 6.81 1.05 +385 1 24.38 34.78 38.27 +386 1 4.63 23.56 0.55 +387 1 33.5 8.38 36.97 +388 1 5.76 27.14 12.06 +389 1 37.45 26.58 32.25 +390 1 2.8 8.96 32.35 +391 1 5.29 39.84 30.1 +392 1 29.2 26.49 31.18 +393 1 33.91 27.39 12.89 +394 1 3.37 14.19 39.34 +395 1 30.68 28.7 27 +396 1 2.59 18.45 19.38 +397 1 13.55 0.75 27.35 +398 1 3.82 20.12 16.1 +399 1 37.72 0.72 34.29 +400 1 23.85 3.32 19.46 +401 1 4.78 0.67 38.23 +402 1 22.78 23.26 38.6 +403 1 11.56 39.29 4.23 +404 1 21.38 32.45 5.39 +405 1 8.32 19.42 9.52 +406 1 28.43 31.07 17.8 +407 1 11.02 5.75 39.84 +408 1 27.36 36.71 7.62 +409 1 34.22 16.74 27.88 +410 1 3.22 22.01 27.42 +411 1 29.2 15.76 32.33 +412 1 25.29 23.44 2.2 +413 1 10.8 32.43 39.96 +414 1 32.2 1.41 4.44 +415 1 32.94 15.59 37.21 +416 1 6.8 8.08 0.84 +417 1 10.42 9.91 37.73 +418 1 1.18 31.39 3.93 +419 1 10.1 36.38 38.57 +420 1 32.89 26.96 35.07 +421 1 28.12 11.93 25.96 +422 1 4.9 29.15 -0.25 +423 1 2.21 27.99 3.72 +424 1 11.33 3.94 25.55 +425 1 3.3 30.26 10.78 +426 1 11.57 27.26 19.31 +427 1 21.79 32.67 13.3 +428 1 4.96 26.53 33.78 +429 1 33.41 32.87 18.46 +430 1 13.92 30.37 20.3 +431 1 16.91 3.5 11.57 +432 1 -0.06 4.42 34.05 +433 1 7.04 24.33 16.85 +434 1 28.66 11.93 19.73 +435 1 30.21 1.75 36.36 +436 1 3.91 6.2 6.26 +437 1 7.01 25.6 27.34 +438 1 34 1.06 18.12 +439 1 29.14 8.5 3.09 +440 1 40.13 23.52 16.94 +441 1 21.69 22.38 26.78 +442 1 18.44 32.85 39.84 +443 1 38.87 1.99 27.63 +444 1 10.47 12.02 33.68 +445 1 9.65 19.94 21.88 +446 1 25.04 8.12 27.89 +447 1 12.18 16.78 31.09 +448 1 38.31 8.2 30.6 +449 1 0.11 5.21 18.12 +450 1 23.48 7.88 38.7 +451 1 7.9 11.99 7.04 +452 1 2.09 34.5 8.64 +453 1 19 18.3 0.42 +454 1 37.94 18.06 15.21 +455 1 25.05 33.33 29.55 +456 1 33.74 37.88 34.54 +457 1 36.07 29.5 17.47 +458 1 27.7 13.54 10.46 +459 1 27.18 23.18 21.06 +460 1 17.49 2.04 23.22 +461 1 23.84 26.31 36.76 +462 1 31.08 32.24 24.92 +463 1 17.7 28.73 16.66 +464 1 1.59 15.5 18.04 +465 1 33.49 18.99 8.75 +466 1 1.19 8.43 28.01 +467 1 5.43 20.26 22.25 +468 1 23.3 5.31 15.05 +469 1 27.09 4.47 21.96 +470 1 26.61 27.48 28.83 +471 1 13 3.18 13.4 +472 1 36.09 34.56 10.58 +473 1 19.09 15.33 7.48 +474 1 12.94 18.16 22.07 +475 1 38.8 16.16 36.73 +476 1 16.73 39.94 -0.46 +477 1 3.64 12.56 9.42 +478 1 27.64 3.31 18.29 +479 1 15.58 12.36 4.52 +480 1 15.37 11.18 18.19 +481 1 37.52 11.23 14.94 +482 1 37.16 2.3 10.01 +483 1 36.19 9.86 21.99 +484 1 36.38 21.09 4.76 +485 1 38.15 12.94 25.35 +486 1 15.1 29.65 24.64 +487 1 16.54 29.12 38.85 +488 1 33.86 11.39 14.4 +489 1 27.99 18.55 9.87 +490 1 0.66 1.26 8.28 +491 1 29.89 33.84 29.75 +492 1 6.64 33.3 6.74 +493 1 31.47 0.39 11.25 +494 1 8.76 15.96 10.74 +495 1 39.6 15.8 21.04 +496 1 22.38 28.55 19.85 +497 1 25.87 6.23 5.4 +498 1 36.24 26.67 38.61 +499 1 23.05 8.79 7.01 +500 1 32.05 4.16 8.87 +501 1 35.3 13.36 38.03 +502 1 39.91 25.91 36.45 +503 1 32.17 17.27 31.82 +504 1 29.99 21.54 20.57 +505 1 9.39 0.57 34.17 +506 1 22.12 17.22 13.03 +507 1 15.23 16.27 24.39 +508 1 26.32 25.89 13.26 +509 1 39.25 3.46 1.34 +510 1 32.56 10.28 7.96 +511 1 25.76 14.8 34.79 +512 1 32.12 5.38 36.94 +513 1 17.74 15.37 14.87 +514 1 21.93 3.26 25.26 +515 1 24.05 0.48 36.27 +516 1 8.2 19.02 33.92 +517 1 33.07 25.88 24.79 +518 1 12.54 0.52 32.8 +519 1 18.5 6.34 23.21 +520 1 35.93 10.26 34.79 +521 1 19.33 11.86 6.94 +522 1 1.63 5.31 25.43 +523 1 30.62 36.78 30.77 +524 1 12.25 26.79 13.74 +525 1 21 1.47 13.99 +526 1 22.24 29.36 34.11 +527 1 29.05 1.74 0.24 +528 1 19.34 25.14 39.77 +529 1 12.9 25.42 35.42 +530 1 4.1 20.69 33.31 +531 1 35.38 5.64 9.17 +532 1 5.01 34.03 23.36 +533 1 15.7 10.01 7.1 +534 1 25.95 19.48 24.73 +535 1 11.15 4.16 21.43 +536 1 1.47 3.23 13.72 +537 1 26.54 36.76 17.48 +538 1 7.65 30.6 27.73 +539 1 18.59 3.05 3.32 +540 1 6.92 36.14 15.67 +541 1 12.72 36.21 32.72 +542 1 16.33 26.24 14.35 +543 1 21.66 12.61 26.18 +544 1 15.72 32.37 10.71 +545 1 27.57 15.75 4.97 +546 1 20.18 39.13 18.44 +547 1 18.77 17.09 4.74 +548 1 12.75 14.08 17.89 +549 1 10.71 37.26 35.13 +550 1 20.88 32.12 9.94 +551 1 8.69 0.06 9.54 +552 1 1.58 12.61 26.42 +553 1 10.29 22.73 13.14 +554 1 23.31 25.7 4.97 +555 1 36.7 30.78 5.26 +556 1 5.6 28.71 23.76 +557 1 13.04 7.91 15.46 +558 1 40.24 33.53 34.5 +559 1 39.7 18.36 34.25 +560 1 23.52 22.84 21.14 +561 1 32.82 27.9 5.02 +562 1 1.52 33.77 27.04 +563 1 31.48 18.68 13.1 +564 1 34 24.07 34.55 +565 1 34.72 25.03 30.45 +566 1 18.92 5.7 16.54 +567 1 15.26 40.2 16.97 +568 1 24.55 16.8 26.26 +569 1 17.59 18.03 31.75 +570 1 12.08 27.38 38.42 +571 1 31.42 21.91 35.27 +572 1 9.68 6.93 36.96 +573 1 22.93 15.19 2.53 +574 1 11.83 24.38 2.24 +575 1 16.02 12.44 31.42 +576 1 20.24 10.7 20.15 +577 1 37.38 17.37 40.63 +578 1 3.74 17.41 22.49 +579 1 23.21 9.86 23.99 +580 1 2.49 36.56 38 +581 1 20.51 1.54 22.62 +582 1 8.23 33.44 33.15 +583 1 30.93 8.12 14.85 +584 1 36.35 3.92 37.65 +585 1 5.57 10.63 28.64 +586 1 30.24 22.84 4.6 +587 1 3.24 15.97 7.43 +588 1 22.64 0.7 27.09 +589 1 1.64 40.37 27.74 +590 1 30.53 35.28 3.5 +591 1 25.55 4.7 2.53 +592 1 22.04 29.56 12.29 +593 1 3.42 8.76 2.28 +594 1 16.37 37.65 7.87 +595 1 20.65 12.75 2.9 +596 1 8.07 20.49 2.6 +597 1 20.04 24.72 28.2 +598 1 29.75 0.33 16.1 +599 1 31.36 33.09 8.02 +600 1 8.6 10.56 2.65 +601 1 20.55 33.93 33.71 +602 1 23.11 -0.42 31.7 +603 1 27.07 6.69 18.5 +604 1 15.65 23.71 11.8 +605 1 23.88 24.17 30.1 +606 1 0.79 32.46 16.99 +607 1 25.96 20.19 2.43 +608 1 35.16 12.33 4.73 +609 1 16.53 17.12 10.45 +610 1 19.74 35.94 8.62 +611 1 -0.24 28.29 28.3 +612 1 33.15 4.39 12.64 +613 1 24.27 18.59 33.59 +614 1 0.3 9.61 23.54 +615 1 5.52 10.89 34.71 +616 1 9.85 26.26 34.42 +617 1 25.54 37.74 39.13 +618 1 4.11 29.65 5.81 +619 1 30.86 22.72 31.07 +620 1 39.54 34.54 23.24 +621 1 15.03 9.34 12.11 +622 1 21.93 38.49 9.53 +623 1 18.21 19.2 16.65 +624 1 38.71 32.83 14.49 +625 1 37.74 36.38 31.43 +626 1 7.57 2.2 1.07 +627 1 12.27 10.05 1.53 +628 1 18.32 19.55 12.51 +629 1 12.49 24.81 16.57 +630 1 35.07 31.62 22.85 +631 1 4.91 19.68 30.45 +632 1 11.36 2.92 36.19 +633 1 26.76 35.53 1.29 +634 1 1.13 14.55 14.77 +635 1 8.2 25.14 37.83 +636 1 -0.5 0.85 23.08 +637 1 17.95 18.01 37.61 +638 1 2.44 37.75 0.71 +639 1 3.77 23.41 17.91 +640 1 3.34 14.41 35.96 +641 1 14.89 31.42 31.76 +642 1 15.72 22.91 30.66 +643 1 37.42 3.13 5.51 +644 1 1.51 38.14 20.78 +645 1 12.55 18.16 25.81 +646 1 18.98 15.88 29.21 +647 1 17.33 32.04 27.87 +648 1 31.21 37.38 22.84 +649 1 11.88 32.4 31 +650 1 25.1 2.19 12.69 +651 1 38.85 39.1 27.87 +652 1 5.9 16.14 33.34 +653 1 6.3 17.5 36.46 +654 1 2.28 25.02 12.53 +655 1 19.33 25.49 6.78 +656 1 8.57 37.22 8.4 +657 1 22 38.61 24.14 +658 1 35.63 3.23 2.15 +659 1 37.35 22.64 9.99 +660 1 25.46 28.22 33.18 +661 1 13.99 4.21 9.07 +662 1 9.04 40.64 37.59 +663 1 17.46 6.49 27.93 +664 1 1.42 6.14 30.2 +665 1 25.82 28.28 10.33 +666 1 30.71 30.2 -0.02 +667 1 8.05 29.32 0.62 +668 1 6.49 3.17 6.65 +669 1 7.77 39.88 26.03 +670 1 28.53 12.14 30.96 +671 1 6.25 12.64 39.55 +672 1 3.78 7.96 25.83 +673 1 28.69 29.58 6.61 +674 1 5.32 18.55 8.6 +675 1 5.3 11.44 14.19 +676 1 39 12.03 36.99 +677 1 11.08 32.51 19.12 +678 1 38.48 1.03 20.34 +679 1 38.47 11.31 10.12 +680 1 3.65 20.3 11.99 +681 1 27.18 11.39 3.4 +682 1 29.61 20.72 38.86 +683 1 31.88 4.82 24.75 +684 1 14.52 36.61 25.66 +685 1 21.68 19.96 24.58 +686 1 1.2 13.59 23.16 +687 1 37.71 5.97 35.28 +688 1 19.81 22.04 37.54 +689 1 40.67 27.07 10.14 +690 1 38.57 13.96 13.75 +691 1 18.15 17.19 21.63 +692 1 3.76 27.51 30.32 +693 1 11.39 25.09 7.96 +694 1 28.95 22.02 13.33 +695 1 31.72 35.46 35.33 +696 1 15.17 6.03 23.94 +697 1 9.63 9.42 22.18 +698 1 27.76 4.1 38.61 +699 1 27.37 37.46 11.07 +700 1 35.69 15.24 6.39 +701 1 21.92 33.09 36.84 +702 1 4.79 15.51 13.28 +703 1 9.31 26.44 22.8 +704 1 30.14 38.31 6.98 +705 1 4.33 6.66 13.77 +706 1 3.66 27.15 37.83 +707 1 0.44 24.06 29.62 +708 1 35.4 9.59 9.8 +709 1 33.77 39.44 21.41 +710 1 29.2 18.74 24.38 +711 1 34.14 30 7.36 +712 1 16.02 4.37 6.43 +713 1 35.75 39.41 40.58 +714 1 15.32 11.84 23.24 +715 1 32.52 24.39 20.97 +716 1 11.45 2.9 7.16 +717 1 7.07 34.28 36.04 +718 1 11.41 8.83 7.57 +719 1 29.29 27.79 16.55 +720 1 2.41 9.16 16.14 +721 1 13.14 38.07 12.01 +722 1 37.45 14.26 18.3 +723 1 34.64 18.37 16.65 +724 1 29.26 34.28 33.46 +725 1 13.67 19.83 3.04 +726 1 19.64 2.6 32.95 +727 1 23.61 23.55 11.34 +728 1 6.87 22.5 36.5 +729 1 36.78 28.34 22.96 +730 1 11.3 13.98 9.84 +731 1 20.82 19.73 9.16 +732 1 12.65 12.61 6.16 +733 1 9.25 7.81 25.28 +734 1 25.4 29.36 5.84 +735 1 17.86 9.06 4.45 +736 1 35.84 40.51 26.06 +737 1 26.97 21.28 31.59 +738 1 39.94 38.14 24.86 +739 1 3.16 17.07 2.49 +740 1 14.08 15.4 36.99 +741 1 26.1 13.88 29.68 +742 1 26.36 20 20.56 +743 1 12.02 6.35 27.65 +744 1 11.21 19.14 15.27 +745 1 35.86 22.93 26.81 +746 1 32.26 12.62 2.68 +747 1 29.36 4.91 6.86 +748 1 20.14 7.97 29.32 +749 1 25.53 11.2 36.18 +750 1 30.36 14.25 24.79 +751 1 29.84 38.37 39.29 +752 1 15.79 36.4 4.26 +753 1 32.59 14.17 10.29 +754 1 13.89 34.54 15.42 +755 1 12.13 33.62 7.27 +756 1 25.86 23.81 33.97 +757 1 18.4 31.27 34.96 +758 1 6.58 40.49 17.57 +759 1 5.64 39.86 23.05 +760 1 25.32 33 16.24 +761 1 0.98 10.99 12.21 +762 1 32.86 23.75 12.41 +763 1 32.91 1.3 26.94 +764 1 9.46 8.66 31.47 +765 1 17.49 15.53 1.82 +766 1 8.17 18.16 15.3 +767 1 4.84 30.63 26.32 +768 1 6.75 37.1 30.8 +769 1 7.16 5.72 15.74 +770 1 20.09 17.82 19.18 +771 1 1.02 27.99 32.54 +772 1 21.44 1.28 38.4 +773 1 21.06 14.62 37.08 +774 1 27.82 18.99 15.96 +775 1 33.51 21.46 22.82 +776 1 8.29 2.79 17.09 +777 1 18.14 11.41 28.62 +778 1 17.94 28.54 32.73 +779 1 36.1 9.54 40.1 +780 1 36.55 2.62 22.97 +781 1 27.29 10.41 39.35 +782 1 22.04 37.76 2.02 +783 1 23.01 30.08 16.58 +784 1 6.34 15.31 21.61 +785 1 7.3 22.39 7.74 +786 1 38 5.77 21.04 +787 1 32.93 12.85 26.58 +788 1 22.43 15.36 16.72 +789 1 18.54 2.38 8.35 +790 1 0.62 31.88 23.84 +791 1 39.56 30.3 21.7 +792 1 7.56 11.78 25.2 +793 1 16.05 3.98 26.72 +794 1 24.33 36.16 13.16 +795 1 26.38 31.24 35.77 +796 1 14.94 26.46 -0.44 +797 1 3.53 28 19.79 +798 1 11.94 32.27 25.88 +799 1 34.59 15.06 19.23 +800 1 3.51 10.62 24.22 +801 1 13.18 21.59 35.52 +802 1 19.95 13.15 16.23 +803 1 24.48 9.63 19.58 +804 1 37.7 34.42 19.19 +805 1 22.84 19.59 5.52 +806 1 34.62 36.75 12.26 +807 1 10.33 21.85 25.15 +808 1 21.51 29.7 7.23 +809 1 34.05 3 30.58 +810 1 12.43 29.67 5.59 +811 1 18.94 21.82 29.31 +812 1 39.21 17.7 4 +813 1 7.04 2.97 37.09 +814 1 30.87 10.8 22.09 +815 1 33.54 7.16 23.15 +816 1 32.82 32.27 11.47 +817 1 21.8 14.54 21.61 +818 1 38.83 6.69 13.68 +819 1 30.37 39.05 18.66 +820 1 31.21 15.08 13.79 +821 1 1.07 11.97 35.04 +822 1 26.02 35.8 35.47 +823 1 27.64 33.32 8.04 +824 1 39.57 36.88 4.39 +825 1 14.48 30.97 36.87 +826 1 36.86 27.04 8.96 +827 1 34.73 26.27 19.55 +828 1 29.24 29.12 10.86 +829 1 8.35 39.9 13.92 +830 1 5.43 5.1 31.85 +831 1 18.36 22.31 5.89 +832 1 2.46 27.35 16.36 +833 1 21.76 37.05 27.45 +834 1 29.32 17.11 2.28 +835 1 3.58 21.98 3.09 +836 1 10.61 9.17 10.69 +837 1 25.15 17.54 6.05 +838 1 3.4 22.81 7.03 +839 1 16.12 23.66 38.29 +840 1 8.67 4.79 31.8 +841 1 27.82 0.02 20.45 +842 1 4.46 2.44 29.46 +843 1 39.11 22.69 36.33 +844 1 4.26 2.45 34.43 +845 1 13.47 3.5 30.9 +846 1 26.92 22.55 26.54 +847 1 5.66 30.07 30.65 +848 1 31.58 35.68 25.46 +849 1 31.23 5.65 27.78 +850 1 8.76 19.49 28.61 +851 1 24.13 8.02 2.3 +852 1 8.27 6.8 4.93 +853 1 15.31 34.36 37.63 +854 1 3.96 35.82 26.97 +855 1 24.95 4.01 29.96 +856 1 26.54 25.95 19.15 +857 1 17.76 29.23 5.35 +858 1 16.95 21.79 0.78 +859 1 17.52 39.02 13.01 +860 1 20.5 22.86 10.41 +861 1 27.67 27.07 2.78 +862 1 37.1 31.02 2.03 +863 1 37.17 2.24 16.34 +864 1 24.51 34.69 10.28 +865 1 17.38 13.41 21.4 +866 1 38 9.37 17.94 +867 1 35.67 25.27 5.3 +868 1 22.66 4.47 0.97 +869 1 20.06 28.17 27.42 +870 1 27.33 2.38 9.79 +871 1 36.4 10.73 31.42 +872 1 0.53 9.45 6.96 +873 1 12.89 9.03 25.13 +874 1 37.5 23.54 21.33 +875 1 7.19 28.87 19.11 +876 1 21.45 32.81 22.71 +877 1 8.76 8.3 13.51 +878 1 10.24 31.46 3.73 +879 1 15.93 9.7 35.82 +880 1 14.92 19.46 39.91 +881 1 13.02 22.03 27.3 +882 1 34.57 1.59 34.73 +883 1 0.5 21.04 30.77 +884 1 24.84 32.67 4.97 +885 1 30.96 4.24 17.34 +886 1 23.63 8.84 32.7 +887 1 6.84 3.83 26.13 +888 1 31.57 9.23 27.06 +889 1 14.99 35.15 0.07 +890 1 36.29 40.01 8.22 +891 1 18 36.86 35.66 +892 1 11.5 29.22 0.37 +893 1 35.18 36.03 24.88 +894 1 14.49 9.41 27.73 +895 1 10.12 12.91 0.99 +896 1 11.91 29.4 27.3 +897 1 25.51 28.68 14.56 +898 1 29.32 12.95 35.59 +899 1 2.96 0.59 0.53 +900 1 5.47 5.35 9.88 +901 1 8.93 39.33 1.78 +902 1 39.68 38.49 12.33 +903 1 3.78 1.24 11.85 +904 1 29.54 33.76 11.99 +905 1 7.48 6.16 28.8 +906 1 10.83 33.63 36.96 +907 1 22.03 19.06 21.39 +908 1 31.68 31 3.71 +909 1 35.32 0.3 30.88 +910 1 9.93 35.42 14.85 +911 1 21.01 10.66 12.97 +912 1 22.54 21.62 33.81 +913 1 12.48 12.46 25.15 +914 1 0.64 27.93 39.01 +915 1 13.88 27.29 3.8 +916 1 13.03 20.93 19.25 +917 1 5.7 37.48 34.09 +918 1 2.27 35.08 14.29 +919 1 21.75 26.44 13.48 +920 1 10.66 11.35 17.49 +921 1 36.67 34.72 27.69 +922 1 8.23 22.8 33.36 +923 1 4.79 4.05 3.48 +924 1 35.61 35 35.21 +925 1 31.38 37.67 10.06 +926 1 26.44 35.58 27.52 +927 1 25.53 4.47 8.03 +928 1 38.81 33.08 31.55 +929 1 29.62 39.68 34.32 +930 1 0.76 3.88 10.61 +931 1 24.06 30.13 24.84 +932 1 18.77 8.38 37.02 +933 1 2.81 24.14 24.45 +934 1 11.33 1.25 19.69 +935 1 1.61 26.53 6.48 +936 1 9.52 29.81 35.98 +937 1 7.83 31.75 20.77 +938 1 9.67 23.93 20.57 +939 1 33.96 16.95 24.79 +940 1 37.55 37.31 37.17 +941 1 6.2 24.19 31.13 +942 1 17.79 4.35 30.56 +943 1 13.51 20.25 30.45 +944 1 14.76 12.48 13.13 +945 1 32.56 27.52 30.41 +946 1 35.81 40.1 4.85 +947 1 39.01 25.43 27.07 +948 1 22.8 5.53 32.22 +949 1 2.35 39.55 32.5 +950 1 3.31 31.51 34.19 +951 1 40.63 37.01 15.9 +952 1 18.43 35.86 30.77 +953 1 37.01 39.18 15.57 +954 1 6.74 6.26 21.64 +955 1 5.22 24.94 22.53 +956 1 25.2 11.08 13.98 +957 1 14.66 -0.14 5 +958 1 14.96 8.38 20.32 +959 1 1.89 23.03 10.1 +960 1 33.01 11.23 39.32 +961 1 32.68 6.79 32.04 +962 1 6.25 25.81 3.82 +963 1 18.37 31.97 14.57 +964 1 9.74 30.21 22.71 +965 1 3.09 1.52 19.38 +966 1 33.98 37.34 5.63 +967 1 32.19 28.35 15.8 +968 1 24.4 15.49 19.39 diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in index a18163175cf35f9d125307df4dc8c7534d5526a5..0fa9c1b74c2c41d9917d21b7167d4761403a2c2b 100644 --- a/examples/USER/diffraction/BulkNi.in +++ b/examples/USER/diffraction/BulkNi.in @@ -20,7 +20,7 @@ compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 & dR_Ewald 0.05 echo manual -fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & +fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & mode vector file $A.hist.xrd fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt new file mode 100644 index 0000000000000000000000000000000000000000..f2dc506ddef28d978d48eb90569302e0de27124b --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt @@ -0,0 +1,52 @@ +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 & + react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz new file mode 100644 index 0000000000000000000000000000000000000000..c620b879a883817b8eb7abe4495e585ecacfaf02 Binary files /dev/null and b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz differ diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..653c7582f8d7aba4c8800e5fcfff5ebb22d44a15 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 @@ -0,0 +1,175 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz + orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 14 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 10 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.20765 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0333156 + estimated relative force accuracy = 0.000100329 + using double precision FFTs + 3d grid and FFT values/proc = 12167 5832 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 15 15 15 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.95238 -9670.9169 0.80366765 31 0 + 100 697.22819 -4624.0512 0.80366765 57 22 + 150 723.60507 -17175.571 0.80366765 76 48 + 200 736.71277 -12961.963 0.80366765 84 64 +Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms + +Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45 +Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01 +Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07 +Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22 +Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40 +Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00 +Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81 +Other | | 0.04545 | | | 0.04 + +Nlocal: 35200 ave 35200 max 35200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 38403 ave 38403 max 38403 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6928101 +Ave neighs/atom = 196.821 +Ave special neighs/atom = 9.83727 +Neighbor list builds = 200 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:43 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..cc0dda60c7dcec4b775d0d5cd6cdad4f6b751124 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 @@ -0,0 +1,175 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz + orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 14 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 10 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +# stable at 800K +fix 1 statted_grp nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.20765 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0333156 + estimated relative force accuracy = 0.000100329 + using double precision FFTs + 3d grid and FFT values/proc = 4508 1620 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 15 15 15 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.95238 -9670.9169 0.80366765 31 0 + 100 697.22819 -4624.0512 0.80366765 57 22 + 150 724.40407 -17166.729 0.80366765 76 49 + 200 737.28582 -12968.224 0.80366765 84 65 +Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms + +Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89 +Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31 +Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19 +Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68 +Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47 +Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00 +Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39 +Other | | 0.03995 | | | 0.08 + +Nlocal: 8800 ave 8913 max 8652 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 18366 ave 18461 max 18190 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 6928132 +Ave neighs/atom = 196.822 +Ave special neighs/atom = 9.83608 +Neighbor list builds = 200 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:52 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map new file mode 100644 index 0000000000000000000000000000000000000000..44f7ad8137549eaa375046e114c59a7aa09c0c65 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map @@ -0,0 +1,35 @@ +this is a nominal superimpose file + +2 edgeIDs +18 equivalences + +BondingIDs + +10 +1 + +EdgeIDs + +16 +8 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..61c0408ce3e57955e736d15e77736b95dccf240b --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template @@ -0,0 +1,189 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + +18 atoms +17 bonds +31 angles +39 dihedrals +20 impropers + +Types + +1 9 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 +16 1 +17 3 +18 3 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -5.522237 -0.752722 1.631158 +2 -5.170398 -0.545733 0.178130 +3 -6.469695 -0.553072 -0.648889 +4 -6.052076 -1.721152 1.744648 +5 -6.183059 0.071387 1.971497 +6 -4.489340 -1.389197 -0.173156 +7 -4.637591 0.453703 0.051252 +8 -5.618658 0.138919 4.386107 +9 -4.669492 -0.989819 3.943591 +10 -4.270194 -0.766405 2.474102 +11 -3.348470 -1.875393 2.024289 +12 -3.569794 0.564183 2.345995 +13 -5.201079 -1.993301 4.044219 +14 -3.736682 -0.984819 4.598305 +15 -4.255402 1.370923 2.679069 +16 -6.136394 -0.339866 -2.136775 +17 -6.996331 -1.555519 -0.517408 +18 -7.153308 0.284949 -0.289930 + +Bonds + +1 9 1 2 +2 10 1 4 +3 10 1 5 +4 11 1 10 +5 1 2 3 +6 2 2 6 +7 2 2 7 +8 1 3 16 +9 2 3 17 +10 2 3 18 +11 1 8 9 +12 6 9 10 +13 2 9 13 +14 2 9 14 +15 7 10 11 +16 5 10 12 +17 8 12 15 + +Angles + +1 14 2 1 4 +2 14 2 1 5 +3 15 2 1 10 +4 16 4 1 5 +5 17 4 1 10 +6 17 5 1 10 +7 18 1 2 3 +8 19 1 2 6 +9 19 1 2 7 +10 1 3 2 6 +11 1 3 2 7 +12 3 6 2 7 +13 2 2 3 16 +14 1 2 3 17 +15 1 2 3 18 +16 1 16 3 17 +17 1 16 3 18 +18 3 17 3 18 +19 12 8 9 10 +20 1 8 9 13 +21 1 8 9 14 +22 13 13 9 10 +23 13 14 9 10 +24 3 13 9 14 +25 10 9 10 11 +26 8 9 10 12 +27 20 1 10 9 +28 21 11 10 12 +29 22 1 10 11 +30 23 1 10 12 +31 11 10 12 15 + +Dihedrals + +1 16 4 1 2 3 +2 17 4 1 2 6 +3 17 4 1 2 7 +4 16 5 1 2 3 +5 17 5 1 2 6 +6 17 5 1 2 7 +7 18 10 1 2 3 +8 19 10 1 2 6 +9 19 10 1 2 7 +10 20 2 1 10 9 +11 21 2 1 10 11 +12 22 2 1 10 12 +13 23 4 1 10 9 +14 24 4 1 10 11 +15 25 4 1 10 12 +16 23 5 1 10 9 +17 24 5 1 10 11 +18 25 5 1 10 12 +19 26 1 2 3 16 +20 27 1 2 3 17 +21 27 1 2 3 18 +22 4 16 3 2 6 +23 2 6 2 3 17 +24 2 6 2 3 18 +25 4 16 3 2 7 +26 2 7 2 3 17 +27 2 7 2 3 18 +28 14 8 9 10 11 +29 12 8 9 10 12 +30 28 8 9 10 1 +31 15 13 9 10 11 +32 13 13 9 10 12 +33 29 13 9 10 1 +34 15 14 9 10 11 +35 13 14 9 10 12 +36 29 14 9 10 1 +37 10 9 10 12 15 +38 11 11 10 12 15 +39 30 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 2 3 16 17 +10 1 2 3 16 18 +11 1 2 3 17 18 +12 1 16 3 17 18 +13 1 8 9 13 10 +14 1 8 9 14 10 +15 1 8 9 13 14 +16 1 13 9 14 10 +17 1 9 10 11 12 +18 1 1 10 9 11 +19 1 1 10 9 12 +20 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..944d6918c57e77d2d96b3a949efac38cfce1c5f6 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template @@ -0,0 +1,160 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + +18 atoms +16 bonds +25 angles +23 dihedrals +14 impropers + +Types + +1 2 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 +16 1 +17 3 +18 3 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 +16 -3.964987 2.900602 -1.551341 +17 -4.460694 2.836102 0.668882 +18 -4.828494 3.219656 -0.122111 + +Bonds + +1 12 1 2 +2 4 1 4 +3 4 1 5 +4 1 2 3 +5 2 2 6 +6 2 2 7 +7 1 3 16 +8 2 3 17 +9 2 3 18 +10 1 8 9 +11 6 9 10 +12 2 9 13 +13 2 9 14 +14 7 10 11 +15 5 10 12 +16 8 12 15 + +Angles + +1 6 2 1 4 +2 6 2 1 5 +3 7 4 1 5 +4 24 1 2 3 +5 5 1 2 6 +6 5 1 2 7 +7 1 3 2 6 +8 1 3 2 7 +9 3 6 2 7 +10 2 2 3 16 +11 1 2 3 17 +12 1 2 3 18 +13 1 16 3 17 +14 1 16 3 18 +15 3 17 3 18 +16 12 8 9 10 +17 1 8 9 13 +18 1 8 9 14 +19 13 13 9 10 +20 13 14 9 10 +21 3 13 9 14 +22 10 9 10 11 +23 8 9 10 12 +24 21 11 10 12 +25 11 10 12 15 + +Dihedrals + +1 31 4 1 2 3 +2 32 4 1 2 6 +3 32 4 1 2 7 +4 31 5 1 2 3 +5 32 5 1 2 6 +6 32 5 1 2 7 +7 33 1 2 3 16 +8 1 1 2 3 17 +9 1 1 2 3 18 +10 4 16 3 2 6 +11 2 6 2 3 17 +12 2 6 2 3 18 +13 4 16 3 2 7 +14 2 7 2 3 17 +15 2 7 2 3 18 +16 14 8 9 10 11 +17 12 8 9 10 12 +18 15 13 9 10 11 +19 13 13 9 10 12 +20 15 14 9 10 11 +21 13 14 9 10 12 +22 10 9 10 12 15 +23 11 11 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 9 9 10 11 12 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 2 3 16 17 +8 1 2 3 16 18 +9 1 2 3 17 18 +10 1 16 3 17 18 +11 1 8 9 13 10 +12 1 8 9 14 10 +13 1 8 9 13 14 +14 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map new file mode 100644 index 0000000000000000000000000000000000000000..35fe47fdb3bdb0386d65b950d45cbfb39fbe6f7f --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map @@ -0,0 +1,32 @@ +this is a nominal superimpose file + +2 edgeIDs +15 equivalences + +BondingIDs + +4 +12 + +EdgeIDs + +8 +3 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..ffd3ef733c0ff4eb28c59ba4d8c657a2710dd8ad --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template @@ -0,0 +1,131 @@ +this is a molecule template for: water condensation, post-reacting + +15 atoms +13 bonds +19 angles +16 dihedrals +10 impropers + +Types + +1 9 +2 1 +3 1 +4 10 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 11 +13 3 +14 3 +15 10 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.410000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 -0.820000 +13 0.000000 +14 0.000000 +15 0.410000 + +Coords + +1 -4.856280 -1.050468 1.432625 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 9 1 2 +2 10 1 5 +3 11 1 10 +4 1 2 3 +5 2 2 6 +6 2 2 7 +7 13 4 12 +8 1 8 9 +9 6 9 10 +10 2 9 13 +11 2 9 14 +12 7 10 11 +13 13 15 12 + +Angles + +1 14 2 1 5 +2 15 2 1 10 +3 17 5 1 10 +4 18 1 2 3 +5 19 1 2 6 +6 19 1 2 7 +7 1 3 2 6 +8 1 3 2 7 +9 3 6 2 7 +10 12 8 9 10 +11 1 8 9 13 +12 1 8 9 14 +13 13 13 9 10 +14 13 14 9 10 +15 3 13 9 14 +16 10 9 10 11 +17 20 1 10 9 +18 22 1 10 11 +19 25 15 12 4 + +Dihedrals + +1 16 5 1 2 3 +2 17 5 1 2 6 +3 17 5 1 2 7 +4 18 10 1 2 3 +5 19 10 1 2 6 +6 19 10 1 2 7 +7 20 2 1 10 9 +8 21 2 1 10 11 +9 23 5 1 10 9 +10 24 5 1 10 11 +11 14 8 9 10 11 +12 28 8 9 10 1 +13 15 13 9 10 11 +14 29 13 9 10 1 +15 15 14 9 10 11 +16 29 14 9 10 1 + +Impropers + +1 10 2 1 5 10 +2 11 1 10 9 11 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 8 9 13 10 +8 1 8 9 14 10 +9 1 8 9 13 14 +10 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..7abe15ada8d2372e4435ef82b5e60b7417865790 --- /dev/null +++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template @@ -0,0 +1,158 @@ +this is a molecule template for: water condensation, pre-reacting + +15 atoms +14 bonds +25 angles +30 dihedrals +16 impropers + +Types + +1 9 +2 1 +3 1 +4 4 +5 4 +6 3 +7 3 +8 1 +9 1 +10 5 +11 8 +12 6 +13 3 +14 3 +15 7 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 9 1 2 +2 10 1 4 +3 10 1 5 +4 11 1 10 +5 1 2 3 +6 2 2 6 +7 2 2 7 +8 1 8 9 +9 6 9 10 +10 2 9 13 +11 2 9 14 +12 7 10 11 +13 5 10 12 +14 8 12 15 + +Angles + +1 14 2 1 4 +2 14 2 1 5 +3 15 2 1 10 +4 16 4 1 5 +5 17 4 1 10 +6 17 5 1 10 +7 18 1 2 3 +8 19 1 2 6 +9 19 1 2 7 +10 1 3 2 6 +11 1 3 2 7 +12 3 6 2 7 +13 12 8 9 10 +14 1 8 9 13 +15 1 8 9 14 +16 13 13 9 10 +17 13 14 9 10 +18 3 13 9 14 +19 10 9 10 11 +20 8 9 10 12 +21 20 1 10 9 +22 21 11 10 12 +23 22 1 10 11 +24 23 1 10 12 +25 11 10 12 15 + +Dihedrals + +1 16 4 1 2 3 +2 17 4 1 2 6 +3 17 4 1 2 7 +4 16 5 1 2 3 +5 17 5 1 2 6 +6 17 5 1 2 7 +7 18 10 1 2 3 +8 19 10 1 2 6 +9 19 10 1 2 7 +10 20 2 1 10 9 +11 21 2 1 10 11 +12 22 2 1 10 12 +13 23 4 1 10 9 +14 24 4 1 10 11 +15 25 4 1 10 12 +16 23 5 1 10 9 +17 24 5 1 10 11 +18 25 5 1 10 12 +19 14 8 9 10 11 +20 12 8 9 10 12 +21 28 8 9 10 1 +22 15 13 9 10 11 +23 13 13 9 10 12 +24 29 13 9 10 1 +25 15 14 9 10 11 +26 13 14 9 10 12 +27 29 14 9 10 1 +28 10 9 10 12 15 +29 11 11 10 12 15 +30 30 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 8 9 13 10 +10 1 8 9 14 10 +11 1 8 9 13 14 +12 1 13 9 14 10 +13 1 9 10 11 12 +14 1 1 10 9 11 +15 1 1 10 9 12 +16 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon new file mode 100644 index 0000000000000000000000000000000000000000..1f7e9c42b7b4098fd355dec8afc696e42631321c --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon @@ -0,0 +1,50 @@ +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +molecule mol2 rxn1_stp1_reacted.data_template +molecule mol3 rxn1_stp2_unreacted.data_template +molecule mol4 rxn1_stp2_reacted.data_template + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 & + react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map & + react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map + +fix 1 statted_grp nvt temp 300 300 100 + +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 + +# write_restart restart_longrun +# write_data restart_longrun.data diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..344439f94c5906e1fc7417921b89434ae0a7b8b5 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 @@ -0,0 +1,370 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +fix 1 statted_grp nvt temp 300 300 100 + +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 343 8 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:786) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 296.70408 -51.30066 0.0034851739 1 0 + 100 274.25324 46.715512 0.0034851739 1 1 + 150 471.61579 31.321598 0.0034851739 1 1 + 200 362.87766 42.061118 0.0034851739 1 1 + 250 367.58058 65.303109 0.0034851739 1 1 + 300 372.38236 -52.421725 0.0034851739 1 1 + 350 297.69957 17.869945 0.0034851739 1 1 + 400 258.30433 49.19156 0.0034851739 1 1 + 450 253.34384 -5.8162637 0.0034851739 1 1 + 500 269.96465 -43.337517 0.0034851739 1 1 + 550 303.23718 10.180246 0.0034851739 1 1 + 600 329.59579 -48.97461 0.0034851739 1 1 + 650 350.42568 50.983183 0.0034851739 1 1 + 700 342.03272 35.43465 0.0034851739 1 1 + 750 269.23405 -41.873166 0.0034851739 1 1 + 800 245.15025 13.953092 0.0034851739 1 1 + 850 257.85421 -3.1492141 0.0034851739 1 1 + 900 316.15644 7.7798301 0.0034851739 1 1 + 950 299.9124 -15.77014 0.0034851739 1 1 + 1000 302.89968 -17.049693 0.0034851739 1 1 + 1050 308.91651 71.84632 0.0034851739 1 1 + 1100 348.43932 -18.742012 0.0034851739 1 1 + 1150 309.03036 50.536311 0.0034851739 1 1 + 1200 318.9761 -16.905746 0.0034851739 1 1 + 1250 320.42806 -0.057975092 0.0034851739 1 1 + 1300 289.7824 18.200772 0.0034851739 1 1 + 1350 284.79836 -9.1978427 0.0034851739 1 1 + 1400 325.43292 42.082833 0.0034851739 1 1 + 1450 261.5041 -37.823325 0.0034851739 1 1 + 1500 298.88723 -5.1647385 0.0034851739 1 1 + 1550 291.37403 -7.7764201 0.0034851739 1 1 + 1600 293.83475 22.2458 0.0034851739 1 1 + 1650 293.80611 24.202512 0.0034851739 1 1 + 1700 291.70205 -23.397884 0.0034851739 1 1 + 1750 292.32437 -10.671214 0.0034851739 1 1 + 1800 302.01367 -11.671025 0.0034851739 1 1 + 1850 322.1651 24.438331 0.0034851739 1 1 + 1900 310.45076 45.343592 0.0034851739 1 1 + 1950 325.91745 -19.847809 0.0034851739 1 1 + 2000 276.89662 63.387098 0.0034851739 1 1 + 2050 311.33783 -24.683247 0.0034851739 1 1 + 2100 346.2336 -27.526891 0.0034851739 1 1 + 2150 345.30604 -15.722411 0.0034851739 1 1 + 2200 346.7718 -17.857633 0.0034851739 1 1 + 2250 304.28676 -1.9965581 0.0034851739 1 1 + 2300 322.56372 -31.786868 0.0034851739 1 1 + 2350 282.64326 6.1982735 0.0034851739 1 1 + 2400 286.65759 -63.207781 0.0034851739 1 1 + 2450 257.05528 32.931491 0.0034851739 1 1 + 2500 283.64386 26.912373 0.0034851739 1 1 + 2550 299.54005 27.277039 0.0034851739 1 1 + 2600 283.92503 14.660972 0.0034851739 1 1 + 2650 321.93453 -18.977358 0.0034851739 1 1 + 2700 376.7189 31.826935 0.0034851739 1 1 + 2750 372.20075 -32.821697 0.0034851739 1 1 + 2800 361.40604 83.035183 0.0034851739 1 1 + 2850 332.27269 -23.927452 0.0034851739 1 1 + 2900 331.14638 -0.12328446 0.0034851739 1 1 + 2950 303.67489 -24.078857 0.0034851739 1 1 + 3000 311.40462 21.563537 0.0034851739 1 1 + 3050 284.72849 -23.849667 0.0034851739 1 1 + 3100 303.48477 39.347763 0.0034851739 1 1 + 3150 264.2739 -0.22299879 0.0034851739 1 1 + 3200 300.03351 31.545323 0.0034851739 1 1 + 3250 288.56663 5.7225228 0.0034851739 1 1 + 3300 200.13238 -31.239655 0.0034851739 1 1 + 3350 231.32512 16.631728 0.0034851739 1 1 + 3400 260.57402 2.1717992 0.0034851739 1 1 + 3450 301.47128 -42.210623 0.0034851739 1 1 + 3500 321.77414 40.074365 0.0034851739 1 1 + 3550 353.21858 28.387783 0.0034851739 1 1 + 3600 331.45989 -57.800858 0.0034851739 1 1 + 3650 303.88123 44.86596 0.0034851739 1 1 + 3700 329.73833 -0.80615652 0.0034851739 1 1 + 3750 297.55588 -0.49626039 0.0034851739 1 1 + 3800 286.38794 -10.010003 0.0034851739 1 1 + 3850 290.17417 -43.51187 0.0034851739 1 1 + 3900 247.88933 51.23735 0.0034851739 1 1 + 3950 332.31324 -18.194985 0.0034851739 1 1 + 4000 325.56802 18.402825 0.0034851739 1 1 + 4050 338.37593 36.430977 0.0034851739 1 1 + 4100 370.95478 39.290285 0.0034851739 1 1 + 4150 348.47859 -7.0779678 0.0034851739 1 1 + 4200 241.30632 -33.371788 0.0034851739 1 1 + 4250 242.17258 -9.986197 0.0034851739 1 1 + 4300 300.85311 -7.9244294 0.0034851739 1 1 + 4350 273.15684 -21.257283 0.0034851739 1 1 + 4400 305.77463 -5.8720722 0.0034851739 1 1 + 4450 314.97697 45.0373 0.0034851739 1 1 + 4500 310.77723 16.958773 0.0034851739 1 1 + 4550 302.1742 12.156862 0.0034851739 1 1 + 4600 319.74799 6.84889 0.0034851739 1 1 + 4650 270.86805 -13.767905 0.0034851739 1 1 + 4700 249.81731 -31.197487 0.0034851739 1 1 + 4750 285.86481 -9.8916364 0.0034851739 1 1 + 4800 233.98321 7.1338571 0.0034851739 1 1 + 4850 302.60551 49.262889 0.0034851739 1 1 + 4900 316.55056 34.663247 0.0034851739 1 1 + 4950 357.32741 11.583006 0.0034851739 1 1 + 5000 400.21045 -8.1781061 0.0034851739 1 1 + 5050 390.01845 -20.490275 0.0034851739 1 1 + 5100 378.84247 -41.328757 0.0034851739 1 1 + 5150 324.02038 -15.023862 0.0034851739 1 1 + 5200 262.08429 10.937354 0.0034851739 1 1 + 5250 255.75508 16.381455 0.0034851739 1 1 + 5300 277.84989 40.68232 0.0034851739 1 1 + 5350 302.92832 9.1989494 0.0034851739 1 1 + 5400 283.7196 -1.6584671 0.0034851739 1 1 + 5450 300.71266 -4.7030295 0.0034851739 1 1 + 5500 343.5499 -0.30550044 0.0034851739 1 1 + 5550 369.51271 21.691649 0.0034851739 1 1 + 5600 372.69789 -38.67994 0.0034851739 1 1 + 5650 327.41266 11.352137 0.0034851739 1 1 + 5700 278.98614 -23.827304 0.0034851739 1 1 + 5750 308.30054 -20.756187 0.0034851739 1 1 + 5800 341.45594 28.058441 0.0034851739 1 1 + 5850 322.97844 -10.731921 0.0034851739 1 1 + 5900 304.53591 32.825279 0.0034851739 1 1 + 5950 287.1752 -36.780091 0.0034851739 1 1 + 6000 296.52681 18.781896 0.0034851739 1 1 + 6050 314.25442 15.992829 0.0034851739 1 1 + 6100 313.86576 3.4342714 0.0034851739 1 1 + 6150 325.64196 32.392039 0.0034851739 1 1 + 6200 367.42931 -27.160706 0.0034851739 1 1 + 6250 369.30798 39.020934 0.0034851739 1 1 + 6300 328.92285 -23.175157 0.0034851739 1 1 + 6350 305.63077 4.9024453 0.0034851739 1 1 + 6400 241.70341 -13.676629 0.0034851739 1 1 + 6450 265.66717 2.40612 0.0034851739 1 1 + 6500 249.36037 13.420255 0.0034851739 1 1 + 6550 294.53814 10.853462 0.0034851739 1 1 + 6600 308.2025 18.995308 0.0034851739 1 1 + 6650 305.43797 -49.56785 0.0034851739 1 1 + 6700 320.27344 11.336281 0.0034851739 1 1 + 6750 321.78666 -23.463899 0.0034851739 1 1 + 6800 303.40388 7.6224553 0.0034851739 1 1 + 6850 297.18966 51.52256 0.0034851739 1 1 + 6900 284.18909 -8.4947203 0.0034851739 1 1 + 6950 331.03663 13.233655 0.0034851739 1 1 + 7000 311.37928 -43.265479 0.0034851739 1 1 + 7050 286.81661 -14.174683 0.0034851739 1 1 + 7100 302.84119 12.048954 0.0034851739 1 1 + 7150 297.19357 -43.111968 0.0034851739 1 1 + 7200 332.47359 26.048249 0.0034851739 1 1 + 7250 262.70677 41.176242 0.0034851739 1 1 + 7300 250.61405 -23.413982 0.0034851739 1 1 + 7350 296.91117 35.88133 0.0034851739 1 1 + 7400 245.09229 -13.447194 0.0034851739 1 1 + 7450 272.28131 -23.322585 0.0034851739 1 1 + 7500 209.04985 13.871239 0.0034851739 1 1 + 7550 255.00955 4.9325621 0.0034851739 1 1 + 7600 312.30937 -37.368274 0.0034851739 1 1 + 7650 305.65903 55.245496 0.0034851739 1 1 + 7700 325.09504 -18.347711 0.0034851739 1 1 + 7750 363.28282 -22.479686 0.0034851739 1 1 + 7800 350.17429 26.849547 0.0034851739 1 1 + 7850 271.70853 -17.764575 0.0034851739 1 1 + 7900 272.66484 -11.701967 0.0034851739 1 1 + 7950 298.60202 -12.765675 0.0034851739 1 1 + 8000 274.58852 49.641532 0.0034851739 1 1 + 8050 304.72347 -0.55414183 0.0034851739 1 1 + 8100 328.30757 -39.861301 0.0034851739 1 1 + 8150 406.67601 2.8999409 0.0034851739 1 1 + 8200 332.20083 -51.217399 0.0034851739 1 1 + 8250 354.50609 53.128769 0.0034851739 1 1 + 8300 337.2758 20.68562 0.0034851739 1 1 + 8350 361.89708 -54.185869 0.0034851739 1 1 + 8400 305.63496 24.058529 0.0034851739 1 1 + 8450 303.27461 4.304683 0.0034851739 1 1 + 8500 253.53694 -10.909021 0.0034851739 1 1 + 8550 277.03017 23.241479 0.0034851739 1 1 + 8600 291.41844 -22.240665 0.0034851739 1 1 + 8650 307.85368 31.919587 0.0034851739 1 1 + 8700 309.19724 0.53529642 0.0034851739 1 1 + 8750 354.6583 11.565515 0.0034851739 1 1 + 8800 329.78598 19.5996 0.0034851739 1 1 + 8850 240.79198 21.803515 0.0034851739 1 1 + 8900 318.40749 -59.816923 0.0034851739 1 1 + 8950 308.47211 -57.808635 0.0034851739 1 1 + 9000 271.51207 50.943482 0.0034851739 1 1 + 9050 249.4005 6.7529187 0.0034851739 1 1 + 9100 221.8772 47.196092 0.0034851739 1 1 + 9150 297.9351 4.0058184 0.0034851739 1 1 + 9200 274.85051 -24.774393 0.0034851739 1 1 + 9250 336.04757 5.3799028 0.0034851739 1 1 + 9300 380.44956 -22.389381 0.0034851739 1 1 + 9350 336.9824 23.050616 0.0034851739 1 1 + 9400 304.46425 32.530218 0.0034851739 1 1 + 9450 317.55591 -22.265425 0.0034851739 1 1 + 9500 323.70901 -7.0159787 0.0034851739 1 1 + 9550 316.07308 28.062131 0.0034851739 1 1 + 9600 262.74608 -0.78519192 0.0034851739 1 1 + 9650 271.55045 -21.430123 0.0034851739 1 1 + 9700 239.6022 14.483637 0.0034851739 1 1 + 9750 338.1437 -0.72765302 0.0034851739 1 1 + 9800 334.50189 19.495144 0.0034851739 1 1 + 9850 354.87554 19.272719 0.0034851739 1 1 + 9900 334.02141 -22.393457 0.0034851739 1 1 + 9950 293.63651 19.178873 0.0034851739 1 1 + 10000 319.81736 21.904414 0.0034851739 1 1 +Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms + +Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14 +Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04 +Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49 +Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62 +Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22 +Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19 +Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40 +Other | | 0.01666 | | | 0.90 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 823 ave 823 max 823 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 823 +Ave neighs/atom = 18.7045 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 10000 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..377781f48f7091dbc910d9ce1ab0f98723abb7bb --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 @@ -0,0 +1,370 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.data + orthogonal box = (-25 -25 -25) to (25 25 25) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.data_template +Read molecule mol1: + 18 atoms with max type 8 + 16 bonds with max type 14 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 14 impropers with max type 11 +molecule mol2 rxn1_stp1_reacted.data_template +Read molecule mol2: + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 20 impropers with max type 1 +molecule mol3 rxn1_stp2_unreacted.data_template +Read molecule mol3: + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 16 impropers with max type 1 +molecule mol4 rxn1_stp2_reacted.data_template +Read molecule mol4: + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 10 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp defined + +fix 1 statted_grp nvt temp 300 300 100 + +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.0534597 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0402256 + estimated relative force accuracy = 0.000121138 + using double precision FFTs + 3d grid and FFT values/proc = 252 2 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10.5 + ghost atom cutoff = 10.5 + binsize = 5.25, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:786) +Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes +Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 296.70408 -51.30066 0.0034851739 1 0 + 100 274.25324 46.715512 0.0034851739 1 1 + 150 471.61579 31.321598 0.0034851739 1 1 + 200 362.87766 42.061118 0.0034851739 1 1 + 250 367.58058 65.303109 0.0034851739 1 1 + 300 372.38236 -52.421725 0.0034851739 1 1 + 350 297.69957 17.869945 0.0034851739 1 1 + 400 258.30433 49.19156 0.0034851739 1 1 + 450 253.34384 -5.8162637 0.0034851739 1 1 + 500 269.96465 -43.337517 0.0034851739 1 1 + 550 303.23718 10.180246 0.0034851739 1 1 + 600 329.59579 -48.97461 0.0034851739 1 1 + 650 350.42568 50.983183 0.0034851739 1 1 + 700 342.03272 35.43465 0.0034851739 1 1 + 750 269.23405 -41.873166 0.0034851739 1 1 + 800 245.15025 13.953092 0.0034851739 1 1 + 850 257.85421 -3.1492141 0.0034851739 1 1 + 900 316.15644 7.7798301 0.0034851739 1 1 + 950 299.9124 -15.77014 0.0034851739 1 1 + 1000 302.89968 -17.049693 0.0034851739 1 1 + 1050 308.91651 71.84632 0.0034851739 1 1 + 1100 348.43932 -18.742012 0.0034851739 1 1 + 1150 309.03036 50.536311 0.0034851739 1 1 + 1200 318.9761 -16.905746 0.0034851739 1 1 + 1250 320.42806 -0.057975092 0.0034851739 1 1 + 1300 289.7824 18.200772 0.0034851739 1 1 + 1350 284.79836 -9.1978427 0.0034851739 1 1 + 1400 325.43292 42.082833 0.0034851739 1 1 + 1450 261.5041 -37.823325 0.0034851739 1 1 + 1500 298.88723 -5.1647385 0.0034851739 1 1 + 1550 291.37403 -7.7764201 0.0034851739 1 1 + 1600 293.83475 22.2458 0.0034851739 1 1 + 1650 293.80611 24.202512 0.0034851739 1 1 + 1700 291.70205 -23.397884 0.0034851739 1 1 + 1750 292.32437 -10.671214 0.0034851739 1 1 + 1800 302.01367 -11.671025 0.0034851739 1 1 + 1850 322.1651 24.438331 0.0034851739 1 1 + 1900 310.45076 45.343592 0.0034851739 1 1 + 1950 325.91745 -19.847809 0.0034851739 1 1 + 2000 276.89662 63.387098 0.0034851739 1 1 + 2050 311.33783 -24.683247 0.0034851739 1 1 + 2100 346.2336 -27.526891 0.0034851739 1 1 + 2150 345.30604 -15.722411 0.0034851739 1 1 + 2200 346.7718 -17.857633 0.0034851739 1 1 + 2250 304.28676 -1.9965581 0.0034851739 1 1 + 2300 322.56372 -31.786868 0.0034851739 1 1 + 2350 282.64326 6.1982735 0.0034851739 1 1 + 2400 286.65759 -63.207781 0.0034851739 1 1 + 2450 257.05528 32.931491 0.0034851739 1 1 + 2500 283.64386 26.912373 0.0034851739 1 1 + 2550 299.54005 27.277039 0.0034851739 1 1 + 2600 283.92503 14.660972 0.0034851739 1 1 + 2650 321.93453 -18.977358 0.0034851739 1 1 + 2700 376.7189 31.826935 0.0034851739 1 1 + 2750 372.20075 -32.821697 0.0034851739 1 1 + 2800 361.40604 83.035183 0.0034851739 1 1 + 2850 332.27269 -23.927452 0.0034851739 1 1 + 2900 331.14638 -0.12328446 0.0034851739 1 1 + 2950 303.67489 -24.078857 0.0034851739 1 1 + 3000 311.40462 21.563537 0.0034851739 1 1 + 3050 284.72849 -23.849667 0.0034851739 1 1 + 3100 303.48477 39.347763 0.0034851739 1 1 + 3150 264.2739 -0.22299878 0.0034851739 1 1 + 3200 300.03351 31.545323 0.0034851739 1 1 + 3250 288.56663 5.7225229 0.0034851739 1 1 + 3300 200.13238 -31.239655 0.0034851739 1 1 + 3350 231.32512 16.631728 0.0034851739 1 1 + 3400 260.57402 2.1717992 0.0034851739 1 1 + 3450 301.47128 -42.210623 0.0034851739 1 1 + 3500 321.77414 40.074365 0.0034851739 1 1 + 3550 353.21858 28.387783 0.0034851739 1 1 + 3600 331.45989 -57.800858 0.0034851739 1 1 + 3650 303.88123 44.86596 0.0034851739 1 1 + 3700 329.73833 -0.8061567 0.0034851739 1 1 + 3750 297.55588 -0.49626022 0.0034851739 1 1 + 3800 286.38794 -10.010003 0.0034851739 1 1 + 3850 290.17417 -43.51187 0.0034851739 1 1 + 3900 247.88933 51.23735 0.0034851739 1 1 + 3950 332.31324 -18.194985 0.0034851739 1 1 + 4000 325.56802 18.402825 0.0034851739 1 1 + 4050 338.37594 36.430977 0.0034851739 1 1 + 4100 370.95478 39.290285 0.0034851739 1 1 + 4150 348.47859 -7.0779683 0.0034851739 1 1 + 4200 241.30632 -33.371789 0.0034851739 1 1 + 4250 242.17258 -9.9861962 0.0034851739 1 1 + 4300 300.85311 -7.924429 0.0034851739 1 1 + 4350 273.15684 -21.257282 0.0034851739 1 1 + 4400 305.77464 -5.8720712 0.0034851739 1 1 + 4450 314.97697 45.037299 0.0034851739 1 1 + 4500 310.77723 16.958771 0.0034851739 1 1 + 4550 302.17421 12.156862 0.0034851739 1 1 + 4600 319.74799 6.8488914 0.0034851739 1 1 + 4650 270.86805 -13.767907 0.0034851739 1 1 + 4700 249.81731 -31.197484 0.0034851739 1 1 + 4750 285.86481 -9.8916332 0.0034851739 1 1 + 4800 233.98321 7.1338518 0.0034851739 1 1 + 4850 302.60551 49.262886 0.0034851739 1 1 + 4900 316.55055 34.663238 0.0034851739 1 1 + 4950 357.32741 11.583013 0.0034851739 1 1 + 5000 400.21044 -8.1780861 0.0034851739 1 1 + 5050 390.01845 -20.490268 0.0034851739 1 1 + 5100 378.84249 -41.328772 0.0034851739 1 1 + 5150 324.02039 -15.023852 0.0034851739 1 1 + 5200 262.08427 10.937367 0.0034851739 1 1 + 5250 255.75506 16.381495 0.0034851739 1 1 + 5300 277.84991 40.682283 0.0034851739 1 1 + 5350 302.92834 9.1989644 0.0034851739 1 1 + 5400 283.71964 -1.6583895 0.0034851739 1 1 + 5450 300.71261 -4.703054 0.0034851739 1 1 + 5500 343.54987 -0.30546396 0.0034851739 1 1 + 5550 369.51272 21.691639 0.0034851739 1 1 + 5600 372.69786 -38.679919 0.0034851739 1 1 + 5650 327.41256 11.352201 0.0034851739 1 1 + 5700 278.9861 -23.82728 0.0034851739 1 1 + 5750 308.30037 -20.756238 0.0034851739 1 1 + 5800 341.4559 28.058314 0.0034851739 1 1 + 5850 322.9786 -10.731862 0.0034851739 1 1 + 5900 304.53598 32.825105 0.0034851739 1 1 + 5950 287.17515 -36.780057 0.0034851739 1 1 + 6000 296.52688 18.782156 0.0034851739 1 1 + 6050 314.25411 15.99272 0.0034851739 1 1 + 6100 313.86572 3.4344108 0.0034851739 1 1 + 6150 325.64197 32.39212 0.0034851739 1 1 + 6200 367.4298 -27.161154 0.0034851739 1 1 + 6250 369.30937 39.020881 0.0034851739 1 1 + 6300 328.92245 -23.175612 0.0034851739 1 1 + 6350 305.6293 4.9011587 0.0034851739 1 1 + 6400 241.70456 -13.675247 0.0034851739 1 1 + 6450 265.66574 2.4049735 0.0034851739 1 1 + 6500 249.3592 13.420453 0.0034851739 1 1 + 6550 294.5367 10.856753 0.0034851739 1 1 + 6600 308.20246 18.992923 0.0034851739 1 1 + 6650 305.43756 -49.57151 0.0034851739 1 1 + 6700 320.27395 11.339101 0.0034851739 1 1 + 6750 321.7875 -23.463361 0.0034851739 1 1 + 6800 303.40316 7.6256997 0.0034851739 1 1 + 6850 297.18652 51.52186 0.0034851739 1 1 + 6900 284.19084 -8.496294 0.0034851739 1 1 + 6950 331.04173 13.227745 0.0034851739 1 1 + 7000 311.38027 -43.26105 0.0034851739 1 1 + 7050 286.82046 -14.171194 0.0034851739 1 1 + 7100 302.81691 12.058085 0.0034851739 1 1 + 7150 297.18018 -43.110658 0.0034851739 1 1 + 7200 332.46131 26.051496 0.0034851739 1 1 + 7250 262.72288 41.161451 0.0034851739 1 1 + 7300 250.62739 -23.440907 0.0034851739 1 1 + 7350 296.92141 35.869216 0.0034851739 1 1 + 7400 245.06807 -13.467896 0.0034851739 1 1 + 7450 272.2659 -23.292836 0.0034851739 1 1 + 7500 209.05776 13.888665 0.0034851739 1 1 + 7550 255.03716 4.9662624 0.0034851739 1 1 + 7600 312.26011 -37.350427 0.0034851739 1 1 + 7650 305.5823 55.208039 0.0034851739 1 1 + 7700 325.13382 -18.370791 0.0034851739 1 1 + 7750 363.24898 -22.473126 0.0034851739 1 1 + 7800 350.19254 26.792307 0.0034851739 1 1 + 7850 271.76418 -17.843445 0.0034851739 1 1 + 7900 272.70301 -11.709349 0.0034851739 1 1 + 7950 298.5993 -12.736235 0.0034851739 1 1 + 8000 274.52611 49.657345 0.0034851739 1 1 + 8050 304.73711 -0.52485689 0.0034851739 1 1 + 8100 328.29239 -39.901891 0.0034851739 1 1 + 8150 406.52096 2.8669076 0.0034851739 1 1 + 8200 332.17309 -51.168754 0.0034851739 1 1 + 8250 354.68419 53.003157 0.0034851739 1 1 + 8300 337.28934 20.766408 0.0034851739 1 1 + 8350 361.81133 -54.159227 0.0034851739 1 1 + 8400 305.59597 24.011667 0.0034851739 1 1 + 8450 303.25823 4.423341 0.0034851739 1 1 + 8500 253.50747 -11.026949 0.0034851739 1 1 + 8550 277.13504 23.204625 0.0034851739 1 1 + 8600 291.40211 -22.253861 0.0034851739 1 1 + 8650 307.93765 32.14162 0.0034851739 1 1 + 8700 309.1529 0.36279434 0.0034851739 1 1 + 8750 355.10326 11.677219 0.0034851739 1 1 + 8800 330.21328 19.235269 0.0034851739 1 1 + 8850 241.29109 21.707386 0.0034851739 1 1 + 8900 319.15363 -60.010115 0.0034851739 1 1 + 8950 308.88552 -57.637014 0.0034851739 1 1 + 9000 272.22373 51.15837 0.0034851739 1 1 + 9050 248.84947 7.3390565 0.0034851739 1 1 + 9100 221.91564 48.387079 0.0034851739 1 1 + 9150 298.03506 2.9058639 0.0034851739 1 1 + 9200 274.25114 -24.597819 0.0034851739 1 1 + 9250 334.08373 5.1079577 0.0034851739 1 1 + 9300 383.07285 -23.274763 0.0034851739 1 1 + 9350 335.00581 20.94212 0.0034851739 1 1 + 9400 309.23862 34.074744 0.0034851739 1 1 + 9450 312.62262 -28.468057 0.0034851739 1 1 + 9500 324.54274 2.851136 0.0034851739 1 1 + 9550 313.32781 22.468182 0.0034851739 1 1 + 9600 269.04372 4.064934 0.0034851739 1 1 + 9650 270.98476 -21.520127 0.0034851739 1 1 + 9700 236.8736 16.250728 0.0034851739 1 1 + 9750 333.94686 1.6864148 0.0034851739 1 1 + 9800 330.91875 12.150018 0.0034851739 1 1 + 9850 343.8603 25.338853 0.0034851739 1 1 + 9900 330.93364 -28.292992 0.0034851739 1 1 + 9950 291.25518 25.795948 0.0034851739 1 1 + 10000 319.25565 25.323846 0.0034851739 1 1 +Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms + +Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s +93.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94 +Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22 +Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39 +Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51 +Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91 +Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33 +Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03 +Other | | 0.02359 | | | 0.66 + +Nlocal: 11 ave 44 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 33 ave 44 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 205.75 ave 823 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 823 +Ave neighs/atom = 18.7045 +Ave special neighs/atom = 9.77273 +Neighbor list builds = 10000 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map new file mode 100644 index 0000000000000000000000000000000000000000..44f7ad8137549eaa375046e114c59a7aa09c0c65 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map @@ -0,0 +1,35 @@ +this is a nominal superimpose file + +2 edgeIDs +18 equivalences + +BondingIDs + +10 +1 + +EdgeIDs + +16 +8 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 +16 16 +17 17 +18 18 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..d7256f43d2b3c659159ef23e3169dc6123d193ec --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template @@ -0,0 +1,189 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + +18 atoms +17 bonds +31 angles +39 dihedrals +20 impropers + +Types + +1 9 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 +16 1 +17 4 +18 4 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -5.522237 -0.752722 1.631158 +2 -5.170398 -0.545733 0.178130 +3 -6.469695 -0.553072 -0.648889 +4 -6.052076 -1.721152 1.744648 +5 -6.183059 0.071387 1.971497 +6 -4.489340 -1.389197 -0.173156 +7 -4.637591 0.453703 0.051252 +8 -5.618658 0.138919 4.386107 +9 -4.669492 -0.989819 3.943591 +10 -4.270194 -0.766405 2.474102 +11 -3.348470 -1.875393 2.024289 +12 -3.569794 0.564183 2.345995 +13 -5.201079 -1.993301 4.044219 +14 -3.736682 -0.984819 4.598305 +15 -4.255402 1.370923 2.679069 +16 -6.136394 -0.339866 -2.136775 +17 -6.996331 -1.555519 -0.517408 +18 -7.153308 0.284949 -0.289930 + +Bonds + +1 11 1 2 +2 12 1 4 +3 12 1 5 +4 13 1 10 +5 2 2 3 +6 1 2 6 +7 1 2 7 +8 2 3 16 +9 1 3 17 +10 1 3 18 +11 2 8 9 +12 4 9 10 +13 1 9 13 +14 1 9 14 +15 5 10 11 +16 3 10 12 +17 6 12 15 + +Angles + +1 17 2 1 4 +2 17 2 1 5 +3 18 2 1 10 +4 19 4 1 5 +5 20 4 1 10 +6 20 5 1 10 +7 21 1 2 3 +8 22 1 2 6 +9 22 1 2 7 +10 2 3 2 6 +11 2 3 2 7 +12 1 6 2 7 +13 3 2 3 16 +14 2 2 3 17 +15 2 2 3 18 +16 2 16 3 17 +17 2 16 3 18 +18 1 17 3 18 +19 8 8 9 10 +20 2 8 9 13 +21 2 8 9 14 +22 23 13 9 10 +23 23 14 9 10 +24 1 13 9 14 +25 6 9 10 11 +26 4 9 10 12 +27 24 1 10 9 +28 25 11 10 12 +29 26 1 10 11 +30 27 1 10 12 +31 7 10 12 15 + +Dihedrals + +1 19 4 1 2 3 +2 20 4 1 2 6 +3 20 4 1 2 7 +4 19 5 1 2 3 +5 20 5 1 2 6 +6 20 5 1 2 7 +7 21 10 1 2 3 +8 22 10 1 2 6 +9 22 10 1 2 7 +10 23 2 1 10 9 +11 24 2 1 10 11 +12 25 2 1 10 12 +13 26 4 1 10 9 +14 27 4 1 10 11 +15 28 4 1 10 12 +16 26 5 1 10 9 +17 27 5 1 10 11 +18 28 5 1 10 12 +19 29 1 2 3 16 +20 30 1 2 3 17 +21 30 1 2 3 18 +22 4 16 3 2 6 +23 2 6 2 3 17 +24 2 6 2 3 18 +25 4 16 3 2 7 +26 2 7 2 3 17 +27 2 7 2 3 18 +28 10 8 9 10 11 +29 8 8 9 10 12 +30 31 8 9 10 1 +31 11 13 9 10 11 +32 9 13 9 10 12 +33 32 13 9 10 1 +34 11 14 9 10 11 +35 9 14 9 10 12 +36 32 14 9 10 1 +37 6 9 10 12 15 +38 7 11 10 12 15 +39 33 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 2 3 16 17 +10 1 2 3 16 18 +11 1 2 3 17 18 +12 1 16 3 17 18 +13 1 8 9 13 10 +14 1 8 9 14 10 +15 1 8 9 13 14 +16 1 13 9 14 10 +17 1 9 10 11 12 +18 1 1 10 9 11 +19 1 1 10 9 12 +20 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..ec3f109d7b50c06c642635693f77257c4ce68c7e --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template @@ -0,0 +1,160 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + +18 atoms +16 bonds +25 angles +23 dihedrals +14 impropers + +Types + +1 7 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 +16 1 +17 4 +18 4 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 +16 0.000000 +17 0.000000 +18 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 +16 -3.964987 2.900602 -1.551341 +17 -4.460694 2.836102 0.668882 +18 -4.828494 3.219656 -0.122111 + +Bonds + +1 14 1 2 +2 10 1 4 +3 10 1 5 +4 2 2 3 +5 1 2 6 +6 1 2 7 +7 2 3 16 +8 1 3 17 +9 1 3 18 +10 2 8 9 +11 4 9 10 +12 1 9 13 +13 1 9 14 +14 5 10 11 +15 3 10 12 +16 6 12 15 + +Angles + +1 15 2 1 4 +2 15 2 1 5 +3 16 4 1 5 +4 28 1 2 3 +5 14 1 2 6 +6 14 1 2 7 +7 2 3 2 6 +8 2 3 2 7 +9 1 6 2 7 +10 3 2 3 16 +11 2 2 3 17 +12 2 2 3 18 +13 2 16 3 17 +14 2 16 3 18 +15 1 17 3 18 +16 8 8 9 10 +17 2 8 9 13 +18 2 8 9 14 +19 23 13 9 10 +20 23 14 9 10 +21 1 13 9 14 +22 6 9 10 11 +23 4 9 10 12 +24 25 11 10 12 +25 7 10 12 15 + +Dihedrals + +1 34 4 1 2 3 +2 35 4 1 2 6 +3 35 4 1 2 7 +4 34 5 1 2 3 +5 35 5 1 2 6 +6 35 5 1 2 7 +7 36 1 2 3 16 +8 12 1 2 3 17 +9 12 1 2 3 18 +10 4 16 3 2 6 +11 2 6 2 3 17 +12 2 6 2 3 18 +13 4 16 3 2 7 +14 2 7 2 3 17 +15 2 7 2 3 18 +16 10 8 9 10 11 +17 8 8 9 10 12 +18 11 13 9 10 11 +19 9 13 9 10 12 +20 11 14 9 10 11 +21 9 14 9 10 12 +22 6 9 10 12 15 +23 7 11 10 12 15 + +Impropers + +1 6 2 1 4 5 +2 11 9 10 11 12 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 2 3 16 17 +8 1 2 3 16 18 +9 1 2 3 17 18 +10 1 16 3 17 18 +11 1 8 9 13 10 +12 1 8 9 14 10 +13 1 8 9 13 14 +14 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map new file mode 100644 index 0000000000000000000000000000000000000000..35fe47fdb3bdb0386d65b950d45cbfb39fbe6f7f --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map @@ -0,0 +1,32 @@ +this is a nominal superimpose file + +2 edgeIDs +15 equivalences + +BondingIDs + +4 +12 + +EdgeIDs + +8 +3 + +Equivalences + +1 1 +2 2 +3 3 +4 4 +5 5 +6 6 +7 7 +8 8 +9 9 +10 10 +11 11 +12 12 +13 13 +14 14 +15 15 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..785363464696967b7938c142043868792546e3cf --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template @@ -0,0 +1,131 @@ +this is a molecule template for: water condensation, post-reacting + +15 atoms +13 bonds +19 angles +16 dihedrals +10 impropers + +Types + +1 9 +2 1 +3 1 +4 10 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 11 +13 4 +14 4 +15 10 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.410000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 -0.820000 +13 0.000000 +14 0.000000 +15 0.410000 + +Coords + +1 -4.856280 -1.050468 1.432625 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 11 1 2 +2 12 1 5 +3 13 1 10 +4 2 2 3 +5 1 2 6 +6 1 2 7 +7 15 4 12 +8 2 8 9 +9 4 9 10 +10 1 9 13 +11 1 9 14 +12 5 10 11 +13 15 15 12 + +Angles + +1 17 2 1 5 +2 18 2 1 10 +3 20 5 1 10 +4 21 1 2 3 +5 22 1 2 6 +6 22 1 2 7 +7 2 3 2 6 +8 2 3 2 7 +9 1 6 2 7 +10 8 8 9 10 +11 2 8 9 13 +12 2 8 9 14 +13 23 13 9 10 +14 23 14 9 10 +15 1 13 9 14 +16 6 9 10 11 +17 24 1 10 9 +18 26 1 10 11 +19 29 15 12 4 + +Dihedrals + +1 19 5 1 2 3 +2 20 5 1 2 6 +3 20 5 1 2 7 +4 21 10 1 2 3 +5 22 10 1 2 6 +6 22 10 1 2 7 +7 23 2 1 10 9 +8 24 2 1 10 11 +9 26 5 1 10 9 +10 27 5 1 10 11 +11 10 8 9 10 11 +12 31 8 9 10 1 +13 11 13 9 10 11 +14 32 13 9 10 1 +15 11 14 9 10 11 +16 32 14 9 10 1 + +Impropers + +1 12 2 1 5 10 +2 13 1 10 9 11 +3 1 1 2 3 6 +4 1 1 2 3 7 +5 1 1 2 6 7 +6 1 3 2 6 7 +7 1 8 9 13 10 +8 1 8 9 14 10 +9 1 8 9 13 14 +10 1 13 9 14 10 diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template new file mode 100644 index 0000000000000000000000000000000000000000..847f0622e506865117fbe542f89de35fb20ccede --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template @@ -0,0 +1,158 @@ +this is a molecule template for: water condensation, pre-reacting + +15 atoms +14 bonds +25 angles +30 dihedrals +16 impropers + +Types + +1 9 +2 1 +3 1 +4 8 +5 8 +6 4 +7 4 +8 1 +9 1 +10 2 +11 6 +12 3 +13 4 +14 4 +15 5 + +Charges + +1 -0.300000 +2 0.000000 +3 0.000000 +4 0.000000 +5 0.000000 +6 0.000000 +7 0.000000 +8 0.000000 +9 0.000000 +10 0.300000 +11 0.000000 +12 0.000000 +13 0.000000 +14 0.000000 +15 0.000000 + +Coords + +1 -4.922858 -0.946982 1.146055 +2 -5.047195 -0.935267 -0.358173 +3 -6.526281 -0.755366 -0.743523 +4 -5.282604 0.020447 1.552710 +5 -3.860697 -1.095850 1.428305 +6 -4.662382 -1.920900 -0.781524 +7 -4.433977 -0.072765 -0.784071 +8 -5.506279 0.202610 4.825816 +9 -4.449177 -0.844592 4.423366 +10 -4.103916 -0.749629 2.925195 +11 -3.376249 -1.886171 2.245643 +12 -4.493235 0.477214 2.137199 +13 -4.849053 -1.888877 4.663994 +14 -3.491823 -0.662913 5.018510 +15 -5.020777 1.189745 2.805427 + +Bonds + +1 11 1 2 +2 12 1 4 +3 12 1 5 +4 13 1 10 +5 2 2 3 +6 1 2 6 +7 1 2 7 +8 2 8 9 +9 4 9 10 +10 1 9 13 +11 1 9 14 +12 5 10 11 +13 3 10 12 +14 6 12 15 + +Angles + +1 17 2 1 4 +2 17 2 1 5 +3 18 2 1 10 +4 19 4 1 5 +5 20 4 1 10 +6 20 5 1 10 +7 21 1 2 3 +8 22 1 2 6 +9 22 1 2 7 +10 2 3 2 6 +11 2 3 2 7 +12 1 6 2 7 +13 8 8 9 10 +14 2 8 9 13 +15 2 8 9 14 +16 23 13 9 10 +17 23 14 9 10 +18 1 13 9 14 +19 6 9 10 11 +20 4 9 10 12 +21 24 1 10 9 +22 25 11 10 12 +23 26 1 10 11 +24 27 1 10 12 +25 7 10 12 15 + +Dihedrals + +1 19 4 1 2 3 +2 20 4 1 2 6 +3 20 4 1 2 7 +4 19 5 1 2 3 +5 20 5 1 2 6 +6 20 5 1 2 7 +7 21 10 1 2 3 +8 22 10 1 2 6 +9 22 10 1 2 7 +10 23 2 1 10 9 +11 24 2 1 10 11 +12 25 2 1 10 12 +13 26 4 1 10 9 +14 27 4 1 10 11 +15 28 4 1 10 12 +16 26 5 1 10 9 +17 27 5 1 10 11 +18 28 5 1 10 12 +19 10 8 9 10 11 +20 8 8 9 10 12 +21 31 8 9 10 1 +22 11 13 9 10 11 +23 9 13 9 10 12 +24 32 13 9 10 1 +25 11 14 9 10 11 +26 9 14 9 10 12 +27 32 14 9 10 1 +28 6 9 10 12 15 +29 7 11 10 12 15 +30 33 1 10 12 15 + +Impropers + +1 1 2 1 4 5 +2 1 2 1 4 10 +3 1 2 1 5 10 +4 1 4 1 5 10 +5 1 1 2 3 6 +6 1 1 2 3 7 +7 1 1 2 6 7 +8 1 3 2 6 7 +9 1 8 9 13 10 +10 1 8 9 14 10 +11 1 8 9 13 14 +12 1 13 9 14 10 +13 1 9 10 11 12 +14 1 1 10 9 11 +15 1 1 10 9 12 +16 1 1 10 11 12 diff --git a/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data new file mode 100644 index 0000000000000000000000000000000000000000..8466e68ea57fed2ddca9851724e4ea1509049435 --- /dev/null +++ b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data @@ -0,0 +1,795 @@ +this is LAMMPS data file containing two nylon monomers + +44 atoms +11 atom types +42 bonds +15 bond types +74 angles +29 angle types +100 dihedrals +36 dihedral types +44 impropers +13 improper types +5 extra bond per atom +15 extra angle per atom +15 extra dihedral per atom +25 extra improper per atom +25 extra special per atom + +-25 25 xlo xhi +-25 25 ylo yhi +-25 25 zlo zhi + +Masses + +1 12.0112 +2 12.0112 +3 15.9994 +4 1.00797 +5 1.00797 +6 15.9994 +7 14.0067 +8 1.00797 +9 14.0067 +10 1.00797 +11 15.9994 + +Pair Coeffs # lj/class2/coul/cut + +1 0.054 4.01 +2 0.12 3.81 +3 0.24 3.535 +4 0.02 2.7 +5 0.013 1.098 +6 0.267 3.3 +7 0.065 4.07 +8 0.013 1.098 +9 0.106 4.07 +10 0.013 1.098 +11 0.26 3.61 + +Bond Coeffs # class2 + +1 1.101 345 -691.89 844.6 +2 1.53 299.67 -501.77 679.81 +3 1.3649 368.731 -832.478 1274.02 +4 1.5202 253.707 -423.037 396.9 +5 1.202 851.14 -1918.49 2160.77 +6 0.965 532.506 -1282.9 2004.77 +7 1.53 299.67 -501.77 679.81 +8 1.101 345 -691.89 844.6 +9 1.457 365.805 -699.637 998.484 +10 1.006 466.74 -1073.6 1251.11 +11 1.452 327.166 -547.899 526.5 +12 1.01 462.75 -1053.63 1545.76 +13 1.416 359.159 -558.473 1146.38 +14 1.457 365.805 -699.637 998.484 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39 44 +43 7 26 42 43 44 +44 7 39 42 43 44 diff --git a/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs b/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs new file mode 100644 index 0000000000000000000000000000000000000000..76ecae7b44401c7a2dc6380514ab33b9fc05f29a --- /dev/null +++ b/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs @@ -0,0 +1,6006 @@ +Source: M.I. Mendelev, unpublished +Contact information: mendelev@ameslab.gov +Tuesday, Sep 2, 2014 The potential was taken from v1_4_bcc (in C:\SIMULATION.MD\Na\Results\v1_4) +1 Na +10000 1.00000000000000E-0002 10000 9.20000000000000E-0004 9.20000000000000E+0000 +11 2.29897700000000E+0001 4.22786798098572E+0000 bcc +0 -1.00000000000000E-0001 -1.41421356237310E-0001 -1.73205080756888E-0001 -2.00000000000000E-0001 +-2.23606797749979E-0001 -2.44948974278318E-0001 -2.64575131106459E-0001 -2.82842712474619E-0001 -3.00000000000000E-0001 +-3.16227766016838E-0001 -3.31662479035540E-0001 -3.46410161513775E-0001 -3.60555127546399E-0001 -3.74165738677394E-0001 +-3.87298334620742E-0001 -4.00000000000000E-0001 -4.12310562561766E-0001 -4.24264068711929E-0001 -4.35889894354067E-0001 +-4.47213595499958E-0001 -4.58257569495584E-0001 -4.69041575982343E-0001 -4.79583152331272E-0001 -4.89897948556636E-0001 +-5.00000000000000E-0001 -5.09901951359279E-0001 -5.19615242270663E-0001 -5.29150262212918E-0001 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4.4461045576277334e+00 2.7023074862421219e+00 6.5761907532557173e-01 +3605 -1.9130986635970524e+00 3.9668547188660113e+00 -6.3242395502805584e+00 +3643 4.2561654139359133e+00 2.7079886942829829e+00 2.7399717274611493e+00 +3679 -2.1411701998224424e+00 -1.6132315381071032e+00 7.2516729511827427e-01 +3324 -8.2027537927136707e-01 -2.7694148205687066e+00 2.4736641085737388e+00 +3274 -4.4417852313637960e+00 -3.1061873476270003e+00 -4.2202494315305700e-01 +3779 -6.8867094633379926e+00 8.9727449535086627e+00 2.8636972542619379e+00 +621 3.0864972952518466e+00 -7.7377722234997837e-01 1.2106492653280587e-01 +3759 4.2946340382075698e+00 -2.7309518923249305e+00 -7.9384037173415658e+00 +3903 5.6188342028914784e+00 -2.7814248255132510e+00 -7.5133775402016285e+00 +3247 -1.6193326128196186e+00 -1.7233073750291210e+00 1.2558642428529292e+00 +3620 3.1413258846560623e+00 4.1189507481056093e+00 -6.3921202343711521e+00 +3984 1.3917530918758356e+00 -2.3497816055013883e+00 -1.4662677833340403e+00 +3359 -9.7958489915505709e-01 -7.9530975508665236e-01 3.6113761736403754e-01 +3728 4.3499495062909288e+00 -3.0962919910136191e+00 2.5291553497464387e+00 +3105 -2.1324777268885367e+00 4.6999502576160301e+00 -1.1831903765756278e+00 +2913 9.6792227860968549e-01 -8.2454190909792562e+00 -3.4600835572456634e+00 +105 1.1598974321010078e+00 6.6642846330522749e+00 -3.1397454859758240e+00 +3786 2.4337460674831185e-01 1.7007163465914101e+00 2.5520406588866820e+00 +4072 -4.0958048708482792e-01 1.1106824876365642e+00 3.0788300199054586e+00 +3160 -5.4524347356962517e+00 4.3156482789948143e+00 -1.3707562648323310e+00 +167 -3.7846180163481380e+00 6.0688805089413700e+00 -9.3209569588631103e-01 +193 -2.2590274085362330e+00 -3.0825410238075674e+00 2.7055352419861740e+00 +848 7.0018093775573365e-01 2.8058409327943159e+00 -2.8664598081555570e+00 +3993 -2.1133573700213573e+00 -3.5509555580404868e+00 1.6428703567042029e+00 +3781 -9.8115460551194134e-01 -3.3293080663104027e+00 -4.8282826681026414e+00 +9 -5.7488885085826680e-01 -3.8370861619809009e+00 -7.2892619744045950e+00 +3599 5.2833107352107955e+00 -8.2925617792090145e-01 -2.5358574431762029e+00 +3518 4.0580253230452010e+00 -3.0945361122357586e+00 -8.8323796705297763e-01 +4089 7.2248060554373073e+00 9.0480655644191388e-01 -9.6284911590930766e-01 +2593 3.2503133857492319e+00 -4.1972151630470256e+00 -1.7952974231313504e-01 diff --git a/examples/USER/misc/entropy/in.entropy b/examples/USER/misc/entropy/in.entropy new file mode 100644 index 0000000000000000000000000000000000000000..2c25dac3205d885b2b84aa4c3aff7df5420bce74 --- /dev/null +++ b/examples/USER/misc/entropy/in.entropy @@ -0,0 +1,34 @@ +echo both + +units metal +atom_style full + +read_data data.interface +mass 1 22.98977 + +neigh_modify delay 10 every 1 +pair_style eam/fs +pair_coeff * * Na_MendelevM_2014.eam.fs Na +timestep 0.002 +thermo 500 + +neighbor 4. bin + +# Define computes +# Global density, no average +compute 1 all entropy/atom 0.25 7.75 +# Local density, no average +compute 2 all entropy/atom 0.25 7.75 local yes +# Global density, average over neighbors +compute 3 all entropy/atom 0.25 7.75 avg yes 5. +# Local density, average over neighbors +compute 4 all entropy/atom 0.25 7.75 avg yes 5. local yes + +dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4 + + +fix 1 all nph x 1. 1. 10. +fix 2 all temp/csvr 350. 350. 0.1 64582 + +run 1000 + diff --git a/examples/USER/misc/entropy/log.entropy b/examples/USER/misc/entropy/log.entropy new file mode 100644 index 0000000000000000000000000000000000000000..c380c62a731b77c6c83d3a36fc822b52843f8c17 --- /dev/null +++ b/examples/USER/misc/entropy/log.entropy @@ -0,0 +1,124 @@ +LAMMPS (30 Mar 2018) + +units metal +atom_style full + +read_data data.interface +Reading data file ... + triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 4096 atoms + reading velocities ... + 4096 velocities +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +mass 1 22.98977 + +neigh_modify delay 10 every 1 +pair_style eam/fs +pair_coeff * * Na_MendelevM_2014.eam.fs Na +timestep 0.002 +thermo 500 + +neighbor 4. bin + +# Define computes +# Global density, no average +compute 1 all entropy/atom 0.25 7.75 +# Local density, no average +compute 2 all entropy/atom 0.25 7.75 local yes +# Global density, average over neighbors +compute 3 all entropy/atom 0.25 7.75 avg yes 5. +# Local density, average over neighbors +compute 4 all entropy/atom 0.25 7.75 avg yes 5. local yes + +dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4 + + +fix 1 all nph x 1. 1. 10. +fix 2 all temp/csvr 350. 350. 0.1 64582 + +run 1000 +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.2 + ghost atom cutoff = 13.2 + binsize = 6.6, bins = 21 6 6 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair eam/fs, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard + (2) compute entropy/atom, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (4) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (5) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.002 +Per MPI rank memory allocation (min/avg/max) = 25.68 | 25.69 | 25.69 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75 + 500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18 + 1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18 +Loop time of 5.3437 on 4 procs for 1000 steps with 4096 atoms + +Performance: 32.337 ns/day, 0.742 hours/ns, 187.136 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.2832 | 4.3257 | 4.3839 | 1.8 | 80.95 +Bond | 0.00018309 | 0.00019825 | 0.00021418 | 0.0 | 0.00 +Neigh | 0.42195 | 0.42512 | 0.42739 | 0.3 | 7.96 +Comm | 0.051679 | 0.1101 | 0.14916 | 10.8 | 2.06 +Output | 0.40909 | 0.4091 | 0.40911 | 0.0 | 7.66 +Modify | 0.060869 | 0.061921 | 0.06327 | 0.4 | 1.16 +Other | | 0.01161 | | | 0.22 + +Nlocal: 1024 ave 1040 max 1001 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 4614.25 ave 4700 max 4540 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 121747 ave 126398 max 116931 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +FullNghs: 243494 ave 252523 max 233842 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 973974 +Ave neighs/atom = 237.787 +Ave special neighs/atom = 0 +Neighbor list builds = 13 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/body/data.cubes b/examples/body/data.cubes new file mode 100644 index 0000000000000000000000000000000000000000..c1323ca3503bb10745df9a9bc176ce531850a4eb --- /dev/null +++ b/examples/body/data.cubes @@ -0,0 +1,76 @@ +LAMMPS data file for polygons: cubes, moment of inertia I = m edge^2/ 6 +2 atoms +2 bodies +1 atom types +0 6 xlo xhi +0 6 ylo yhi +0 6 zlo zhi + +Atoms + +1 1 1 1 1.5 1.5 1.5 +2 1 1 1 4.0 4.0 4.0 + +Bodies + +1 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 +2 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 + diff --git a/examples/body/data.squares b/examples/body/data.squares new file mode 100755 index 0000000000000000000000000000000000000000..6b198fd422dc0e5d8f736d70bcd9906ca133898e --- /dev/null +++ b/examples/body/data.squares @@ -0,0 +1,32 @@ +LAMMPS data file for polygons: squares of edge length L: Izz = 1/6mL^2 +2 atoms +2 bodies +1 atom types +0 12 xlo xhi +0 12 ylo yhi +-0.5 0.5 zlo zhi + +Atoms + +1 1 1 1 4 5 0 +2 1 1 1 9 6 0 + +Bodies + +1 1 19 +4 +1 1 2.67 0 0 0 +-2 -2 0 +-2 2 0 +2 2 0 +2 -2 0 +0.5 +2 1 19 +4 +1 1 2.67 0 0 0 +-2 -2 0 +-2 2 0 +2 2 0 +2 -2 0 +0.5 + diff --git a/examples/body/in.body b/examples/body/in.body index 5879ed5e45bc8810e82df81fdac0928306ae9e23..815b8531545a4348fb54dd1553abcfb642f44bf5 100644 --- a/examples/body/in.body +++ b/examples/body/in.body @@ -8,7 +8,7 @@ read_data data.body velocity all create 1.44 87287 loop geom -pair_style body 5.0 +pair_style body/nparticle 5.0 pair_coeff * * 1.0 1.0 neighbor 0.5 bin diff --git a/examples/body/in.cubes b/examples/body/in.cubes new file mode 100644 index 0000000000000000000000000000000000000000..a22599fe9607873aab7bc2214f59b8268415814d --- /dev/null +++ b/examples/body/in.cubes @@ -0,0 +1,53 @@ +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + +replicate $r $r $r + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} + diff --git a/examples/body/in.pour3d b/examples/body/in.pour3d new file mode 100644 index 0000000000000000000000000000000000000000..bcba950e593606065837cdbaeb85a4376fd0c4c4 --- /dev/null +++ b/examples/body/in.pour3d @@ -0,0 +1,57 @@ +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 & + molecule.rod3d toff 2 molecule.point3d toff 3 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object & + molfrac 0.25 0.25 0.25 0.25 + +fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL + +#compute 1 all body/local type 1 2 3 +#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] +#dump 10 all custom 1000 tmp.dump id type x y z radius + +thermo_style custom step atoms ke pe etotal press + +thermo 1000 + +#dump 2 all image 500 image.*.jpg type type & +# zoom 1.5 adiam 1.5 body type 0 0 view 75 15 +#dump_modify 2 pad 6 + +run ${steps} + + diff --git a/examples/body/in.squares b/examples/body/in.squares new file mode 100755 index 0000000000000000000000000000000000000000..3b05b5cead88cd6265b17ce2772873b97c475383 --- /dev/null +++ b/examples/body/in.squares @@ -0,0 +1,55 @@ +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + +replicate $r $r 1 + +velocity all create $T ${seed} dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 & + y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 & +# adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} diff --git a/examples/body/in.wall2d b/examples/body/in.wall2d new file mode 100755 index 0000000000000000000000000000000000000000..04e7f31cb6810151570f164353f683ac6b675afa --- /dev/null +++ b/examples/body/in.wall2d @@ -0,0 +1,57 @@ +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + +replicate $r $r 1 + +velocity all create $T ${seed} dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 & +# adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} diff --git a/examples/body/log.9Jul18.body.cubes.g++.1 b/examples/body/log.9Jul18.body.cubes.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c9a799c0b51192a5420fb75fb8aeaa32a0b1a3df --- /dev/null +++ b/examples/body/log.9Jul18.body.cubes.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (29 Jun 2018) +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + orthogonal box = (0 0 0) to (6 6 6) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r $r +replicate 3 $r $r +replicate 3 3 $r +replicate 3 3 3 + orthogonal box = (0 0 0) to (18 18 18) + 1 by 1 by 1 MPI processor grid + 54 atoms + Time spent = 0.000217915 secs + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 1 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.9641 + ghost atom cutoff = 3.9641 + binsize = 1.98205, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes +Step KinEng PotEng TotEng c_p2 c_1_temp + 0 1.7666667 0 1.7666667 0.01090535 0.59439252 + 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 + 2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624 + 3000 3.090491 0.16511199 3.255603 0.018691142 1.23672 + 4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839 + 5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154 + 6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839 + 7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326 + 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 + 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 + 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 +Loop time of 38.5686 on 1 procs for 10000 steps with 54 atoms + +Performance: 22401.653 tau/day, 259.278 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 38.426 | 38.426 | 38.426 | 0.0 | 99.63 +Neigh | 0.0043154 | 0.0043154 | 0.0043154 | 0.0 | 0.01 +Comm | 0.047616 | 0.047616 | 0.047616 | 0.0 | 0.12 +Output | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00 +Modify | 0.082948 | 0.082948 | 0.082948 | 0.0 | 0.22 +Other | | 0.007761 | | | 0.02 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 96 ave 96 max 96 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 100 +Ave neighs/atom = 1.85185 +Neighbor list builds = 268 +Dangerous builds = 0 + +Total wall time: 0:00:38 diff --git a/examples/body/log.9Jul18.body.cubes.g++.4 b/examples/body/log.9Jul18.body.cubes.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..e2407e972532938d39ba0e62964d74dc9c69740f --- /dev/null +++ b/examples/body/log.9Jul18.body.cubes.g++.4 @@ -0,0 +1,125 @@ +LAMMPS (29 Jun 2018) +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + orthogonal box = (0 0 0) to (6 6 6) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r $r +replicate 3 $r $r +replicate 3 3 $r +replicate 3 3 3 + orthogonal box = (0 0 0) to (18 18 18) + 1 by 2 by 2 MPI processor grid + 54 atoms + Time spent = 0.00103807 secs + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 1 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.9641 + ghost atom cutoff = 3.9641 + binsize = 1.98205, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.879 | 5.068 | 5.256 Mbytes +Step KinEng PotEng TotEng c_p2 c_1_temp + 0 1.7666667 0 1.7666667 0.01090535 0.59439252 + 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 + 2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624 + 3000 3.090491 0.16511199 3.255603 0.018691142 1.23672 + 4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839 + 5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154 + 6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839 + 7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326 + 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 + 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 + 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 +Loop time of 20.5306 on 4 procs for 10000 steps with 54 atoms + +Performance: 42083.509 tau/day, 487.078 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.5288 | 10.878 | 19.952 | 159.0 | 52.98 +Neigh | 0.0014424 | 0.0016552 | 0.0021195 | 0.7 | 0.01 +Comm | 0.50623 | 9.5805 | 12.93 | 169.4 | 46.66 +Output | 0.00011921 | 0.00014341 | 0.00021386 | 0.0 | 0.00 +Modify | 0.044663 | 0.047684 | 0.05382 | 1.6 | 0.23 +Other | | 0.023 | | | 0.11 + +Nlocal: 13.5 ave 17 max 9 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 63.5 ave 68 max 58 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 25 ave 38 max 6 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 100 +Ave neighs/atom = 1.85185 +Neighbor list builds = 268 +Dangerous builds = 0 + +Total wall time: 0:00:20 diff --git a/examples/body/log.9Jul18.body.pour3d.g++.1 b/examples/body/log.9Jul18.body.pour3d.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..213dd2e18fa9959a87ca922760e53508cace973d --- /dev/null +++ b/examples/body/log.9Jul18.body.pour3d.g++.1 @@ -0,0 +1,138 @@ +LAMMPS (29 Jun 2018) +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg +Created orthogonal box = (0 0 0) to (50 50 50) + 1 by 1 by 1 MPI processor grid + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 5 + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3 +Read molecule object: + 1 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 2 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 3 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 4 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 +Particle insertion: 134 every 4472 steps, 500 by step 13417 + +fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL + +#compute 1 all body/local type 1 2 3 +#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] +#dump 10 all custom 1000 tmp.dump id type x y z radius + +thermo_style custom step atoms ke pe etotal press + +thermo 1000 + +#dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15 +#dump_modify 2 pad 6 + +run ${steps} +run 6000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5 + ghost atom cutoff = 5 + binsize = 2.5, bins = 20 20 20 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.5065 | 0.5065 | 0.5065 Mbytes +Step Atoms KinEng PotEng TotEng Press + 0 0 -0 0 0 0 + 1000 134 -0 0.00083010524 0.00083010524 -2.1515152e-06 + 2000 134 -0 -0.00069962476 -0.00069962476 -1.4170663e-08 + 3000 134 -0 -0.00069962687 -0.00069962687 -4.1478181e-11 + 4000 134 -0 -0.00069962687 -0.00069962687 -1.2141026e-13 + 5000 268 -0 0.014969705 0.014969705 3.0797164e-05 + 6000 268 -0 0.042467887 0.042467887 0.00056148005 +Loop time of 0.634737 on 1 procs for 6000 steps with 268 atoms + +Performance: 816716.196 tau/day, 9452.734 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41391 | 0.41391 | 0.41391 | 0.0 | 65.21 +Neigh | 0.010547 | 0.010547 | 0.010547 | 0.0 | 1.66 +Comm | 0.0030921 | 0.0030921 | 0.0030921 | 0.0 | 0.49 +Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.02 +Modify | 0.19736 | 0.19736 | 0.19736 | 0.0 | 31.09 +Other | | 0.009719 | | | 1.53 + +Nlocal: 268 ave 268 max 268 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 68 ave 68 max 68 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 68 +Ave neighs/atom = 0.253731 +Neighbor list builds = 168 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/examples/body/log.9Jul18.body.squares.g++.1 b/examples/body/log.9Jul18.body.squares.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..7b539797bd6d399ade37eeb28d580447c8721d9e --- /dev/null +++ b/examples/body/log.9Jul18.body.squares.g++.1 @@ -0,0 +1,221 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.00020504 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 + 2000 0.42284177 0.01346585 0.43630762 0.0029377883 + 3000 0.58154405 0.011321689 0.59286574 0.003667871 + 4000 0.73518304 0.034603175 0.76978621 0.0018689207 + 5000 0.84367476 0.025292163 0.86896692 0.0089161373 + 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 + 7000 0.56206452 0.10453031 0.66659483 0.010255161 + 8000 0.64538994 0.088817673 0.73420761 0.0037633655 + 9000 0.90540819 0.063696004 0.96910419 0.0077673359 + 10000 0.68632042 0.093265016 0.77958544 0.0057864838 + 11000 0.59118074 0.025654748 0.61683549 0.012518759 + 12000 0.67522767 0.038176401 0.71340407 0.01741153 + 13000 0.7644843 0.10429844 0.86878274 0.013161339 + 14000 0.56152694 0.067836655 0.62936359 0.016852121 + 15000 0.41895506 0.019513348 0.43846841 0.015225695 + 16000 0.55799421 0.1564559 0.71445011 0.011703561 + 17000 0.59391964 0.034450221 0.62836986 0.026215002 + 18000 0.75911858 0.030885726 0.7900043 0.018396366 + 19000 0.64417995 0.12110912 0.76528907 0.010247952 + 20000 0.57751435 0.16965651 0.74717086 0.023392323 + 21000 0.7613368 0.13405354 0.89539034 0.021498982 + 22000 0.57676692 0.18011879 0.75688571 0.024469161 + 23000 0.54043723 0.11842026 0.65885749 0.019799067 + 24000 0.62276061 0.038967924 0.66172853 0.019080086 + 25000 0.53157536 0.11651937 0.64809473 0.017019298 + 26000 0.72213293 0.039012448 0.76114538 0.015434904 + 27000 0.62157832 0.13697494 0.75855326 0.028711011 + 28000 0.41323738 0.16301101 0.57624839 0.041792632 + 29000 0.45774328 0.17569066 0.63343394 0.019975231 + 30000 0.78901796 0.099791386 0.88880934 0.024116947 + 31000 0.85205397 0.11977547 0.97182945 0.026667489 + 32000 0.37137095 0.1232622 0.49463315 0.00087637364 + 33000 0.26860871 0.26056381 0.52917252 0.036110517 + 34000 0.3018636 0.21336905 0.51523265 0.040315549 + 35000 0.39915129 0.28245957 0.68161085 0.034876856 + 36000 0.25761236 0.2352705 0.49288286 0.022772767 + 37000 0.1071233 0.31692858 0.42405188 0.017994666 + 38000 0.083729577 0.28473145 0.36846103 -0.0045370431 + 39000 0.070355565 0.26682083 0.33717639 0.017921556 + 40000 0.075894079 0.20077896 0.27667304 0.014873186 + 41000 0.05891028 0.15989064 0.21880092 0.025547873 + 42000 0.1225107 0.16583605 0.28834675 0.038842785 + 43000 0.17049189 0.14323991 0.3137318 0.029550161 + 44000 0.26823939 0.15208257 0.42032196 0.028113612 + 45000 0.10172203 0.1729706 0.27469264 -0.013769913 + 46000 0.14841355 0.19085074 0.33926429 -0.00073741985 + 47000 0.27654927 0.19097937 0.46752864 0.04021431 + 48000 0.53432331 0.080769923 0.61509323 0.029932845 + 49000 0.69111634 0.13064951 0.82176585 0.028985406 + 50000 0.24520806 0.18317453 0.42838258 0.05179746 + 51000 0.23541368 0.14281364 0.37822732 0.071884238 + 52000 0.25464996 0.095730242 0.3503802 0.034488204 + 53000 0.53677633 0.1058745 0.64265084 0.059932498 + 54000 0.32970921 0.27979128 0.60950049 0.062869716 + 55000 0.49094054 0.096735015 0.58767556 0.04728005 + 56000 0.54398249 0.2216472 0.76562969 0.056712022 + 57000 0.60869068 0.2338422 0.84253288 0.077143302 + 58000 0.72175509 0.18687368 0.90862877 0.019357656 + 59000 0.79442757 0.092502981 0.88693055 0.066882632 + 60000 0.6810555 0.077699385 0.75875488 0.095975173 + 61000 0.63178834 0.05071143 0.68249977 0.043586668 + 62000 0.76589344 0.044615704 0.81050914 0.085718411 + 63000 0.84815889 0.030527848 0.87868674 0.053072795 + 64000 0.7309043 0.051938637 0.78284294 0.058887766 + 65000 0.62498816 0.034474465 0.65946262 0.068446407 + 66000 0.69817494 0.068546004 0.76672094 0.062634433 + 67000 0.86444275 0.010184259 0.87462701 0.073635055 + 68000 0.77820319 0.0079319524 0.78613515 0.090330925 + 69000 0.56938919 0.0092629332 0.57865213 0.061838729 + 70000 0.61870712 0.010047381 0.6287545 0.066501338 + 71000 0.71651803 0.0088366199 0.72535465 0.079136316 + 72000 0.76278925 0.008828151 0.77161741 0.063672771 + 73000 0.75447428 0.0083985526 0.76287283 0.078256913 + 74000 0.66185251 0.0091910052 0.67104351 0.069840511 + 75000 0.58458829 0.0097671568 0.59435544 0.076123422 + 76000 0.7487564 0.0100022 0.7587586 0.076171741 + 77000 0.89505465 0.009250681 0.90430533 0.074921699 + 78000 0.73738164 0.0092029279 0.74658457 0.078835344 + 79000 0.65735281 0.010099528 0.66745233 0.077940627 + 80000 0.70247542 0.010306464 0.71278189 0.079560093 + 81000 0.74839505 0.010199092 0.75859415 0.080835104 + 82000 0.75193767 0.010274058 0.76221173 0.081086684 + 83000 0.71392598 0.010495573 0.72442156 0.082746145 + 84000 0.58498928 0.011027388 0.59601667 0.08356465 + 85000 0.59022869 0.011729474 0.60195817 0.084519397 + 86000 0.81753578 0.011208964 0.82874475 0.085490261 + 87000 0.83480682 0.010542579 0.8453494 0.086268527 + 88000 0.67322538 0.011170734 0.68439611 0.08751623 + 89000 0.62637389 0.012033316 0.6384072 0.088548094 + 90000 0.92828557 0.011750388 0.94003596 0.089199823 + 91000 0.96072564 0.010324509 0.97105015 0.090204803 + 92000 0.72105071 0.011484152 0.73253486 0.09140819 + 93000 0.65762527 0.012558219 0.67018349 0.092453474 + 94000 0.73991591 0.01261909 0.752535 0.093373477 + 95000 0.91791653 0.011980455 0.92989699 0.094182136 + 96000 0.76562561 0.011807085 0.7774327 0.095323684 + 97000 0.57292104 0.013610205 0.58653124 0.096505977 + 98000 0.68141076 0.013863204 0.69527396 0.097380069 + 99000 0.82390969 0.013002341 0.83691203 0.098235926 + 100000 0.77639728 0.012989342 0.78938662 0.099274147 +Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms + +Performance: 2221655.884 tau/day, 25713.610 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.056 | 3.056 | 3.056 | 0.0 | 78.58 +Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13 +Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35 +Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03 +Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98 +Other | | 0.03616 | | | 0.93 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 57 ave 57 max 57 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 57 +Ave neighs/atom = 1.78125 +Neighbor list builds = 1445 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/body/log.9Jul18.body.squares.g++.4 b/examples/body/log.9Jul18.body.squares.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..56d7734b7ba2a1919c1581799bb2eb83660aa4c9 --- /dev/null +++ b/examples/body/log.9Jul18.body.squares.g++.4 @@ -0,0 +1,221 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000324011 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 + 2000 0.42284177 0.01346585 0.43630762 0.0029377883 + 3000 0.58154405 0.011321689 0.59286574 0.003667871 + 4000 0.73518304 0.034603175 0.76978621 0.0018689207 + 5000 0.84367476 0.025292163 0.86896692 0.0089161373 + 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 + 7000 0.56206452 0.10453031 0.66659483 0.010255161 + 8000 0.64538994 0.088817673 0.73420761 0.0037633655 + 9000 0.90540819 0.063696004 0.96910419 0.0077673359 + 10000 0.68632042 0.093265016 0.77958544 0.0057864837 + 11000 0.59118074 0.025654748 0.61683549 0.012518759 + 12000 0.67522767 0.038176401 0.71340407 0.01741153 + 13000 0.7644843 0.10429844 0.86878274 0.013161339 + 14000 0.56152694 0.067836656 0.6293636 0.016852113 + 15000 0.41895505 0.019513353 0.43846841 0.015225696 + 16000 0.55799443 0.15645637 0.7144508 0.011703646 + 17000 0.59385248 0.03451986 0.62837234 0.025482966 + 18000 0.75902169 0.031103586 0.79012527 0.018263354 + 19000 0.64266826 0.12535314 0.76802141 0.014884119 + 20000 0.57836261 0.16581188 0.74417449 0.024667165 + 21000 0.78281936 0.11877527 0.90159464 -0.0090089213 + 22000 0.5312006 0.13300874 0.66420934 0.025797278 + 23000 0.56458861 0.084369128 0.64895774 0.024630917 + 24000 0.65126875 0.06122992 0.71249867 0.034377198 + 25000 0.55173441 0.15694886 0.70868327 0.021634086 + 26000 0.59121615 0.17071182 0.76192797 0.024758366 + 27000 0.6394843 0.17442949 0.81391378 0.034919937 + 28000 0.31144221 0.41243036 0.72387256 0.074115225 + 29000 0.13516917 0.3075419 0.44271107 0.023861298 + 30000 0.14094934 0.24407203 0.38502137 0.037030438 + 31000 0.26313749 0.087395422 0.35053291 0.042347005 + 32000 0.51602457 0.063012079 0.57903664 0.018550299 + 33000 0.55628829 0.200213 0.75650129 0.026507686 + 34000 0.97399408 0.082504517 1.0564986 0.037889878 + 35000 0.64710533 0.17662002 0.82372535 0.058295508 + 36000 0.45769083 0.08241194 0.54010277 0.014957415 + 37000 0.72850105 0.053874061 0.78237512 0.037194593 + 38000 0.44177995 0.28939498 0.73117493 0.045194029 + 39000 0.46828451 0.077630686 0.54591519 0.089849009 + 40000 0.46786451 0.092828423 0.56069294 0.028042052 + 41000 0.71861856 0.097085715 0.81570427 0.036473296 + 42000 0.74121021 0.10553127 0.84674148 0.054058843 + 43000 0.62945489 0.12770673 0.75716161 0.047267994 + 44000 0.49900638 0.085150056 0.58415644 0.054798793 + 45000 0.70199572 0.063415877 0.7654116 0.038363546 + 46000 0.49513142 0.10649384 0.60162526 0.059392561 + 47000 0.3858898 0.079458749 0.46534855 0.051825764 + 48000 0.62585854 0.028585902 0.65444444 0.054074424 + 49000 0.65934482 0.51865062 1.1779954 -0.035272836 + 50000 0.5420438 0.082056756 0.62410056 0.031187494 + 51000 0.36685223 0.14224019 0.50909241 0.073790397 + 52000 0.19044627 0.15368389 0.34413016 0.059034266 + 53000 0.26847678 0.075693324 0.3441701 0.032276915 + 54000 0.3593711 0.19034549 0.54971659 0.070827883 + 55000 0.21659198 0.1929074 0.40949939 0.035916364 + 56000 0.28242715 0.12313241 0.40555956 0.062083926 + 57000 0.34067475 0.14711992 0.48779467 0.059321458 + 58000 0.4842796 0.16143425 0.64571385 0.059048247 + 59000 0.84438871 0.076546849 0.92093556 0.048046901 + 60000 0.92794849 0.054331626 0.98228012 0.058392272 + 61000 0.6916736 0.076168342 0.76784194 0.058654987 + 62000 0.63317965 0.094506389 0.72768604 0.061044719 + 63000 0.63317266 0.038785593 0.67195825 0.097236147 + 64000 0.81696668 0.121811 0.93877769 0.064935373 + 65000 0.82644758 0.25188344 1.078331 0.093352359 + 66000 0.64975019 0.17930857 0.82905876 0.058805254 + 67000 0.63487678 0.16877059 0.80364737 0.070254696 + 68000 0.79140717 0.11631004 0.9077172 0.064646394 + 69000 0.85687272 0.057835331 0.91470805 0.071057291 + 70000 0.67785976 0.040686768 0.71854653 0.074687222 + 71000 0.60594577 0.032193155 0.63813893 0.069349268 + 72000 0.77586745 0.024068533 0.79993598 0.083394193 + 73000 0.88877625 0.025746326 0.91452258 0.081511105 + 74000 0.73507888 0.036574786 0.77165367 0.075360233 + 75000 0.68787782 0.042098622 0.72997644 0.068651098 + 76000 0.72515745 0.04360868 0.76876613 0.069594624 + 77000 0.77580944 0.041826702 0.81763614 0.071937144 + 78000 0.76640394 0.039285046 0.80568899 0.074274921 + 79000 0.62504309 0.039593585 0.66463667 0.076443295 + 80000 0.60001642 0.043468215 0.64348464 0.094547719 + 81000 0.82175037 0.045608873 0.86735924 0.080186295 + 82000 0.85783276 0.042692576 0.90052534 0.081576548 + 83000 0.71367707 0.042172193 0.75584926 0.08256625 + 84000 0.68532406 0.044724759 0.73004882 0.083672013 + 85000 0.72576789 0.046982462 0.77275035 0.084789331 + 86000 0.75597701 0.04765086 0.80362787 0.085758056 + 87000 0.74190598 0.047629096 0.78953507 0.086679976 + 88000 0.60967704 0.049906172 0.65958321 0.085526191 + 89000 0.54490288 0.054768238 0.59967112 0.090604027 + 90000 0.75398341 0.057153453 0.81113686 0.091900858 + 91000 0.84577472 0.052753512 0.89852823 0.091913909 + 92000 0.7176235 0.050677427 0.76830093 0.092032507 + 93000 0.61699446 0.054097013 0.67109147 0.092071275 + 94000 0.76330752 0.057398618 0.82070614 0.092435043 + 95000 0.98754458 0.053801311 1.0413459 0.093526707 + 96000 0.7405897 0.052135628 0.79272533 0.095011929 + 97000 0.65587599 0.057011962 0.71288795 0.096692123 + 98000 0.72345634 0.060700171 0.78415651 0.097510345 + 99000 0.88283624 0.061795247 0.94463149 0.09799633 + 100000 0.86303812 0.058912988 0.92195111 0.09892993 +Loop time of 2.80074 on 4 procs for 100000 steps with 32 atoms + +Performance: 3084895.573 tau/day, 35704.810 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.81169 | 0.89466 | 0.97669 | 8.4 | 31.94 +Neigh | 0.0017524 | 0.0018129 | 0.0018773 | 0.1 | 0.06 +Comm | 0.91307 | 0.99193 | 1.0691 | 7.3 | 35.42 +Output | 0.00076914 | 0.00093722 | 0.0013936 | 0.0 | 0.03 +Modify | 0.75335 | 0.75779 | 0.76346 | 0.4 | 27.06 +Other | | 0.1536 | | | 5.48 + +Nlocal: 8 ave 10 max 4 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 17.25 ave 19 max 15 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 13.5 ave 21 max 5 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 54 +Ave neighs/atom = 1.6875 +Neighbor list builds = 1443 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.1 b/examples/body/log.9Jul18.body.wall2d.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..f22c3663802a487158fffc74c13931f9d83a9416 --- /dev/null +++ b/examples/body/log.9Jul18.body.wall2d.g++.1 @@ -0,0 +1,223 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.00029707 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.49241101 0.0031318767 0.49554289 0.017768281 + 2000 0.56118632 0.0026068888 0.56379321 0.003410416 + 3000 0.75565115 0.025578366 0.78122951 0.0071862988 + 4000 0.72298647 0.093150646 0.81613712 0.003190158 + 5000 0.51684166 0.049164868 0.56600653 0.0096960168 + 6000 0.56627905 0.048132853 0.6144119 0.020733586 + 7000 0.58122129 0.018223718 0.59944501 0.0038160759 + 8000 0.64297977 0.025934821 0.66891459 0.0041091784 + 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 + 10000 0.35738377 0.078487805 0.43587158 3.9079782e-05 + 11000 0.41529308 0.13619284 0.55148592 -0.0067482285 + 12000 0.43274718 0.071315497 0.50406268 0.007006378 + 13000 0.4748331 0.069904647 0.54473775 0.0010384372 + 14000 0.6287791 0.12721033 0.75598943 0.0047792448 + 15000 0.4692413 0.12344005 0.59268136 0.018033616 + 16000 0.43157074 0.14306789 0.57463862 0.042356676 + 17000 0.53085999 0.22126296 0.75212294 0.027509646 + 18000 0.52688968 0.13225282 0.6591425 0.0021558013 + 19000 0.55032328 0.12513047 0.67545375 0.025036251 + 20000 0.48465097 0.1431055 0.62775647 0.017193781 + 21000 0.53166734 0.21928574 0.75095307 0.011564317 + 22000 0.62177353 0.09296159 0.71473512 0.017660922 + 23000 0.6972939 0.12434123 0.82163514 0.024432327 + 24000 0.42767372 0.22152311 0.64919684 -0.013712449 + 25000 0.4816037 0.19272865 0.67433236 0.052386055 + 26000 0.72642579 0.19697046 0.92339625 0.020407694 + 27000 0.39649144 0.15058326 0.5470747 0.023705766 + 28000 0.44896324 0.18500106 0.6339643 -0.0089410286 + 29000 0.5565759 0.11085772 0.66743362 0.048437166 + 30000 0.58173584 0.21773281 0.79946865 0.0057357773 + 31000 0.49199415 0.23601982 0.72801397 0.046744152 + 32000 0.55665496 0.20542161 0.76207658 -0.0038756805 + 33000 0.62730739 0.24460524 0.87191263 0.045330682 + 34000 0.58107044 0.16395278 0.74502322 -0.0049496051 + 35000 0.56838849 0.21842922 0.78681771 0.0062086036 + 36000 0.45910273 0.28464172 0.74374445 -0.011700747 + 37000 0.37092037 0.27646862 0.647389 0.022305679 + 38000 0.7278047 0.30674438 1.0345491 0.07698342 + 39000 0.5132923 0.27395066 0.78724295 0.026898634 + 40000 0.62348649 0.24424644 0.86773293 0.039403899 + 41000 0.3658401 0.15512326 0.52096337 0.022559003 + 42000 0.4912253 0.35712978 0.84835508 -0.010336341 + 43000 0.70225957 0.36314638 1.0654059 0.004148866 + 44000 0.56958157 0.25488927 0.82447084 0.067537066 + 45000 0.45854352 0.30149439 0.76003791 -0.017002401 + 46000 0.62787247 0.34567995 0.97355242 0.11894801 + 47000 0.61348914 0.29378625 0.90727539 0.067873976 + 48000 0.71301829 0.34135284 1.0543711 0.021077736 + 49000 0.53520804 0.30593196 0.84113999 0.0059257647 + 50000 0.44966403 0.35370793 0.80337195 0.0020395669 + 51000 0.5236113 0.32296924 0.84658054 -0.051011506 + 52000 0.53905573 0.351771 0.89082672 0.013720106 + 53000 0.55978158 0.41293947 0.97272106 0.068558589 + 54000 0.52170459 0.2718066 0.7935112 0.0093138985 + 55000 0.61078876 0.43353897 1.0443277 0.045377392 + 56000 0.51300655 0.33182278 0.84482933 -0.018418487 + 57000 0.54882822 0.38380093 0.93262915 0.10249946 + 58000 0.72106212 0.45361279 1.1746749 0.030313481 + 59000 0.55871447 0.63823029 1.1969448 0.019079703 + 60000 0.49395192 0.58283102 1.0767829 0.0179349 + 61000 0.45991079 0.62540573 1.0853165 0.074398804 + 62000 0.4655788 0.60862262 1.0742014 0.11472976 + 63000 0.55634524 0.63069255 1.1870378 -0.0025676135 + 64000 0.57688903 0.45435264 1.0312417 0.0083813852 + 65000 0.57168922 0.42217005 0.99385927 0.044931269 + 66000 0.6206044 0.46727538 1.0878798 0.019686229 + 67000 0.61037155 0.41840109 1.0287726 0.0195109 + 68000 0.63848598 0.41305347 1.0515395 0.072940144 + 69000 0.49244916 0.3834095 0.87585866 0.07963677 + 70000 0.41847062 0.51907975 0.93755037 0.18447904 + 71000 0.45198986 0.52973709 0.98172695 0.078419371 + 72000 0.47064262 0.37808165 0.84872427 -0.00046308054 + 73000 0.6690143 0.37549359 1.0445079 0.061208432 + 74000 0.60444955 0.33779636 0.94224592 -0.068840321 + 75000 0.61762382 0.3916421 1.0092659 0.16253292 + 76000 0.63657961 0.50277989 1.1393595 0.013857508 + 77000 0.52524028 0.43597896 0.96121924 -0.03296482 + 78000 0.43803533 0.33172284 0.76975817 0.078763029 + 79000 0.67156089 0.55272177 1.2242827 0.080822223 + 80000 0.68678238 0.46061627 1.1473987 0.0027036992 + 81000 0.64956678 0.44959229 1.0991591 0.11201483 + 82000 0.51060477 0.43508342 0.9456882 0.028000608 + 83000 0.59550548 0.69026083 1.2857663 -0.0015809004 + 84000 0.64222145 0.38768816 1.0299096 0.014153173 + 85000 0.7661229 0.43445261 1.2005755 0.048034534 + 86000 0.60025257 0.53027929 1.1305319 0.0056865157 + 87000 0.46220939 0.47470035 0.93690974 0.075311946 + 88000 0.54123847 0.62899839 1.1702369 0.13260162 + 89000 0.61212272 0.6114241 1.2235468 0.033284822 + 90000 0.63924773 0.6916249 1.3308726 0.045088296 + 91000 0.49316865 0.51037033 1.003539 0.023203598 + 92000 0.57572123 0.43496319 1.0106844 0.297092 + 93000 0.65187559 0.56815972 1.2200353 0.1538215 + 94000 0.64107331 0.58948521 1.2305585 0.031117778 + 95000 0.64584158 0.6364688 1.2823104 0.096154676 + 96000 0.60509093 0.601487 1.2065779 0.03457172 + 97000 0.68837218 0.77974186 1.468114 0.17801164 + 98000 0.62725266 0.64137144 1.2686241 0.17449001 + 99000 0.46861221 0.67000291 1.1386151 0.2429588 + 100000 0.5879119 0.7140612 1.3019731 0.064634257 +Loop time of 2.50594 on 1 procs for 100000 steps with 32 atoms + +Performance: 3447804.126 tau/day, 39905.140 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5639 | 1.5639 | 1.5639 | 0.0 | 62.41 +Neigh | 0.0086911 | 0.0086911 | 0.0086911 | 0.0 | 0.35 +Comm | 0.058926 | 0.058926 | 0.058926 | 0.0 | 2.35 +Output | 0.0012379 | 0.0012379 | 0.0012379 | 0.0 | 0.05 +Modify | 0.83537 | 0.83537 | 0.83537 | 0.0 | 33.34 +Other | | 0.03781 | | | 1.51 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 20 ave 20 max 20 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 57 ave 57 max 57 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 57 +Ave neighs/atom = 1.78125 +Neighbor list builds = 2705 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.4 b/examples/body/log.9Jul18.body.wall2d.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..7239fd4dcd4fc6a55886d0bfd11a401ab3e97f23 --- /dev/null +++ b/examples/body/log.9Jul18.body.wall2d.g++.4 @@ -0,0 +1,223 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000386 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.49241101 0.0031318767 0.49554289 0.017768281 + 2000 0.56118632 0.0026068888 0.56379321 0.003410416 + 3000 0.75565115 0.025578366 0.78122951 0.0071862988 + 4000 0.72298647 0.093150646 0.81613712 0.003190158 + 5000 0.51684166 0.049164868 0.56600653 0.0096960168 + 6000 0.56627905 0.048132853 0.6144119 0.020733586 + 7000 0.58122129 0.018223718 0.59944501 0.0038160759 + 8000 0.64297977 0.025934821 0.66891459 0.0041091784 + 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 + 10000 0.35738377 0.078487805 0.43587158 3.9079865e-05 + 11000 0.41529307 0.13619284 0.55148591 -0.0067482285 + 12000 0.43274718 0.071315527 0.50406271 0.007006369 + 13000 0.4748324 0.069905666 0.54473807 0.0010385254 + 14000 0.62603727 0.098905625 0.7249429 0.0048876764 + 15000 0.44512086 0.10415235 0.54927321 0.01902062 + 16000 0.47460177 0.18053316 0.65513493 0.045013976 + 17000 0.52742676 0.10110706 0.62853382 0.013615471 + 18000 0.46111734 0.096118795 0.55723613 0.0073676834 + 19000 0.59668439 0.13652292 0.73320731 0.029403553 + 20000 0.46840192 0.11611719 0.58451911 -0.00034412499 + 21000 0.53550533 0.096457461 0.6319628 0.0019785732 + 22000 0.46599715 0.13206373 0.59806087 0.031970672 + 23000 0.49280776 0.20404726 0.69685501 0.03657433 + 24000 0.60901688 0.18255214 0.79156902 0.044955017 + 25000 0.47345185 0.13671357 0.61016542 0.020313539 + 26000 0.47653832 0.12448225 0.60102057 0.01878099 + 27000 0.50008212 0.24740634 0.74748845 0.021862639 + 28000 0.41627204 0.2519463 0.66821834 0.054683701 + 29000 0.55608273 0.23100212 0.78708485 -0.0043318497 + 30000 0.53884537 0.3001584 0.83900377 -0.012838186 + 31000 0.53036238 0.2300328 0.76039518 -0.0061688449 + 32000 0.42666792 0.20536256 0.63203048 0.045305282 + 33000 0.62908185 0.1652033 0.79428515 0.0072777588 + 34000 0.47028154 0.388736 0.85901754 0.04332288 + 35000 0.54602322 0.2775624 0.82358562 0.02898206 + 36000 0.59860544 0.21824655 0.81685199 0.0025936194 + 37000 0.62467827 0.11983499 0.74451326 0.050052743 + 38000 0.72594229 0.36584781 1.0917901 0.04280621 + 39000 0.51129656 0.23859043 0.74988699 0.050817447 + 40000 0.53263836 0.24212889 0.77476725 0.036245922 + 41000 0.50288088 0.36668283 0.86956371 0.018381415 + 42000 0.46653688 0.21974887 0.68628574 0.012661062 + 43000 0.61738785 0.32131037 0.93869821 0.012709433 + 44000 0.56603903 0.26515554 0.83119457 0.03315102 + 45000 0.56231638 0.32111693 0.88343331 0.06079756 + 46000 0.7096208 0.2570131 0.96663391 0.048770468 + 47000 0.588755 0.1880748 0.7768298 0.035962604 + 48000 0.56296339 0.25783519 0.82079858 0.053019928 + 49000 0.419885 0.42328618 0.84317118 0.038105269 + 50000 0.63073351 0.41426285 1.0449964 0.0015271048 + 51000 0.59357935 0.184222 0.77780136 0.015996218 + 52000 0.60608471 0.36247533 0.96856003 0.10984665 + 53000 0.5227842 0.27686739 0.79965159 0.02761699 + 54000 0.39435923 0.34197355 0.73633278 0.061183263 + 55000 0.46748455 0.34230903 0.80979358 0.077441382 + 56000 0.59819827 0.29212061 0.89031889 0.043772353 + 57000 0.61682559 0.32788566 0.94471124 0.03992069 + 58000 0.52702478 0.24891506 0.77593984 0.058480883 + 59000 0.66925719 0.4109031 1.0801603 0.072434423 + 60000 0.66807714 0.39233068 1.0604078 0.082370324 + 61000 0.5724275 0.43308567 1.0055132 0.0072945426 + 62000 0.49433556 0.38453743 0.87887299 0.0036097443 + 63000 0.57575143 0.54067119 1.1164226 0.073339638 + 64000 0.68045383 0.38246533 1.0629192 0.025314593 + 65000 0.59843527 0.42928622 1.0277215 -0.030096445 + 66000 0.60274797 0.50186417 1.1046121 0.069797184 + 67000 0.47450407 0.52689807 1.0014021 0.008758012 + 68000 0.5514135 0.64113187 1.1925454 0.093863314 + 69000 0.52008074 0.45749565 0.97757639 -0.066061381 + 70000 0.69042662 0.50416006 1.1945867 0.014128617 + 71000 0.63925854 0.35153425 0.9907928 -0.01134957 + 72000 0.52088835 0.47626986 0.99715821 0.10198133 + 73000 0.46333852 0.5515537 1.0148922 0.00060582772 + 74000 0.53481418 0.50409531 1.0389095 0.00919451 + 75000 0.67182749 0.50380162 1.1756291 0.043301985 + 76000 0.70492289 0.4112122 1.1161351 0.14880484 + 77000 0.59781817 0.50197661 1.0997948 -0.057111711 + 78000 0.51677429 0.4348232 0.95159749 -0.0074619446 + 79000 0.50663297 0.55000424 1.0566372 0.0052071216 + 80000 0.59392006 0.48394003 1.0778601 -0.018990234 + 81000 0.66323593 0.40358336 1.0668193 -0.02961345 + 82000 0.61596979 0.49177944 1.1077492 0.1314853 + 83000 0.63917554 0.61656584 1.2557414 0.11908351 + 84000 0.49305291 0.46161646 0.95466937 0.033558488 + 85000 0.52552044 0.54250555 1.068026 0.13015174 + 86000 0.55140914 0.38924725 0.94065638 0.047412499 + 87000 0.60952504 0.52603688 1.1355619 0.039230066 + 88000 0.50119735 0.547539 1.0487364 0.019659933 + 89000 0.40331401 0.50331134 0.90662535 -0.056906034 + 90000 0.47067839 0.51306911 0.9837475 0.11918166 + 91000 0.45564995 0.38693455 0.8425845 0.12040045 + 92000 0.64163032 0.34232532 0.98395564 0.0057051641 + 93000 0.70375593 0.53646186 1.2402178 0.16044241 + 94000 0.53378112 0.51971406 1.0534952 0.11389004 + 95000 0.47055342 0.50396004 0.97451346 0.079424215 + 96000 0.59543473 0.40204536 0.99748009 0.096813093 + 97000 0.64821917 0.50051728 1.1487365 0.054071312 + 98000 0.55723937 0.4945909 1.0518303 0.047316424 + 99000 0.56044424 0.50773312 1.0681774 0.0149959 + 100000 0.68254229 0.32704484 1.0095871 0.0069212661 +Loop time of 2.20043 on 4 procs for 100000 steps with 32 atoms + +Performance: 3926501.701 tau/day, 45445.622 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41008 | 0.41366 | 0.41719 | 0.4 | 18.80 +Neigh | 0.0027823 | 0.0030481 | 0.0034747 | 0.5 | 0.14 +Comm | 0.74581 | 0.7675 | 0.78684 | 2.0 | 34.88 +Output | 0.00082111 | 0.0010884 | 0.0016899 | 1.1 | 0.05 +Modify | 0.83828 | 0.85329 | 0.86656 | 1.4 | 38.78 +Other | | 0.1618 | | | 7.36 + +Nlocal: 8 ave 9 max 7 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 12.75 ave 14 max 12 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 11 ave 19 max 5 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 44 +Ave neighs/atom = 1.375 +Neighbor list builds = 2663 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/molecule.cube b/examples/body/molecule.cube new file mode 100644 index 0000000000000000000000000000000000000000..2a8a7bca5023155889095b303b22d3aef201d2cc --- /dev/null +++ b/examples/body/molecule.cube @@ -0,0 +1,52 @@ +# 3d polygon body: cubes, moment of inertia I = m edge^2/ 6 + +1 atoms +3 79 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +8 12 6 + +Body Doubles + +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 + diff --git a/examples/body/molecule.point3d b/examples/body/molecule.point3d new file mode 100644 index 0000000000000000000000000000000000000000..d22bfbe6fa9d58e0df10b2cba22dd1b402185e9a --- /dev/null +++ b/examples/body/molecule.point3d @@ -0,0 +1,26 @@ +# 2d polygon body: disks Izz = 1/2 m radius^2 + +1 atoms +3 10 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +1 0 0 + +Body Doubles + +1 1 1.125 0 0 0 +0 0 0 +3.0 diff --git a/examples/body/molecule.rod3d b/examples/body/molecule.rod3d new file mode 100644 index 0000000000000000000000000000000000000000..1c8a0a8cd3eecfa325d2a1c99a38edca26d0a789 --- /dev/null +++ b/examples/body/molecule.rod3d @@ -0,0 +1,27 @@ +# 2d polygon body: rods Izz = 1/12 m length^2 + +1 atoms +3 13 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +2 1 0 + +Body Doubles + +1 1 1.333 0 0 0 +-2 0 0 +2 0 0 +0.5 diff --git a/examples/body/molecule.tetra b/examples/body/molecule.tetra new file mode 100644 index 0000000000000000000000000000000000000000..d67ec906c64868521eaae59f8284697e18ff7d72 --- /dev/null +++ b/examples/body/molecule.tetra @@ -0,0 +1,39 @@ +# 3d polygon body: regular tetrahedra, moment of inertia I = m edge^2/ 20 + +1 atoms +3 47 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +4 6 4 + +Body Doubles + +0.4 0.4 0.4 0 0 0 +1 1 1 +1 -1 -1 +-1 1 -1 +-1 -1 1 +0 1 +0 2 +0 3 +1 2 +2 3 +3 1 +0 1 2 -1 +0 1 3 -1 +0 2 3 -1 +1 2 3 -1 +0.5 diff --git a/examples/gcmc/in.gcmc.co2 b/examples/gcmc/in.gcmc.co2 index bb6916fc4847df10707f2712c10955d921878601..b5e11d212dafb99f71acfc0a6870163dc9705723 100644 --- a/examples/gcmc/in.gcmc.co2 +++ b/examples/gcmc/in.gcmc.co2 @@ -59,7 +59,9 @@ timestep 1.0 # rigid constraints with thermostat fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix_modify myrigidnvt dynamic/dof no + +# dynamically update fix rigid/nvt/small temperature ndof +fix_modify myrigidnvt dynamic/dof yes # gcmc @@ -82,7 +84,10 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) + +# dynamically update default temperature ndof compute_modify thermo_temp dynamic/dof yes + thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO thermo 1000 diff --git a/examples/gcmc/in.gcmc.h2o b/examples/gcmc/in.gcmc.h2o index 2c03b1ab78cc9dad8626ef76241e2dae1ab37955..f689711c2147a621e3937948df7d7bb494135587 100644 --- a/examples/gcmc/in.gcmc.h2o +++ b/examples/gcmc/in.gcmc.h2o @@ -30,8 +30,6 @@ create_box 2 box & extra/angle/per/atom 1 & extra/special/per/atom 2 -# we can load multiple molecule templates, but don't have to use them all -molecule co2mol CO2.txt molecule h2omol H2O.txt create_atoms 0 box mol h2omol 464563 units box @@ -58,18 +56,24 @@ timestep 1.0 minimize 0.0 0.0 100 1000 reset_timestep 0 + # rigid constraints with thermostat -fix mynvt all nvt temp ${temp} ${temp} 100 -fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol -# gcmc +fix mynvt h2o nvt temp ${temp} ${temp} 100 +fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol +# important to make temperature dofs dynamic +compute_modify thermo_temp dynamic/dof yes +compute_modify mynvt_temp dynamic/dof yes run 1000 +reset_timestep 0 + +# gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & +fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol & h2omol tfac_insert ${tfac} group h2o shake wshake # atom counts @@ -87,7 +91,6 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) -compute_modify thermo_temp dynamic/dof yes thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH thermo 1000 diff --git a/examples/gcmc/log.23Oct17.gcmc.co2.g++.4 b/examples/gcmc/log.23Oct17.gcmc.co2.g++.4 deleted file mode 100644 index b344c7b0685eb0e19deb26e363e9cc43cd292f24..0000000000000000000000000000000000000000 --- a/examples/gcmc/log.23Oct17.gcmc.co2.g++.4 +++ /dev/null @@ -1,192 +0,0 @@ -LAMMPS (23 Oct 2017) - using 1 OpenMP thread(s) per MPI task -# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics -# Rigid CO2 TraPPE model -# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of -# mixtures containing alkanes, carbon dioxide and -# nitrogen AIChE J., 47,1676-1682 (2001)]. - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -create_atoms 0 box mol co2mol 464563 units box -Created 24 atoms - Time spent = 0.00261331 secs - -# rigid CO2 TraPPE model - -pair_coeff 1 1 0.053649 2.8 -pair_coeff 2 2 0.156973 3.05 -bond_coeff 1 0 1.16 -angle_coeff 1 0 180 - -# masses - -mass 1 12.0107 -mass 2 15.9994 - -# MD settings - -group co2 type 1 2 -24 atoms in group co2 -neighbor 2.0 bin -neigh_modify every 1 delay 10 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -# rigid constraints with thermostat - -fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol -8 rigid bodies with 24 atoms - 1.16 = max distance from body owner to body atom -fix_modify myrigidnvt dynamic/dof no - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt - -# atom counts - -variable carbon atom "type==1" -variable oxygen atom "type==2" -group carbon dynamic all var carbon -dynamic group carbon defined -group oxygen dynamic all var oxygen -dynamic group oxygen defined -variable nC equal count(carbon) -variable nO equal count(oxygen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) -compute_modify thermo_temp dynamic/dof yes -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO -thermo 1000 - -# run - -run 20000 -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.164636 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 2 2 2 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO - 0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0 8 16 -WARNING: Using kspace solver on system with no charge (../kspace.cpp:289) - 1000 335.66829 -3.7743052 -4.6268612 7.3374649 0.36539744 15 0.20601899 0.20787963 0 0 5 10 - 2000 459.73529 238.91592 -0.42937831 5.4815343 0.21923846 9 0.30392058 0.30105616 0 0 3 6 - 3000 255.47773 -479.67802 -36.850434 15.738299 0.95003334 39 0.22220744 0.2197582 0 0 13 26 - 4000 182.70803 -1059.2262 -43.044833 12.163134 1.0231128 42 0.16781689 0.16716177 0 0 14 28 - 5000 234.00907 -1821.0444 -46.04795 15.578317 1.0231128 42 0.13498091 0.13704201 0 0 14 28 - 6000 163.42759 -774.67294 -49.686261 11.691518 1.0961923 45 0.11401677 0.11296973 0 0 15 30 - 7000 171.64616 -355.23516 -49.323434 12.27947 1.0961923 45 0.098302308 0.098552065 0 0 15 30 - 8000 251.29791 -905.47863 -37.841209 15.480807 0.95003334 39 0.086856972 0.08638658 0 0 13 26 - 9000 143.69498 -849.95393 -49.073188 10.279858 1.0961923 45 0.078261061 0.077955243 0 0 15 30 - 10000 239.35727 -1158.1879 -43.562047 15.934355 1.0231128 42 0.070789792 0.070807529 0 0 14 28 - 11000 169.51213 -1574.7885 -51.125228 12.126803 1.0961923 45 0.065008734 0.06498871 0 0 15 30 - 12000 181.39739 160.11631 -46.850937 12.977068 1.0961923 45 0.059648717 0.059514803 0 0 15 30 - 13000 164.14601 -1107.7629 -50.726722 11.742914 1.0961923 45 0.055207333 0.055097701 0 0 15 30 - 14000 287.26285 418.51463 -41.664766 19.123497 1.0231128 42 0.051346789 0.051222285 0 0 14 28 - 15000 256.94593 -532.36615 -41.651618 17.105257 1.0231128 42 0.047870301 0.047861685 0 0 14 28 - 16000 166.92132 151.15933 -39.957018 11.11219 1.0231128 42 0.045205599 0.045042211 0 0 14 28 - 17000 163.22452 -1299.8119 -42.677558 10.866089 1.0231128 42 0.043122086 0.042993687 0 0 14 28 - 18000 158.01154 475.77329 -48.803162 11.304057 1.0961923 45 0.041016683 0.040647229 0 0 15 30 - 19000 138.49297 -1585.1508 -47.517099 9.9077098 1.0961923 45 0.038929287 0.038436764 0 0 15 30 - 20000 173.84439 -1362.6301 -53.002743 12.436731 1.0961923 45 0.036973919 0.036523816 0 0 15 30 -Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms - -Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1687 | 1.6702 | 2.1864 | 30.8 | 5.15 -Bond | 0.018828 | 0.020035 | 0.020975 | 0.6 | 0.06 -Kspace | 0.57506 | 1.0931 | 1.5898 | 37.7 | 3.37 -Neigh | 0.068863 | 0.069524 | 0.070128 | 0.2 | 0.21 -Comm | 2.0735 | 2.0865 | 2.0979 | 0.7 | 6.43 -Output | 0.0025017 | 0.0025966 | 0.0027781 | 0.2 | 0.01 -Modify | 27.335 | 27.344 | 27.363 | 0.2 | 84.27 -Other | | 0.1621 | | | 0.50 - -Nlocal: 11.25 ave 14 max 8 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Nghost: 2639.75 ave 2656 max 2617 min -Histogram: 1 0 0 0 0 0 2 0 0 1 -Neighs: 4320 ave 5824 max 2201 min -Histogram: 1 0 0 0 0 0 1 1 0 1 - -Total # of neighbors = 17280 -Ave neighs/atom = 384 -Ave special neighs/atom = 2 -Neighbor list builds = 20394 -Dangerous builds = 0 - -Total wall time: 0:00:32 diff --git a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4 b/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4 deleted file mode 100644 index 4eeab969ddc8c578baf028394c39064f2b57aace..0000000000000000000000000000000000000000 --- a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.4 +++ /dev/null @@ -1,293 +0,0 @@ -LAMMPS (23 Oct 2017) - using 1 OpenMP thread(s) per MPI task -# fix gcmc example with fix shake - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid - -# we can load multiple molecule templates, but don't have to use them all -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -molecule h2omol H2O.txt -Read molecule h2omol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types -create_atoms 0 box mol h2omol 464563 units box -Created 24 atoms - Time spent = 0.00174451 secs - -# rigid SPC/E water model - -pair_coeff 1 1 0.15535 3.166 -pair_coeff * 2 0.0000 0.0000 - -bond_coeff 1 1000 1.0 -angle_coeff 1 100 109.47 - -# masses - -mass 1 15.9994 -mass 2 1.0 - -# MD settings - -group h2o type 1 2 -24 atoms in group h2o -neighbor 2.0 bin -neigh_modify every 1 delay 1 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -minimize 0.0 0.0 100 1000 -WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 2 2 2 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 338 -4.9610706 9.2628112e-06 18.211756 730.90791 - 100 338 -15.742442 0.14954269 7.579918 -637.49568 -Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms - -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -4.96106135393 -15.5388622715 -15.592899346 - Force two-norm initial, final = 15.474 18.1478 - Force max component initial, final = 5.80042 7.56514 - Final line search alpha, max atom move = 0.00151131 0.0114333 - Iterations, force evaluations = 100 328 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41 -Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55 -Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84 -Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.005213 | | | 9.21 - -Nlocal: 6 ave 8 max 3 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Nghost: 1722 ave 1725 max 1720 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 1256.75 ave 2101 max 667 min -Histogram: 1 0 1 0 1 0 0 0 0 1 - -Total # of neighbors = 5027 -Ave neighs/atom = 209.458 -Ave special neighs/atom = 2 -Neighbor list builds = 0 -Dangerous builds = 0 -reset_timestep 0 -# rigid constraints with thermostat - -fix mynvt all nvt temp ${temp} ${temp} 100 -fix mynvt all nvt temp 338.0 ${temp} 100 -fix mynvt all nvt temp 338.0 338.0 100 -fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 8 = # of frozen angles -# gcmc - - - -run 1000 -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 518.26667 -15.742442 0 7.4303753 -613.0781 - 1000 369.81793 -54.202686 0 -37.667331 294.98823 -Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms - -Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72 -Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12 -Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15 -Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43 -Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62 -Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02 -Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77 -Other | | 0.004909 | | | 3.17 - -Nlocal: 6 ave 8 max 3 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 1331.5 ave 1369 max 1290 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 1259.75 ave 1642 max 428 min -Histogram: 1 0 0 0 0 0 0 1 0 2 - -Total # of neighbors = 5039 -Ave neighs/atom = 209.958 -Ave special neighs/atom = 2 -Neighbor list builds = 27 -Dangerous builds = 0 - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake - -# atom counts - -variable oxygen atom "type==1" -variable hydrogen atom "type==2" -group oxygen dynamic all var oxygen -dynamic group oxygen defined -group hydrogen dynamic all var hydrogen -dynamic group hydrogen defined -variable nO equal count(oxygen) -variable nH equal count(hydrogen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) -compute_modify thermo_temp dynamic/dof yes -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH -thermo 1000 - -# run - -run 20000 -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) -Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes -Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH - 1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16 - 2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58 - 3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66 - 4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66 - 5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66 - 6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66 - 7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66 - 8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66 - 9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68 - 10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68 - 11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68 - 12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68 - 13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68 - 14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68 - 15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68 - 16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68 - 17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68 - 18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68 - 19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70 - 20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70 - 21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70 -Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms - -Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56 -Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04 -Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67 -Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41 -Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87 -Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00 -Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17 -Other | | 0.2281 | | | 0.27 - -Nlocal: 26.25 ave 31 max 22 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 6049.25 ave 6133 max 5962 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Neighs: 23613 ave 35083 max 14025 min -Histogram: 1 0 0 1 1 0 0 0 0 1 - -Total # of neighbors = 94452 -Ave neighs/atom = 899.543 -Ave special neighs/atom = 2 -Neighbor list builds = 20428 -Dangerous builds = 0 - -Total wall time: 0:01:24 diff --git a/examples/gcmc/log.23Oct17.gcmc.co2.g++.1 b/examples/gcmc/log.30Mar18.gcmc.co2.g++.1 similarity index 52% rename from examples/gcmc/log.23Oct17.gcmc.co2.g++.1 rename to examples/gcmc/log.30Mar18.gcmc.co2.g++.1 index e7b7c6afda0f28e4bb4b7c7dd5aaa5b86635d39d..46afe5ea2ae15af56f9fed995edd9462182f235e 100644 --- a/examples/gcmc/log.23Oct17.gcmc.co2.g++.1 +++ b/examples/gcmc/log.30Mar18.gcmc.co2.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (23 Oct 2017) +LAMMPS (30 Mar 2018) using 1 OpenMP thread(s) per MPI task # GCMC for CO2 molecular fluid, rigid/small/nvt dynamics # Rigid CO2 TraPPE model @@ -39,14 +39,14 @@ Created orthogonal box = (0 0 0) to (10 10 10) 1 by 1 by 1 MPI processor grid molecule co2mol CO2.txt Read molecule co2mol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 create_atoms 0 box mol co2mol 464563 units box Created 24 atoms - Time spent = 0.00196958 secs + Time spent = 0.00241756 secs # rigid CO2 TraPPE model @@ -72,29 +72,31 @@ timestep 1.0 # rigid constraints with thermostat -fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol +fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol +fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol +fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol 8 rigid bodies with 24 atoms 1.16 = max distance from body owner to body atom -fix_modify myrigidnvt dynamic/dof no + +# dynamically update fix rigid/nvt/small temperature ndof +fix_modify myrigidnvt dynamic/dof yes # gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt # atom counts variable carbon atom "type==1" variable oxygen atom "type==2" -group carbon dynamic all var carbon +group carbon dynamic co2 var carbon dynamic group carbon defined -group oxygen dynamic all var oxygen +group oxygen dynamic co2 var oxygen dynamic group oxygen defined variable nC equal count(carbon) variable nO equal count(oxygen) @@ -105,7 +107,10 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) + +# dynamically update default temperature ndof compute_modify thermo_temp dynamic/dof yes + thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO thermo 1000 @@ -113,13 +118,13 @@ thermo 1000 run 20000 Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.164636 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445) +WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) @@ -138,55 +143,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16 -WARNING: Using kspace solver on system with no charge (../kspace.cpp:289) - 1000 420.43475 1722.4052 -9.6956123 15.456579 0.5846359 24 0.20879341 0.20713005 0 0 8 16 - 2000 302.29516 -547.83641 -22.017674 14.11699 0.73079488 30 0.1742478 0.1678018 0 0 10 20 - 3000 316.6934 -1080.2672 -8.2218891 10.069364 0.51155641 21 0.13544917 0.13720634 0 0 7 14 - 4000 246.81618 -679.83642 -14.577244 10.29997 0.65771539 27 0.1568939 0.15860229 0 0 9 18 - 5000 260.22849 -896.29914 -16.097593 10.859684 0.65771539 27 0.13138744 0.13547049 0 0 9 18 - 6000 291.70796 -1521.99 -22.303136 13.622574 0.73079488 30 0.12615476 0.12717694 0 0 10 20 - 7000 236.02638 -599.92186 -27.580831 13.367447 0.87695385 36 0.119703 0.12145398 0 0 12 24 - 8000 321.45341 688.10577 -10.09204 11.817696 0.5846359 24 0.10917411 0.11032646 0 0 8 16 - 9000 502.85382 -302.31056 -0.22330142 0.99927447 0.073079488 3 0.1254105 0.12905828 0 0 1 2 - 10000 249.98239 -510.0091 -32.815145 15.399767 0.95003334 39 0.1274504 0.12875623 0 0 13 26 - 11000 247.59424 -1129.0274 -25.320205 12.792544 0.80387436 33 0.11739076 0.11916784 0 0 11 22 - 12000 0 -20.39554 -0.14872889 -0 0 0 0.1254933 0.12920375 0 0 0 0 - 13000 1272.2738 -474.79484 -0.29450485 8.8489483 0.14615898 6 0.13767133 0.14112496 0 0 2 4 - 14000 516.54246 -36.296516 -5.0012009 11.291243 0.36539744 15 0.15632744 0.15955377 0 0 5 10 - 15000 307.09233 1951.9301 -14.820362 12.815375 0.65771539 27 0.15393544 0.15716192 0 0 9 18 - 16000 198.31989 -559.48443 -30.459487 11.231925 0.87695385 36 0.1482565 0.15025652 0 0 12 24 - 17000 246.99311 657.85683 -18.579206 11.53442 0.73079488 30 0.14143958 0.14375423 0 0 10 20 - 18000 467.13468 167.03738 -1.0945268 5.569759 0.21923846 9 0.13847359 0.14098533 0 0 3 6 - 19000 359.54027 -1413.5407 -12.156233 13.217895 0.5846359 24 0.15169146 0.15294205 0 0 8 16 - 20000 227.79597 -1204.5652 -23.24144 10.637925 0.73079488 30 0.14917199 0.15022946 0 0 10 20 -Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms - -Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s -99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + 1000 330.05964 -376.0111 -13.936335 13.773831 0.65771539 27 0.21142067 0.21453147 0 0 9 18 + 2000 293.79769 -321.3209 -19.049256 13.720163 0.73079488 30 0.25170944 0.25426294 0 0 10 20 + 3000 348.9085 259.04079 -0.23347965 2.4267366 0.14615898 6 0.22016906 0.23200597 0 0 2 4 + 4000 360.54577 -329.12072 -16.584234 15.046059 0.65771539 27 0.19173099 0.19785362 0 0 9 18 + 5000 275.58628 -58.283006 -12.520856 11.500585 0.65771539 27 0.16490585 0.17329884 0 0 9 18 + 6000 338.59574 364.93514 -19.866569 17.494353 0.80387436 33 0.17971759 0.18331589 0 0 11 22 + 7000 286.11586 -1252.5069 -19.588667 13.361427 0.73079488 30 0.15729895 0.16220459 0 0 10 20 + 8000 454.86786 -642.89382 -20.818357 21.242037 0.73079488 30 0.15500235 0.15802382 0 0 10 20 + 9000 326.36695 -364.71382 -31.376162 18.48392 0.87695385 36 0.14203985 0.14510714 0 0 12 24 + 10000 348.46961 -387.75245 -21.068466 18.00451 0.80387436 33 0.14000907 0.14343389 0 0 11 22 + 11000 409.74257 -15.843895 -20.648252 21.170323 0.80387436 33 0.14689306 0.15117074 0 0 11 22 + 12000 523.93502 1003.0729 -6.0563102 14.055757 0.43847693 18 0.15337575 0.1580166 0 0 6 12 + 13000 278.14441 -717.1097 -2.3488496 4.6982087 0.29231795 12 0.15952356 0.16422306 0 0 4 8 + 14000 367.89375 1239.0841 -11.203323 13.524997 0.5846359 24 0.17002439 0.17460294 0 0 8 16 + 15000 197.05319 -471.14343 -9.3890758 6.2653668 0.51155641 21 0.17702612 0.18155802 0 0 7 14 + 16000 138.17147 -935.93437 -2.3846783 2.3338898 0.29231795 12 0.17884346 0.18268758 0 0 4 8 + 17000 245.61833 -166.1694 -5.0970057 5.3690384 0.36539744 15 0.18909252 0.19317817 0 0 5 10 + 18000 232.0142 -175.732 -14.320198 9.6822635 0.65771539 27 0.18977089 0.19280537 0 0 9 18 + 19000 362.01189 864.87258 -6.4515321 9.7117982 0.43847693 18 0.19207244 0.19488984 0 0 6 12 + 20000 441.19548 186.19779 -18.147268 20.603546 0.73079488 30 0.19713351 0.199073 0 0 10 20 +Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms + +Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5462 | 2.5462 | 2.5462 | 0.0 | 12.30 -Bond | 0.029783 | 0.029783 | 0.029783 | 0.0 | 0.14 -Kspace | 0.26167 | 0.26167 | 0.26167 | 0.0 | 1.26 -Neigh | 0.10705 | 0.10705 | 0.10705 | 0.0 | 0.52 -Comm | 0.23409 | 0.23409 | 0.23409 | 0.0 | 1.13 -Output | 0.0013416 | 0.0013416 | 0.0013416 | 0.0 | 0.01 -Modify | 17.458 | 17.458 | 17.458 | 0.0 | 84.37 -Other | | 0.05433 | | | 0.26 +Pair | 1.8955 | 1.8955 | 1.8955 | 0.0 | 11.49 +Bond | 0.026564 | 0.026564 | 0.026564 | 0.0 | 0.16 +Kspace | 0.21215 | 0.21215 | 0.21215 | 0.0 | 1.29 +Neigh | 0.088336 | 0.088336 | 0.088336 | 0.0 | 0.54 +Comm | 0.19828 | 0.19828 | 0.19828 | 0.0 | 1.20 +Output | 0.001025 | 0.001025 | 0.001025 | 0.0 | 0.01 +Modify | 14.024 | 14.024 | 14.024 | 0.0 | 85.02 +Other | | 0.0491 | | | 0.30 Nlocal: 30 ave 30 max 30 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2310 ave 2310 max 2310 min +Nghost: 2094 ave 2094 max 2094 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 7736 ave 7736 max 7736 min +Neighs: 7664 ave 7664 max 7664 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 7736 -Ave neighs/atom = 257.867 +Total # of neighbors = 7664 +Ave neighs/atom = 255.467 Ave special neighs/atom = 2 -Neighbor list builds = 20349 +Neighbor list builds = 20076 Dangerous builds = 0 -Total wall time: 0:00:20 +Total wall time: 0:00:16 diff --git a/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 b/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..a824945cbfc79b18c8d023c8d9d766ae3abd439a --- /dev/null +++ b/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 @@ -0,0 +1,131 @@ +LAMMPS (30 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics +# Rigid CO2 TraPPE model +# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of +# mixtures containing alkanes, carbon dioxide and +# nitrogen AIChE J., 47,1676-1682 (2001)]. + +# variables available on command line + +variable mu index -8.1 +variable disp index 0.5 +variable temp index 338.0 +variable lbox index 10.0 +variable spacing index 5.0 + +# global model settings + +units real +atom_style full +boundary p p p +pair_style lj/cut/coul/long 14 +pair_modify mix arithmetic tail yes +kspace_style ewald 0.0001 +bond_style harmonic +angle_style harmonic + +# box, start molecules on simple cubic lattice + +lattice sc ${spacing} +lattice sc 5.0 +Lattice spacing in x,y,z = 5 5 5 +region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 10.0 units box +create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 +Created orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid +molecule co2mol CO2.txt +Read molecule co2mol: + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +create_atoms 0 box mol co2mol 464563 units box +Created 24 atoms + Time spent = 0.00257635 secs + +# rigid CO2 TraPPE model + +pair_coeff 1 1 0.053649 2.8 +pair_coeff 2 2 0.156973 3.05 +bond_coeff 1 0 1.16 +angle_coeff 1 0 180 + +# masses + +mass 1 12.0107 +mass 2 15.9994 + +# MD settings + +group co2 type 1 2 +24 atoms in group co2 +neighbor 2.0 bin +neigh_modify every 1 delay 10 check yes +velocity all create ${temp} 54654 +velocity all create 338.0 54654 +timestep 1.0 + +# rigid constraints with thermostat + +fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol +fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol +fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol +8 rigid bodies with 24 atoms + 1.16 = max distance from body owner to body atom + +# dynamically update fix rigid/nvt/small temperature ndof +fix_modify myrigidnvt dynamic/dof yes + +# gcmc + +variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) +fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt +fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt + +# atom counts + +variable carbon atom "type==1" +variable oxygen atom "type==2" +group carbon dynamic co2 var carbon +dynamic group carbon defined +group oxygen dynamic co2 var oxygen +dynamic group oxygen defined +variable nC equal count(carbon) +variable nO equal count(oxygen) + +# output + +variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) +variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) +variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) +variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) + +# dynamically update default temperature ndof +compute_modify thermo_temp dynamic/dof yes + +thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO +thermo 1000 + +# run + +run 20000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.164636 + estimated absolute RMS force accuracy = 0.0332064 + estimated relative force accuracy = 0.0001 + KSpace vectors: actual max1d max3d = 16 2 62 + kxmax kymax kzmax = 2 2 2 +WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) +0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc +0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc +ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721) +Last command: run 20000 diff --git a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.1 b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 similarity index 54% rename from examples/gcmc/log.23Oct17.gcmc.h2o.g++.1 rename to examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 index bc7c3af4541e58dea45b6d917d2645a2fb64683c..2f11cb116e0df82c40d7fa8797bf3c559df1265e 100644 --- a/examples/gcmc/log.23Oct17.gcmc.h2o.g++.1 +++ b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (23 Oct 2017) +LAMMPS (30 Mar 2018) using 1 OpenMP thread(s) per MPI task # fix gcmc example with fix shake @@ -34,24 +34,16 @@ create_box 2 box bond/types 1 Created orthogonal box = (0 0 0) to (10 10 10) 1 by 1 by 1 MPI processor grid -# we can load multiple molecule templates, but don't have to use them all -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types molecule h2omol H2O.txt Read molecule h2omol: - 3 atoms with 2 types - 2 bonds with 1 types - 1 angles with 1 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 create_atoms 0 box mol h2omol 464563 units box Created 24 atoms - Time spent = 0.00201297 secs + Time spent = 0.00204968 secs # rigid SPC/E water model @@ -79,7 +71,7 @@ timestep 1.0 minimize 0.0 0.0 100 1000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 @@ -101,9 +93,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 338 -4.1890564 9.2628112e-06 18.98377 739.06991 100 338 -30.182886 0.85607237 -6.1539961 -2535.3207 -Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms +Loop time of 0.0512006 on 1 procs for 100 steps with 24 atoms -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations @@ -117,14 +109,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.042597 | 0.042597 | 0.042597 | 0.0 | 83.93 -Bond | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.94 -Kspace | 0.0031135 | 0.0031135 | 0.0031135 | 0.0 | 6.13 +Pair | 0.04303 | 0.04303 | 0.04303 | 0.0 | 84.04 +Bond | 0.00047088 | 0.00047088 | 0.00047088 | 0.0 | 0.92 +Kspace | 0.0029728 | 0.0029728 | 0.0029728 | 0.0 | 5.81 Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90 -Comm | 0.0032997 | 0.0032997 | 0.0032997 | 0.0 | 6.50 -Output | 1.359e-05 | 1.359e-05 | 1.359e-05 | 0.0 | 0.03 +Comm | 0.003406 | 0.003406 | 0.003406 | 0.0 | 6.65 +Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.04 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0007946 | | | 1.57 +Other | | 0.0008392 | | | 1.64 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -139,23 +131,26 @@ Ave special neighs/atom = 2 Neighbor list builds = 2 Dangerous builds = 0 reset_timestep 0 + # rigid constraints with thermostat -fix mynvt all nvt temp ${temp} ${temp} 100 -fix mynvt all nvt temp 338.0 ${temp} 100 -fix mynvt all nvt temp 338.0 338.0 100 -fix wshake all shake 0.0001 50 0 b 1 a 1 mol h2omol +fix mynvt h2o nvt temp ${temp} ${temp} 100 +fix mynvt h2o nvt temp 338.0 ${temp} 100 +fix mynvt h2o nvt temp 338.0 338.0 100 +fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 8 = # of frozen angles -# gcmc +# important to make temperature dofs dynamic +compute_modify thermo_temp dynamic/dof yes +compute_modify mynvt_temp dynamic/dof yes run 1000 Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 @@ -164,23 +159,23 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 518.26667 -30.182886 0 -7.0100684 993.1985 - 1000 326.9865 -62.258445 0 -47.638175 -5.3440813 -Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms + 1000 326.9865 -62.258443 0 -47.638173 -5.3439918 +Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms -Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.10788 | 0.10788 | 0.10788 | 0.0 | 76.27 -Bond | 0.00018954 | 0.00018954 | 0.00018954 | 0.0 | 0.13 -Kspace | 0.011867 | 0.011867 | 0.011867 | 0.0 | 8.39 -Neigh | 0.0045254 | 0.0045254 | 0.0045254 | 0.0 | 3.20 -Comm | 0.011277 | 0.011277 | 0.011277 | 0.0 | 7.97 -Output | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 | 0.0 | 0.01 -Modify | 0.00383 | 0.00383 | 0.00383 | 0.0 | 2.71 -Other | | 0.001868 | | | 1.32 +Pair | 0.10588 | 0.10588 | 0.10588 | 0.0 | 75.94 +Bond | 0.00015759 | 0.00015759 | 0.00015759 | 0.0 | 0.11 +Kspace | 0.011144 | 0.011144 | 0.011144 | 0.0 | 7.99 +Neigh | 0.00459 | 0.00459 | 0.00459 | 0.0 | 3.29 +Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 8.17 +Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.01 +Modify | 0.0043328 | 0.0043328 | 0.0043328 | 0.0 | 3.11 +Other | | 0.001914 | | | 1.37 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -194,13 +189,16 @@ Ave neighs/atom = 213 Ave special neighs/atom = 2 Neighbor list builds = 25 Dangerous builds = 0 +reset_timestep 0 + +# gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake # atom counts @@ -219,7 +217,6 @@ variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) -compute_modify thermo_temp dynamic/dof yes thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH thermo 1000 @@ -227,67 +224,67 @@ thermo 1000 run 20000 Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445) +WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH - 1000 326.9865 -4.3509713 -62.258445 14.62027 0.23910963 24 0 0 0 0 8 16 - 2000 116.99793 -5344.1527 -286.61595 17.088682 0.74721761 75 0.048183096 0.013941446 0 0 25 50 - 3000 106.86746 -3920.4926 -361.60598 18.794545 0.89666113 90 0.035637919 0.012768883 0 0 30 60 - 4000 75.002668 540.46846 -414.8511 14.531966 0.98632724 99 0.025963651 0.0093451705 0 0 33 66 - 5000 79.924788 -2131.1173 -437.21216 15.962121 1.0162159 102 0.019879728 0.0070418993 0 0 34 68 - 6000 95.552773 -3647.0233 -438.24276 19.083253 1.0162159 102 0.015753613 0.0056885133 0 0 34 68 - 7000 79.501736 -2071.5369 -440.77351 15.877631 1.0162159 102 0.01326216 0.0046915318 0 0 34 68 - 8000 62.567091 -3102.9616 -442.21884 12.495541 1.0162159 102 0.011305503 0.0040437885 0 0 34 68 - 9000 68.324047 -3812.7866 -440.46835 13.645287 1.0162159 102 0.0099549538 0.0035157329 0 0 34 68 - 10000 83.857631 -2158.2659 -444.8183 16.747566 1.0162159 102 0.0088200922 0.0031354281 0 0 34 68 - 11000 68.350984 -2084.0789 -440.14081 13.650667 1.0162159 102 0.0081331455 0.0030247424 0 0 34 68 - 12000 76.867315 -1585.6723 -443.36199 15.3515 1.0162159 102 0.0073845932 0.0027532534 0 0 34 68 - 13000 59.74266 -2211.0211 -446.07791 11.931462 1.0162159 102 0.0067756276 0.0025213898 0 0 34 68 - 14000 81.154979 -907.0176 -441.53368 16.207808 1.0162159 102 0.0062527642 0.0023280719 0 0 34 68 - 15000 66.814346 -2804.5134 -455.80704 13.7421 1.0461046 105 0.0059590528 0.0021576214 0 0 35 70 - 16000 71.42983 -3930.4004 -458.43218 14.691394 1.0461046 105 0.0055547473 0.0020163729 0 0 35 70 - 17000 89.624855 -3569.8136 -455.18164 18.433672 1.0461046 105 0.0052173265 0.0018867687 0 0 35 70 - 18000 63.519962 -1882.8157 -456.58939 13.064525 1.0461046 105 0.0049082049 0.0017765986 0 0 35 70 - 19000 71.872698 -2243.5046 -454.93359 14.782481 1.0461046 105 0.0046439115 0.0016748361 0 0 35 70 - 20000 73.660765 -2285.3173 -476.35473 15.589381 1.0759934 108 0.0045124933 0.0015837653 0 0 36 72 - 21000 95.675868 987.92089 -475.46736 20.248603 1.0759934 108 0.004285814 0.0015049513 0 0 36 72 -Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms - -Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + 0 326.9865 -4.3508819 -62.258443 14.62027 0.23910963 24 0 0 0 0 8 16 + 1000 354.423 -3760.1354 -235.34169 51.766914 0.74721761 75 0.046175467 0.011949811 0 0 25 50 + 2000 335.19661 -3018.659 -270.44089 52.955344 0.80699501 81 0.026473882 0.0068755525 0 0 27 54 + 3000 333.47175 2657.2052 -336.48359 64.611037 0.98632724 99 0.022634978 0.0060076096 0 0 33 66 + 4000 321.48504 2055.4786 -345.06113 62.288579 0.98632724 99 0.016897769 0.0045269353 0 0 33 66 + 5000 333.45735 1918.5375 -368.5463 66.596193 1.0162159 102 0.013784412 0.0036569014 0 0 34 68 + 6000 301.90666 -698.74074 -371.32122 60.295069 1.0162159 102 0.01160439 0.0030159847 0 0 34 68 + 7000 336.42505 1537.9483 -378.51731 69.194524 1.0461046 105 0.010174953 0.0025995783 0 0 35 70 + 8000 338.95331 -1032.1084 -390.7067 69.714524 1.0461046 105 0.0089594585 0.002260114 0 0 35 70 + 9000 311.44605 -1494.7788 -383.9272 64.056945 1.0461046 105 0.007938083 0.0020156323 0 0 35 70 + 10000 330.70877 2082.4597 -366.57249 68.018822 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70 + 11000 286.34718 2238.3752 -370.91119 60.601806 1.0759934 108 0.0066641451 0.0016519521 0 0 36 72 + 12000 371.02522 3048.7157 -398.51333 78.522854 1.0759934 108 0.0061145907 0.0015128339 0 0 36 72 + 13000 392.87611 4486.1134 -387.07077 83.147323 1.0759934 108 0.0056427384 0.0013968431 0 0 36 72 + 14000 332.80747 3586.2698 -406.12151 70.434545 1.0759934 108 0.0052496417 0.0012945729 0 0 36 72 + 15000 325.61844 4198.3864 -387.5733 68.913077 1.0759934 108 0.0048934679 0.0012098238 0 0 36 72 + 16000 254.10285 1560.976 -409.98615 55.292559 1.1058821 111 0.0047204383 0.0011320612 0 0 37 74 + 17000 367.46414 2750.8283 -412.22037 79.959878 1.1058821 111 0.0044407568 0.0010659592 0 0 37 74 + 18000 407.74215 2308.5027 -408.73046 88.724338 1.1058821 111 0.0042016342 0.0010049017 0 0 37 74 + 19000 341.53799 5777.9814 -407.00637 74.31837 1.1058821 111 0.0039877848 0.00095025921 0 0 37 74 + 20000 395.75303 3159.4677 -403.82798 86.115516 1.1058821 111 0.0037874635 0.00090297077 0 0 37 74 +Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms + +Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 37.459 | 37.459 | 37.459 | 0.0 | 16.98 -Bond | 0.087067 | 0.087067 | 0.087067 | 0.0 | 0.04 -Kspace | 0.90234 | 0.90234 | 0.90234 | 0.0 | 0.41 -Neigh | 1.2299 | 1.2299 | 1.2299 | 0.0 | 0.56 -Comm | 0.95437 | 0.95437 | 0.95437 | 0.0 | 0.43 -Output | 0.0010636 | 0.0010636 | 0.0010636 | 0.0 | 0.00 -Modify | 179.85 | 179.85 | 179.85 | 0.0 | 81.51 -Other | | 0.1754 | | | 0.08 - -Nlocal: 108 ave 108 max 108 min +Pair | 39.09 | 39.09 | 39.09 | 0.0 | 16.90 +Bond | 0.092728 | 0.092728 | 0.092728 | 0.0 | 0.04 +Kspace | 0.87751 | 0.87751 | 0.87751 | 0.0 | 0.38 +Neigh | 3.9658 | 3.9658 | 3.9658 | 0.0 | 1.71 +Comm | 1.0608 | 1.0608 | 1.0608 | 0.0 | 0.46 +Output | 0.00096035 | 0.00096035 | 0.00096035 | 0.0 | 0.00 +Modify | 186.07 | 186.07 | 186.07 | 0.0 | 80.43 +Other | | 0.1892 | | | 0.08 + +Nlocal: 111 ave 111 max 111 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7850 ave 7850 max 7850 min +Nghost: 8070 ave 8070 max 8070 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 99828 ave 99828 max 99828 min +Neighs: 105469 ave 105469 max 105469 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 99828 -Ave neighs/atom = 924.333 +Total # of neighbors = 105469 +Ave neighs/atom = 950.171 Ave special neighs/atom = 2 -Neighbor list builds = 20439 +Neighbor list builds = 20910 Dangerous builds = 0 -Total wall time: 0:03:40 +Total wall time: 0:03:51 diff --git a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..c5caf57113594ce82deedc9f24df1e5b94b2fcd6 --- /dev/null +++ b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 @@ -0,0 +1,237 @@ +LAMMPS (30 Mar 2018) + using 1 OpenMP thread(s) per MPI task +# fix gcmc example with fix shake + +# variables available on command line + +variable mu index -8.1 +variable disp index 0.5 +variable temp index 338.0 +variable lbox index 10.0 +variable spacing index 5.0 + +# global model settings + +units real +atom_style full +boundary p p p +pair_style lj/cut/coul/long 14 +pair_modify mix arithmetic tail yes +kspace_style ewald 0.0001 +bond_style harmonic +angle_style harmonic + +# box, start molecules on simple cubic lattice + +lattice sc ${spacing} +lattice sc 5.0 +Lattice spacing in x,y,z = 5 5 5 +region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 ${lbox} 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 ${lbox} units box +region box block 0 10.0 0 10.0 0 10.0 units box +create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 +Created orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + +molecule h2omol H2O.txt +Read molecule h2omol: + 3 atoms with max type 2 + 2 bonds with max type 1 + 1 angles with max type 1 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +create_atoms 0 box mol h2omol 464563 units box +Created 24 atoms + Time spent = 0.00285625 secs + +# rigid SPC/E water model + +pair_coeff 1 1 0.15535 3.166 +pair_coeff * 2 0.0000 0.0000 + +bond_coeff 1 1000 1.0 +angle_coeff 1 100 109.47 + +# masses + +mass 1 15.9994 +mass 2 1.0 + +# MD settings + +group h2o type 1 2 +24 atoms in group h2o +neighbor 2.0 bin +neigh_modify every 1 delay 1 check yes +velocity all create ${temp} 54654 +velocity all create 338.0 54654 +timestep 1.0 + +minimize 0.0 0.0 100 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) +Ewald initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.170448 + estimated absolute RMS force accuracy = 0.0332064 + estimated relative force accuracy = 0.0001 + KSpace vectors: actual max1d max3d = 16 2 62 + kxmax kymax kzmax = 2 2 2 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 16 + ghost atom cutoff = 16 + binsize = 8, bins = 2 2 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 338 -4.9610706 9.2628112e-06 18.211756 730.90791 + 100 338 -15.742442 0.14954269 7.579918 -637.49568 +Loop time of 0.0695416 on 4 procs for 100 steps with 24 atoms + +94.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = max iterations + Energy initial, next-to-last, final = + -4.96106135393 -15.5388622715 -15.592899346 + Force two-norm initial, final = 15.474 18.1478 + Force max component initial, final = 5.80042 7.56514 + Final line search alpha, max atom move = 0.00151131 0.0114333 + Iterations, force evaluations = 100 328 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0093951 | 0.017625 | 0.028943 | 5.3 | 25.34 +Bond | 0.00035357 | 0.00042325 | 0.00055075 | 0.0 | 0.61 +Kspace | 0.00664 | 0.019695 | 0.029924 | 6.1 | 28.32 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.022505 | 0.02509 | 0.027851 | 1.3 | 36.08 +Output | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 | 0.0 | 0.05 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.006672 | | | 9.59 + +Nlocal: 6 ave 8 max 3 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Nghost: 1722 ave 1725 max 1720 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 1256.75 ave 2101 max 667 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 5027 +Ave neighs/atom = 209.458 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +reset_timestep 0 + +# rigid constraints with thermostat + +fix mynvt h2o nvt temp ${temp} ${temp} 100 +fix mynvt h2o nvt temp 338.0 ${temp} 100 +fix mynvt h2o nvt temp 338.0 338.0 100 +fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 8 = # of frozen angles + +# important to make temperature dofs dynamic + +compute_modify thermo_temp dynamic/dof yes +compute_modify mynvt_temp dynamic/dof yes + +run 1000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.170448 + estimated absolute RMS force accuracy = 0.0332064 + estimated relative force accuracy = 0.0001 + KSpace vectors: actual max1d max3d = 16 2 62 + kxmax kymax kzmax = 2 2 2 +Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 518.26667 -15.742442 0 7.4303753 -613.0781 + 1000 369.81793 -54.202682 0 -37.667327 294.98832 +Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms + +Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s +96.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.015873 | 0.028989 | 0.040172 | 5.3 | 15.13 +Bond | 0.00024271 | 0.00027657 | 0.00034404 | 0.0 | 0.14 +Kspace | 0.022896 | 0.034492 | 0.047924 | 5.1 | 18.00 +Neigh | 0.0025764 | 0.0025961 | 0.0026152 | 0.0 | 1.35 +Comm | 0.068467 | 0.070095 | 0.071535 | 0.4 | 36.58 +Output | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 | 0.0 | 0.03 +Modify | 0.049141 | 0.049894 | 0.05072 | 0.3 | 26.04 +Other | | 0.005226 | | | 2.73 + +Nlocal: 6 ave 8 max 3 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 1331.5 ave 1369 max 1290 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 1259.75 ave 1642 max 428 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 5039 +Ave neighs/atom = 209.958 +Ave special neighs/atom = 2 +Neighbor list builds = 27 +Dangerous builds = 0 +reset_timestep 0 + +# gcmc + +variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) +fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake +fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake + +# atom counts + +variable oxygen atom "type==1" +variable hydrogen atom "type==2" +group oxygen dynamic all var oxygen +dynamic group oxygen defined +group hydrogen dynamic all var hydrogen +dynamic group hydrogen defined +variable nO equal count(oxygen) +variable nH equal count(hydrogen) + +# output + +variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) +variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) +variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) +variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) +thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH +thermo 1000 + +# run + +run 20000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.170448 + estimated absolute RMS force accuracy = 0.0332064 + estimated relative force accuracy = 0.0001 + KSpace vectors: actual max1d max3d = 16 2 62 + kxmax kymax kzmax = 2 2 2 +WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) +0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc +0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc +ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721) +Last command: run 20000 diff --git a/examples/gcmc/log.23Oct17.gcmc.lj.g++.1 b/examples/gcmc/log.30Mar18.gcmc.lj.g++.1 similarity index 52% rename from examples/gcmc/log.23Oct17.gcmc.lj.g++.1 rename to examples/gcmc/log.30Mar18.gcmc.lj.g++.1 index a38dfeee77897b740bfecfaedd046676a6ad56b3..20a25c0f954627cd3445b1fbb6406f5610fb8cd0 100644 --- a/examples/gcmc/log.23Oct17.gcmc.lj.g++.1 +++ b/examples/gcmc/log.30Mar18.gcmc.lj.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (23 Oct 2017) +LAMMPS (30 Mar 2018) using 1 OpenMP thread(s) per MPI task # GCMC for LJ simple fluid, no dynamics # T = 2.0 @@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5) pair_coeff * * 1.0 1.0 mass * 1.0 +# we recommend setting up a dedicated group for gcmc + +group gcmcgroup type 1 +0 atoms in group gcmcgroup + # gcmc -fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0 +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0 # atom count variable type1 atom "type==1" -group type1 dynamic all var type1 +group type1 dynamic gcmcgroup var type1 dynamic group type1 defined variable n1 equal count(type1) @@ -97,40 +102,40 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 - 1000 2.4038954 2.1735585 -2.7041368 3.5476844 0.496 62 0.064790036 0.06313096 0.1081294 0.54304 1.4513524 -0.025479219 64.98 - 2000 2.0461168 1.1913842 -2.9880181 3.0212194 0.512 64 0.067416408 0.066335853 0.11306166 0.52736 1.3274665 0.034690004 62.97 - 3000 1.7930436 1.3788681 -3.2212667 2.6505861 0.552 69 0.067733191 0.066877836 0.1133516 0.5344 1.3834744 0.0070582537 63.5 - 4000 1.981449 1.2541054 -2.8222868 2.9217977 0.472 59 0.068546991 0.067856412 0.11442807 0.52504 1.3815629 0.043309657 62.17 - 5000 2.0946818 1.0701629 -3.5213291 3.0977688 0.568 71 0.06813743 0.067567891 0.11342906 0.53824 1.4049567 -0.0054539777 64.15 - 6000 1.9793484 0.68224187 -3.410211 2.9247088 0.536 67 0.067797628 0.067420108 0.11295333 0.5384 1.401683 -0.0066894359 64.37 - 7000 2.1885798 1.6745012 -3.185499 3.2345922 0.544 68 0.068630201 0.068261832 0.11403705 0.5244 1.449239 0.045987399 62.33 - 8000 2.2175324 1.5897263 -3.078898 3.2759002 0.528 66 0.068180395 0.067899629 0.11332691 0.53928 1.5488388 -0.01075766 64.29 - 9000 1.8610779 1.0396231 -2.923262 2.7465908 0.496 62 0.068346453 0.068028117 0.1134132 0.52912 1.4352871 0.027082544 62.87 - 10000 2.1079271 1.1746643 -2.9112062 3.1091925 0.48 60 0.068352878 0.068054948 0.11335434 0.5316 1.4462327 0.018503094 63.2 -Loop time of 20.4081 on 1 procs for 10000 steps with 60 atoms - -Performance: 211680.375 tau/day, 490.001 timesteps/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + 1000 2.0603874 2.9024736 -3.2576986 3.0482443 0.584 73 0.069266074 0.066959582 0.11158434 0.53624 1.3978532 0.0014407586 64.19 + 2000 2.1586837 1.5581387 -2.8420766 3.1857993 0.496 62 0.068487803 0.067570935 0.1126652 0.53128 1.3713694 0.020274019 63.41 + 3000 2.4664064 0.65471138 -3.3428236 3.6435549 0.528 66 0.068182273 0.067547792 0.11226502 0.53472 1.3892234 0.0070204504 63.68 + 4000 1.8880496 1.4802782 -2.7846019 2.785647 0.488 61 0.068250075 0.067843541 0.11299989 0.52744 1.299496 0.033918563 63.1 + 5000 2.0578649 1.3204331 -3.5571862 3.0433213 0.568 71 0.067858571 0.067732262 0.11271981 0.5364 1.4237505 0.00065741209 64 + 6000 2.3627973 0.97064566 -3.1107668 3.4879388 0.504 63 0.067846204 0.06757018 0.11272207 0.5332 1.3945131 0.014216594 63.7 + 7000 1.6629817 0.98138972 -2.7780297 2.4514644 0.464 58 0.067451389 0.067269791 0.11263692 0.53688 1.4207486 -0.0012887793 63.82 + 8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43 + 9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23 + 10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44 +Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms + +Performance: 203381.368 tau/day, 470.790 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.46484 | 0.46484 | 0.46484 | 0.0 | 2.28 -Neigh | 1.1447 | 1.1447 | 1.1447 | 0.0 | 5.61 -Comm | 0.1696 | 0.1696 | 0.1696 | 0.0 | 0.83 -Output | 0.000319 | 0.000319 | 0.000319 | 0.0 | 0.00 -Modify | 18.607 | 18.607 | 18.607 | 0.0 | 91.17 -Other | | 0.02194 | | | 0.11 - -Nlocal: 60 ave 60 max 60 min +Pair | 0.45931 | 0.45931 | 0.45931 | 0.0 | 2.16 +Neigh | 1.1637 | 1.1637 | 1.1637 | 0.0 | 5.48 +Comm | 0.17294 | 0.17294 | 0.17294 | 0.0 | 0.81 +Output | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.00 +Modify | 19.416 | 19.416 | 19.416 | 0.0 | 91.41 +Other | | 0.02919 | | | 0.14 + +Nlocal: 64 ave 64 max 64 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 663 ave 663 max 663 min +Nghost: 714 ave 714 max 714 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2133 ave 2133 max 2133 min +Neighs: 2423 ave 2423 max 2423 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2133 -Ave neighs/atom = 35.55 +Total # of neighbors = 2423 +Ave neighs/atom = 37.8594 Neighbor list builds = 10000 Dangerous builds = 0 -Total wall time: 0:00:20 +Total wall time: 0:00:21 diff --git a/examples/gcmc/log.23Oct17.gcmc.lj.g++.4 b/examples/gcmc/log.30Mar18.gcmc.lj.g++.4 similarity index 50% rename from examples/gcmc/log.23Oct17.gcmc.lj.g++.4 rename to examples/gcmc/log.30Mar18.gcmc.lj.g++.4 index ea7dc8116febce3c356ca8782599656cf6250986..819d0ed0869038a7b0bd61a2a7fab6038eff996c 100644 --- a/examples/gcmc/log.23Oct17.gcmc.lj.g++.4 +++ b/examples/gcmc/log.30Mar18.gcmc.lj.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (23 Oct 2017) +LAMMPS (30 Mar 2018) using 1 OpenMP thread(s) per MPI task # GCMC for LJ simple fluid, no dynamics # T = 2.0 @@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5) pair_coeff * * 1.0 1.0 mass * 1.0 +# we recommend setting up a dedicated group for gcmc + +group gcmcgroup type 1 +0 atoms in group gcmcgroup + # gcmc -fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp} -fix mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0 +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp} +fix mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0 # atom count variable type1 atom "type==1" -group type1 dynamic all var type1 +group type1 dynamic gcmcgroup var type1 dynamic group type1 defined variable n1 equal count(type1) @@ -97,40 +102,40 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av 0 0 0 0 -0 0 0 0 0 0 0 0 0 0 - 1000 1.956397 1.7699101 -2.7889468 2.8864874 0.488 61 0.068894746 0.067229075 0.1141726 0.53288 1.3832798 0.013392866 63.44 - 2000 2.040943 0.56060899 -2.8001647 3.0077055 0.456 57 0.069858594 0.068831934 0.11629114 0.5232 1.3587174 0.049995794 62.19 - 3000 2.0004866 1.5736515 -3.3098044 2.9572411 0.552 69 0.069594029 0.068727791 0.11592543 0.53096 1.4129434 0.020022578 63.23 - 4000 2.1127942 2.642809 -2.8865084 3.1211733 0.528 66 0.070268697 0.069533235 0.11693806 0.52424 1.3444615 0.046884078 62.57 - 5000 2.3663648 1.354269 -3.1917346 3.4957662 0.528 66 0.070519633 0.069960064 0.11710321 0.52688 1.3595814 0.036270867 62.56 - 6000 1.9224136 0.82756699 -3.1965 2.839257 0.52 65 0.06985018 0.069474645 0.11628632 0.536 1.47062 0.00141549 63.76 - 7000 2.0266192 1.5593811 -2.9972341 2.9931606 0.52 65 0.070244693 0.069880791 0.11666541 0.52528 1.3246332 0.040754793 62.2 - 8000 1.7790467 1.8680568 -2.8028819 2.6275151 0.52 65 0.070454494 0.070172368 0.11736806 0.524 1.4213649 0.047985191 62.03 - 9000 1.7968847 1.3195587 -3.261001 2.6550983 0.536 67 0.069952011 0.069618327 0.11650087 0.53904 1.4624201 -0.01069837 64.36 - 10000 2.1566109 1.1015729 -3.4999837 3.1880335 0.552 69 0.069603309 0.069284134 0.11625548 0.53128 1.3587249 0.02075238 63.24 -Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms - -Performance: 181350.388 tau/day, 419.793 timesteps/s -97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + 1000 2.4378552 1.9014939 -3.23439 3.6030066 0.544 68 0.073050445 0.070796636 0.11934255 0.52552 1.3006333 0.04152087 62.56 + 2000 1.9339159 1.0360287 -3.5001391 2.8594327 0.56 70 0.069588893 0.068587488 0.11319584 0.542 1.4012888 -0.020696665 64.56 + 3000 1.8891807 2.2857708 -3.3755633 2.7954769 0.592 74 0.068329031 0.067640916 0.11187803 0.53536 1.3380926 0.0062359288 64.21 + 4000 2.0436517 1.7600211 -3.4067452 3.0229014 0.576 72 0.067464211 0.067003868 0.11060324 0.54144 1.4484907 -0.016246603 64.75 + 5000 2.1512268 1.0811095 -3.2418366 3.1786785 0.536 67 0.066830654 0.066717982 0.1094094 0.54368 1.4962073 -0.025791643 65.04 + 6000 2.128931 1.5444487 -3.1904474 3.1450116 0.528 66 0.067479197 0.067193531 0.1104464 0.53112 1.4247377 0.019908014 63.01 + 7000 1.8194311 0.72981963 -3.6601329 2.6912418 0.576 72 0.068131849 0.067910074 0.11182024 0.51968 1.4517098 0.063444774 61.72 + 8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45 + 9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73 + 10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04 +Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms + +Performance: 147733.999 tau/day, 341.977 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.10935 | 0.11844 | 0.12741 | 2.1 | 0.50 -Neigh | 0.33 | 0.33945 | 0.35091 | 1.6 | 1.42 -Comm | 0.49249 | 0.51745 | 0.53856 | 2.7 | 2.17 -Output | 0.00053334 | 0.0007208 | 0.0007906 | 0.0 | 0.00 -Modify | 22.82 | 22.822 | 22.825 | 0.0 | 95.81 -Other | | 0.02289 | | | 0.10 - -Nlocal: 17.25 ave 23 max 10 min -Histogram: 1 0 0 0 0 0 2 0 0 1 -Nghost: 506.5 ave 519 max 490 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 705.75 ave 998 max 369 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 2823 -Ave neighs/atom = 40.913 +Pair | 0.11648 | 0.1221 | 0.13001 | 1.5 | 0.42 +Neigh | 0.34452 | 0.35618 | 0.36328 | 1.2 | 1.22 +Comm | 0.63561 | 0.65617 | 0.67542 | 1.8 | 2.24 +Output | 0.00056601 | 0.00069755 | 0.00074744 | 0.0 | 0.00 +Modify | 28.069 | 28.076 | 28.082 | 0.1 | 96.01 +Other | | 0.03094 | | | 0.11 + +Nlocal: 15 ave 16 max 14 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 437 ave 446 max 431 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 529 ave 595 max 437 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 2116 +Ave neighs/atom = 35.2667 Neighbor list builds = 10000 Dangerous builds = 0 -Total wall time: 0:00:23 +Total wall time: 0:00:29 diff --git a/examples/latte/data.ch4 b/examples/latte/data.ch4 new file mode 100644 index 0000000000000000000000000000000000000000..fc8d48d244305c0b4f64c523bb7021418ea4c439 --- /dev/null +++ b/examples/latte/data.ch4 @@ -0,0 +1,23 @@ + LAMMPS Description + + 5 atoms + + 2 atom types + + 0.0000000000000000 19.523000000000000 xlo xhi + 0.0000000000000000 12.757999999999999 ylo yhi + 0.0000000000000000 11.692000000000000 zlo zhi + 0.0000000000000000 0.0000000000000000 0.0000000000000000 xy xz yz + + Masses + + 1 12.010000000000000 + 2 1.0078250169754028 + + Atoms + + 1 1 1 0.0 -9.16600 2.05200 0.00000 + 2 1 2 0.0 -8.09600 2.05200 0.00000 + 3 1 2 0.0 -9.52300 2.75800 -0.72000 + 4 1 2 0.0 -9.52300 2.32200 0.97200 + 5 1 2 0.0 -9.52300 1.07500 -0.25200 diff --git a/examples/latte/data.graphene b/examples/latte/data.graphene new file mode 100644 index 0000000000000000000000000000000000000000..5455a2eeb6cc1756e6c5ad5af01069aa5f01d866 --- /dev/null +++ b/examples/latte/data.graphene @@ -0,0 +1,49 @@ + LAMMPS Description + + 32 atoms + + 1 atom types + + 0.0000000000000000 10.000000000000000 xlo xhi + 0.0000000000000000 8.0000000000000000 ylo yhi + 0.0000000000000000 20.000000000000000 zlo zhi + 4.8985871965894128E-016 1.2246467991473533E-015 1.2246467991473533E-015 xy xz yz + + Masses + + 1 12.010000000000000 + + Atoms + + 1 1 1 0.0 4.93100 4.25000 0.00500 + 2 1 1 0.0 8.62100 2.12100 0.14000 + 3 1 1 0.0 3.70700 2.12600 0.14700 + 4 1 1 0.0 7.38200 4.25400 0.07800 + 5 1 1 0.0 2.47900 4.25400 0.08000 + 6 1 1 0.0 6.15800 6.37400 -0.01000 + 7 1 1 0.0 1.23700 6.38300 0.06600 + 8 1 1 0.0 1.24000 2.12100 0.14600 + 9 1 1 0.0 6.15500 2.12600 0.12900 + 10 1 1 0.0 0.00700 4.25200 0.12200 + 11 1 1 0.0 8.62100 6.38500 0.04100 + 12 1 1 0.0 3.70000 6.37400 -0.01000 + 13 1 1 0.0 0.00600 1.41600 0.13000 + 14 1 1 0.0 4.93000 1.40800 0.14700 + 15 1 1 0.0 8.61800 3.54600 0.11500 + 16 1 1 0.0 3.70800 3.55300 0.08400 + 17 1 1 0.0 7.39400 5.68000 0.03500 + 18 1 1 0.0 2.46500 5.68000 0.03500 + 19 1 1 0.0 6.16000 7.80500 0.02700 + 20 1 1 0.0 1.23800 7.81100 0.06000 + 21 1 1 0.0 2.47300 1.41800 0.16100 + 22 1 1 0.0 7.38900 1.41700 0.14800 + 23 1 1 0.0 1.24200 3.54700 0.12600 + 24 1 1 0.0 6.15300 3.55300 0.07400 + 25 1 1 0.0 0.00700 5.67800 0.09700 + 26 1 1 0.0 4.93100 5.66800 -0.03100 + 27 1 1 0.0 8.62000 7.81300 0.03900 + 28 1 1 0.0 3.70100 7.80200 0.03700 + 29 1 1 0.0 0.00700 -0.01000 0.08900 + 30 1 1 0.0 4.93100 -0.01500 0.16100 + 31 1 1 0.0 2.47300 -0.01200 0.14400 + 32 1 1 0.0 7.38900 -0.01300 0.14800 diff --git a/examples/latte/in.graphene.boxrel b/examples/latte/in.graphene.boxrel new file mode 100644 index 0000000000000000000000000000000000000000..721b7f014f0981bdc8672e2d1bdc2f7bb9f6932d --- /dev/null +++ b/examples/latte/in.graphene.boxrel @@ -0,0 +1,44 @@ +# Simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.graphene + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all box/relax iso 0.0 vmax 0.001 + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom etotal + +# minimization + +thermo 1 +fix 3 all print 1 "Total Energy =" +min_style cg +min_modify dmax 0.1 +min_modify line quadratic +minimize 1.0e-4 1.0e-4 10000 10000 diff --git a/examples/latte/in.latte.multiple b/examples/latte/in.latte.multiple new file mode 100644 index 0000000000000000000000000000000000000000..4888d14ebc6fe862b8d98e2520879cdd11488f01 --- /dev/null +++ b/examples/latte/in.latte.multiple @@ -0,0 +1,65 @@ +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 + +# Clear up previus calculation + +clear + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 + diff --git a/examples/latte/in.latte.sucrose.md b/examples/latte/in.latte.sucrose.md new file mode 100644 index 0000000000000000000000000000000000000000..a10dae5c5ea9451d7733de60d695d559cd340b78 --- /dev/null +++ b/examples/latte/in.latte.sucrose.md @@ -0,0 +1,40 @@ +# simple sucrose model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.sucrose + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 diff --git a/examples/latte/in.latte.water.md b/examples/latte/in.latte.water.md new file mode 100644 index 0000000000000000000000000000000000000000..e1185602b43ec5990e27f904cb97cfc2f725a3df --- /dev/null +++ b/examples/latte/in.latte.water.md @@ -0,0 +1,40 @@ +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 diff --git a/examples/latte/in.latte.water.min b/examples/latte/in.latte.water.min index 503e45a300b25802bde6ae646d317c15774dd355..173afee96a8b8d5987a7bd92ebda8ddb24996408 100644 --- a/examples/latte/in.latte.water.min +++ b/examples/latte/in.latte.water.min @@ -37,5 +37,6 @@ thermo_style custom step temp pe etotal press # minimization thermo 10 -min_style fire -minimize 1.0e-9 1.0e-9 500 500 + +min_style fire +minimize 1.0e-4 1.0e-4 500 500 diff --git a/examples/latte/latte.in b/examples/latte/latte.in index b8b214b78b4847ee4a58c0a03e6f8a94adc78e4b..f927313457cafdf39b762db9b73ec10dd77a82ab 100644 --- a/examples/latte/latte.in +++ b/examples/latte/latte.in @@ -9,9 +9,8 @@ LATTE INPUT FILE #General controls CONTROL{ - xControl= 1 + XCONTROL= 1 BASISTYPE= NONORTHO - COORDSFILE= "./coords.dat" PARAMPATH= "./TBparam" KBT= 0.0 ENTROPYKIND= 1 @@ -22,9 +21,8 @@ CONTROL{ BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL FULLQCONV= 1 QITER= 3 QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25 - SPARSEON= 1 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4 + SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4 MSPARSE= 1500 - RELAX= 0 RELAXTYPE= SD MAXITER= 100000 RLXFTOL= 0.0000001 SKIN= 1.0 CHARGE= 0 XBO= 1 @@ -32,9 +30,3 @@ CONTROL{ XBODISORDER= 5 KON= 0 } - -#Controls for QMD (if using lammps MAXITER must be set to -1) -MDCONTROL{ - MAXITER= -1 -} - diff --git a/examples/latte/log.19Sep17.latte.sucrose.g++.1 b/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 similarity index 100% rename from examples/latte/log.19Sep17.latte.sucrose.g++.1 rename to examples/latte/log.19Sep17.latte.sucrose.md.g++.1 diff --git a/examples/latte/log.19Sep17.latte.water.g++.1 b/examples/latte/log.19Sep17.latte.water.md.g++.1 similarity index 100% rename from examples/latte/log.19Sep17.latte.water.g++.1 rename to examples/latte/log.19Sep17.latte.water.md.g++.1 diff --git a/examples/latte/log.19Sep17.latte.water.min.g++.1 b/examples/latte/log.19Sep17.latte.water.min.g++.1 deleted file mode 100644 index 4b96bd26682bcb3162250bc48ecd8cd3eb60387d..0000000000000000000000000000000000000000 --- a/examples/latte/log.19Sep17.latte.water.min.g++.1 +++ /dev/null @@ -1,152 +0,0 @@ -LAMMPS (1 Sep 2017) -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - orthogonal box = (0 0 0) to (6.267 6.267 6.267) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 24 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# minimization - -thermo 10 -min_style fire -minimize 1.0e-9 1.0e-9 500 500 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes -Step Temp PotEng TotEng Press - 0 0 -104.95614 -104.95614 48229.712 - 10 349.44219 -105.50971 -104.47083 62149.591 - 20 1253.6752 -107.00898 -103.28182 116444.44 - 30 134.63588 -107.56184 -107.16157 59854.143 - 40 2.4043703 -108.15301 -108.14586 32685.77 - 50 162.13426 -108.40551 -107.92349 62104.273 - 60 134.03149 -108.70118 -108.30271 49400.525 - 70 64.159014 -108.78034 -108.5896 37243.303 - 80 240.49926 -109.10766 -108.39266 42158.884 - 90 0.60467192 -109.61818 -109.61639 14107.515 - 100 1.4691163 -109.65556 -109.65119 21596.775 - 110 30.500628 -109.69267 -109.602 16104.639 - 120 120.62379 -109.83749 -109.47888 9474.971 - 130 8.4742975 -109.99986 -109.97467 10104.102 - 140 3.4732679 -110.01209 -110.00176 11990.442 - 150 24.749482 -110.04313 -109.96955 10851.569 - 160 4.1106505 -110.13288 -110.12066 8257.3969 - 170 0.0065628716 -110.18061 -110.18059 7876.8748 - 180 2.0542078 -110.1837 -110.17759 7996.0533 - 190 20.134782 -110.21071 -110.15085 7556.1811 - 200 2.3397267 -110.3244 -110.31745 3767.062 - 210 4.3544709 -110.34438 -110.33143 4889.145 - 220 1.1872367 -110.37457 -110.37104 4162.6543 - 230 2.2798399 -110.38081 -110.37403 4321.0943 - 240 11.835907 -110.39611 -110.36092 4187.5757 - 250 0.13741849 -110.41453 -110.41412 3720.7527 - 260 4.2283185 -110.42036 -110.40779 3743.3494 - 270 0.47243724 -110.44349 -110.44208 3172.1866 - 280 0.06090137 -110.45428 -110.4541 3065.9348 - 290 5.3413962 -110.46285 -110.44697 3121.2924 - 300 8.2032986 -110.48519 -110.4608 2705.5001 - 310 2.0783529 -110.48807 -110.48189 2740.7989 - 320 16.629185 -110.51002 -110.46058 2581.7434 - 330 0.19723065 -110.53444 -110.53385 1942.0228 - 340 6.2758334 -110.54361 -110.52495 1924.0965 - 350 1.4539052 -110.59108 -110.58676 -449.41056 - 360 0.0514233 -110.60143 -110.60128 1284.8259 - 370 1.7240145 -110.60394 -110.59881 1468.0004 - 380 13.28516 -110.62337 -110.58387 1573.4714 - 390 1.2247432 -110.63525 -110.63161 1113.4557 - 400 0.3946985 -110.63694 -110.63576 1083.0801 - 410 2.9831433 -110.641 -110.63213 1112.419 - 420 0.068550589 -110.66029 -110.66009 897.09211 - 430 0.83976182 -110.66259 -110.66009 918.69832 - 440 4.4760907 -110.66844 -110.65513 915.24435 - 450 1.2841241 -110.67482 -110.671 953.30422 - 460 2.5707455 -110.68509 -110.67745 775.21273 - 470 0.99721544 -110.68646 -110.6835 812.74984 - 480 6.8379261 -110.69468 -110.67435 787.9705 - 490 0.18134438 -110.69628 -110.69574 675.52792 - 500 2.0946523 -110.69918 -110.69295 696.82065 -Loop time of 31.775 on 1 procs for 500 steps with 24 atoms - -884.8% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -104.95614332 -110.698546127 -110.699182193 - Force two-norm initial, final = 19.119 0.234621 - Force max component initial, final = 11.7759 0.0903198 - Final line search alpha, max atom move = 0 0 - Iterations, force evaluations = 500 500 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.00 -Bond | 2.8372e-05 | 2.8372e-05 | 2.8372e-05 | 0.0 | 0.00 -Neigh | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.00 -Comm | 0.00060034 | 0.00060034 | 0.00060034 | 0.0 | 0.00 -Output | 0.00057817 | 0.00057817 | 0.00057817 | 0.0 | 0.00 -Modify | 31.771 | 31.771 | 31.771 | 0.0 | 99.99 -Other | | 0.002469 | | | 0.01 - -Nlocal: 24 ave 24 max 24 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 71 ave 71 max 71 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 27 ave 27 max 27 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 27 -Ave neighs/atom = 1.125 -Ave special neighs/atom = 0 -Neighbor list builds = 2 -Dangerous builds = 0 -Total wall time: 0:00:31 diff --git a/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 b/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..3a37136fd36595826ab3e5d51b5ef31bca1f3b96 --- /dev/null +++ b/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 @@ -0,0 +1,170 @@ +LAMMPS (11 May 2018) +# Simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.graphene.boxrel + triclinic box = (0 0 0) to (10 8 20) with tilt (4.89859e-16 1.22465e-15 1.22465e-15) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 32 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all box/relax iso 0.0 vmax 0.001 + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom etotal + +# minimization + +thermo 1 +fix 3 all print 1 "Total Energy =" +min_style cg +min_modify dmax 0.1 +min_modify line quadratic +minimize 1.0e-4 1.0e-4 10000 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 11 9 20 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.779 | 6.779 | 6.779 Mbytes +TotEng + -247.46002 + -247.67224 + -247.87937 + -248.08148 + -248.27865 + -248.47096 + -248.65851 + -248.84137 + -249.01964 + -249.19342 + -249.36281 + -249.52791 + -249.68883 + -249.8457 + -249.99865 + -250.1478 + -250.29332 + -250.43535 + -250.57409 + -250.70972 + -250.84247 + -250.97258 + -251.10035 + -251.2261 + -251.35021 + -251.47314 + -251.59543 + -251.71776 + -251.84096 + -251.9661 + -252.09459 + -252.22833 + -252.37003 + -252.52371 + -252.69578 + -252.89752 + -253.15197 + -253.52044 + -254.31418 + -255.6175 + -256.8162 + -258.1227 + -259.38401 + -260.74831 + -262.03991 + -263.5463 + -264.70486 + -267.69144 + -267.88682 + -269.03519 + -270.60187 + -270.65382 + -270.74279 + -271.55883 + -271.81248 + -271.87529 + -273.01494 + -273.23948 + -273.28719 + -273.35272 + -273.41591 + -273.46274 + -273.54755 + -273.58318 + -273.73111 + -273.75754 +Loop time of 39.4155 on 1 procs for 65 steps with 32 atoms + +1582.4% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -247.460020579 -273.731112592 -273.757543461 + Force two-norm initial, final = 201.608 9.43485 + Force max component initial, final = 188.924 2.41297 + Final line search alpha, max atom move = 0.000223273 0.00053875 + Iterations, force evaluations = 65 65 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.00 +Bond | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00 +Neigh | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00 +Comm | 0.00026107 | 0.00026107 | 0.00026107 | 0.0 | 0.00 +Output | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.00 +Modify | 39.412 | 39.412 | 39.412 | 0.0 | 99.99 +Other | | 0.00127 | | | 0.00 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 48 ave 48 max 48 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 48 +Ave neighs/atom = 1.5 +Ave special neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:40 diff --git a/examples/latte/log.21Jun18.latte.multiple.g++.1 b/examples/latte/log.21Jun18.latte.multiple.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..2c624e4371277f587328241857e38a7e354e719a --- /dev/null +++ b/examples/latte/log.21Jun18.latte.multiple.g++.1 @@ -0,0 +1,171 @@ +LAMMPS (22 Jun 2018) +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes +Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 336.53107 -105.96027 -104.95977 97996.851 +Loop time of 0.912921 on 1 procs for 10 steps with 24 atoms + +Performance: 0.237 ns/day, 101.436 hours/ns, 10.954 timesteps/s +6614.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00 +Bond | 3.8862e-05 | 3.8862e-05 | 3.8862e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00036955 | 0.00036955 | 0.00036955 | 0.0 | 0.04 +Output | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.01 +Modify | 0.91199 | 0.91199 | 0.91199 | 0.0 | 99.90 +Other | | 0.0003812 | | | 0.04 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 1.54167 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# Clear up previus calculation + +clear + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 + triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 20 13 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes +Step Temp PotEng TotEng Press + 0 0 -23.980353 -23.980353 348.02716 + 10 19.123149 -23.990297 -23.98041 18.774332 +Loop time of 0.0415399 on 1 procs for 10 steps with 5 atoms + +Performance: 5.200 ns/day, 4.616 hours/ns, 240.732 timesteps/s +6674.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.722e-06 | 5.722e-06 | 5.722e-06 | 0.0 | 0.01 +Bond | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.02 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.04 +Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.05 +Modify | 0.041394 | 0.041394 | 0.041394 | 0.0 | 99.65 +Other | | 9.322e-05 | | | 0.22 + +Nlocal: 5 ave 5 max 5 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7 ave 7 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10 +Ave neighs/atom = 2 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/latte/log.21Jun18.latte.sucrose.g++.1 b/examples/latte/log.21Jun18.latte.sucrose.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..cb4526587cccc40da331b1dceed633550e87158f --- /dev/null +++ b/examples/latte/log.21Jun18.latte.sucrose.g++.1 @@ -0,0 +1,103 @@ +LAMMPS (11 May 2018) +# simple sucrose model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.sucrose + orthogonal box = (0 0 0) to (17.203 18.009 21.643) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 45 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 18 19 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.5064 | 0.5064 | 0.5064 Mbytes +Step Temp PotEng TotEng Press + 0 0 -251.26617 -251.26617 16.617234 + 10 0.025263709 -251.26631 -251.26617 8.0576708 + 20 0.034232467 -251.26636 -251.26617 1.6673442 + 30 0.059079556 -251.2665 -251.26617 11.058458 + 40 0.055499766 -251.26648 -251.26617 14.837775 + 50 0.058499509 -251.2665 -251.26617 6.7183113 + 60 0.071094535 -251.26657 -251.26617 6.6133687 + 70 0.084309439 -251.26665 -251.26617 12.372721 + 80 0.1089929 -251.26679 -251.26617 8.8355516 + 90 0.11378257 -251.26681 -251.26617 5.1177922 + 100 0.13003966 -251.26691 -251.26617 8.2431185 +Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms + +Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s +1799.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00 +Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00 +Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 +Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00 +Other | | 0.0005403 | | | 0.00 + +Nlocal: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 59 ave 59 max 59 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 59 +Ave neighs/atom = 1.31111 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:28 diff --git a/examples/latte/log.21Jun18.latte.water.g++.1 b/examples/latte/log.21Jun18.latte.water.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..0decce1f985aa32cd18220ae15f9ca07373748ef --- /dev/null +++ b/examples/latte/log.21Jun18.latte.water.g++.1 @@ -0,0 +1,103 @@ +LAMMPS (11 May 2018) +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes +Step Temp PotEng TotEng Press + 0 0 -104.95594 -104.95594 48236.006 + 10 336.5303 -105.96026 -104.95976 97997.303 + 20 529.06385 -106.53021 -104.95731 131520.49 + 30 753.62616 -107.1995 -104.95898 49297.371 + 40 716.6565 -107.08802 -104.95741 28307.272 + 50 824.04417 -107.40822 -104.95835 102167.48 + 60 933.56056 -107.73478 -104.95932 92508.792 + 70 851.18518 -107.48766 -104.95711 13993.28 + 80 999.80265 -107.93146 -104.95906 36700.417 + 90 998.77707 -107.92569 -104.95634 107233.7 + 100 1281.4446 -108.76961 -104.95989 49703.193 +Loop time of 10.6388 on 1 procs for 100 steps with 24 atoms + +Performance: 0.203 ns/day, 118.209 hours/ns, 9.400 timesteps/s +6459.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.6771e-05 | 7.6771e-05 | 7.6771e-05 | 0.0 | 0.00 +Bond | 7.5817e-05 | 7.5817e-05 | 7.5817e-05 | 0.0 | 0.00 +Neigh | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 +Comm | 0.00031829 | 0.00031829 | 0.00031829 | 0.0 | 0.00 +Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 +Modify | 10.637 | 10.637 | 10.637 | 0.0 | 99.99 +Other | | 0.00052 | | | 0.00 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 77 ave 77 max 77 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31 ave 31 max 31 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31 +Ave neighs/atom = 1.29167 +Ave special neighs/atom = 0 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:10 diff --git a/examples/latte/log.21Jun18.latte.water.min.g++.1 b/examples/latte/log.21Jun18.latte.water.min.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..1c8921fd60cdb482ffb3650e14bb3250ee83e011 --- /dev/null +++ b/examples/latte/log.21Jun18.latte.water.min.g++.1 @@ -0,0 +1,108 @@ +LAMMPS (11 May 2018) +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# minimization + +thermo 10 + +min_style fire +minimize 1.0e-4 1.0e-4 500 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes +Step Temp PotEng TotEng Press + 0 0 -104.95594 -104.95594 48236.006 + 10 349.4534 -105.50948 -104.47056 62157.729 + 20 1253.6636 -107.00863 -103.28151 116456.71 + 30 134.64051 -107.56155 -107.16127 59864.196 + 40 2.4044989 -108.1527 -108.14556 32695.648 + 47 137.26885 -108.30413 -107.89603 60177.442 +Loop time of 6.42677 on 1 procs for 47 steps with 24 atoms + +6481.9% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -104.955944301 -108.302982895 -108.304126127 + Force two-norm initial, final = 19.119 3.44609 + Force max component initial, final = 11.7758 1.3408 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 47 47 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 | 0.0 | 0.00 +Bond | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00014353 | 0.00014353 | 0.00014353 | 0.0 | 0.00 +Output | 0.00012302 | 0.00012302 | 0.00012302 | 0.0 | 0.00 +Modify | 6.426 | 6.426 | 6.426 | 0.0 | 99.99 +Other | | 0.0004699 | | | 0.01 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 1.54167 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/rigid/in.rigid-atomfile b/examples/rigid/in.rigid.atomfile similarity index 100% rename from examples/rigid/in.rigid-atomfile rename to examples/rigid/in.rigid.atomfile diff --git a/examples/rigid/in.rigid-atomvar b/examples/rigid/in.rigid.atomvar similarity index 100% rename from examples/rigid/in.rigid-atomvar rename to examples/rigid/in.rigid.atomvar diff --git a/examples/rigid/in.rigid.early b/examples/rigid/in.rigid.early new file mode 100644 index 0000000000000000000000000000000000000000..6f04ba40f4fb3ca879f9955c964cdc7716014656 --- /dev/null +++ b/examples/rigid/in.rigid.early @@ -0,0 +1,83 @@ +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +group clump2 id <> 10 18 +group clump3 id <> 19 27 +group clump4 id <> 28 36 +group clump5 id <> 37 45 +group clump6 id <> 46 54 +group clump7 id <> 55 63 +group clump8 id <> 64 72 +group clump9 id <> 73 81 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 & + clump6 clump7 clump8 clump9 + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & +# clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/in.rigid.nve b/examples/rigid/in.rigid.nve new file mode 100644 index 0000000000000000000000000000000000000000..d61cdecfe8ac021110939746c5d908fe741d7523 --- /dev/null +++ b/examples/rigid/in.rigid.nve @@ -0,0 +1,81 @@ +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +group clump2 id <> 10 18 +group clump3 id <> 19 27 +group clump4 id <> 28 36 +group clump5 id <> 37 45 +group clump6 id <> 46 54 +group clump7 id <> 55 63 +group clump8 id <> 64 72 +group clump9 id <> 73 81 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 & + clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & +# clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/in.rigid.nve.early b/examples/rigid/in.rigid.nve.early new file mode 100644 index 0000000000000000000000000000000000000000..86e970ee75151de0d51f253585b80b9dc2a081f0 --- /dev/null +++ b/examples/rigid/in.rigid.nve.early @@ -0,0 +1,83 @@ +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +group clump2 id <> 10 18 +group clump3 id <> 19 27 +group clump4 id <> 28 36 +group clump5 id <> 37 45 +group clump6 id <> 46 54 +group clump7 id <> 55 63 +group clump8 id <> 64 72 +group clump9 id <> 73 81 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 & + clump6 clump7 clump8 clump9 + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & +# clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/in.rigid-property b/examples/rigid/in.rigid.property similarity index 100% rename from examples/rigid/in.rigid-property rename to examples/rigid/in.rigid.property diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.1 b/examples/rigid/log.20Apr18.rigid.atomfile.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c66711c41c26e15490051359a8990e3c6fbd402b --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.atomfile.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atomfile bodies.txt +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 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+ 9750 16738.013 0.13550102 0 5269.5101 11.407246 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms + +Performance: 615179.112 tau/day, 71201.286 timesteps/s +98.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37 +Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06 +Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58 +Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70 +Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01 +Other | | 0.006017 | | | 4.28 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.4 b/examples/rigid/log.20Apr18.rigid.atomfile.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..70f86f32bbee23abe600df2cf540dd2624d5292e --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.atomfile.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atomfile bodies.txt +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 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12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 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12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589887 0 5269.4979 12.062708 + 9750 16738.013 0.135501 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms + +Performance: 451214.099 tau/day, 52223.854 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91 +Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27 +Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59 +Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38 +Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82 +Other | | 0.009611 | | | 5.02 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.1 b/examples/rigid/log.20Apr18.rigid.atomvar.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..99098d04d21db9221011b9f511c469eb180e213f --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.atomvar.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589893 0 5269.4979 12.062708 + 9750 16738.013 0.13550102 0 5269.5101 11.407246 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms + +Performance: 621477.474 tau/day, 71930.263 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40 +Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59 +Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57 +Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73 +Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24 +Other | | 0.006207 | | | 4.46 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.4 b/examples/rigid/log.20Apr18.rigid.atomvar.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..76344d09952c3346a80847688e6398edebf5d765 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.atomvar.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9) +fix 1 all rigid custom v_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589887 0 5269.4979 12.062708 + 9750 16738.013 0.135501 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.202733 on 4 procs for 10000 steps with 81 atoms + +Performance: 426175.966 tau/day, 49325.922 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0025222 | 0.0037088 | 0.0044038 | 1.2 | 1.83 +Neigh | 0.01135 | 0.012003 | 0.013654 | 0.9 | 5.92 +Comm | 0.088217 | 0.089948 | 0.091659 | 0.4 | 44.37 +Output | 0.0044014 | 0.0047023 | 0.0055132 | 0.7 | 2.32 +Modify | 0.080218 | 0.082638 | 0.084872 | 0.6 | 40.76 +Other | | 0.009733 | | | 4.80 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.1 b/examples/rigid/log.20Apr18.rigid.early.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..5402647b9814753bbcfd831d54d12823586a59f1 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.early.g++.1 @@ -0,0 +1,337 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589893 0 5269.4979 12.062708 + 9750 16738.013 0.13550102 0 5269.5101 11.407246 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.142284 on 1 procs for 10000 steps with 81 atoms + +Performance: 607236.588 tau/day, 70282.013 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010693 | 0.010693 | 0.010693 | 0.0 | 7.52 +Neigh | 0.037908 | 0.037908 | 0.037908 | 0.0 | 26.64 +Comm | 0.0087049 | 0.0087049 | 0.0087049 | 0.0 | 6.12 +Output | 0.0025849 | 0.0025849 | 0.0025849 | 0.0 | 1.82 +Modify | 0.076329 | 0.076329 | 0.076329 | 0.0 | 53.65 +Other | | 0.006064 | | | 4.26 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.4 b/examples/rigid/log.20Apr18.rigid.early.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..c9513a211e9fbc42cfb70bea162e3791cbd98abc --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.early.g++.4 @@ -0,0 +1,337 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589887 0 5269.4979 12.062708 + 9750 16738.013 0.135501 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.170899 on 4 procs for 10000 steps with 81 atoms + +Performance: 505560.431 tau/day, 58513.939 timesteps/s +96.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0024047 | 0.0038016 | 0.0044513 | 1.3 | 2.22 +Neigh | 0.011313 | 0.012043 | 0.013355 | 0.7 | 7.05 +Comm | 0.066761 | 0.069035 | 0.071617 | 0.7 | 40.40 +Output | 0.0038884 | 0.0041398 | 0.0048923 | 0.7 | 2.42 +Modify | 0.071143 | 0.072567 | 0.074478 | 0.4 | 42.46 +Other | | 0.009313 | | | 5.45 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.5Oct16.rigid.g++.4 b/examples/rigid/log.20Apr18.rigid.g++.1 similarity index 91% rename from examples/rigid/log.5Oct16.rigid.g++.4 rename to examples/rigid/log.20Apr18.rigid.g++.1 index 968f3a2d99bab33a911e22007e3ebc8548aba0ab..ca76376e320f83b2172b8d71b901e500c6b9314f 100644 --- a/examples/rigid/log.5Oct16.rigid.g++.4 +++ b/examples/rigid/log.20Apr18.rigid.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task # Simple rigid body system units lj @@ -8,7 +9,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 81 atoms @@ -91,13 +92,18 @@ timestep 0.0001 thermo 50 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 18 18 18 -Memory usage per processor = 3.62803 Mbytes + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -151,7 +157,7 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 + 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 2650 16733.017 1.705148 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 @@ -173,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press 3550 16713.405 7.846062 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3700 16738.602 -0.070934367 0 5269.4889 12.025288 3750 16737.731 0.20706557 0 5269.4927 12.061948 3800 16738.578 -0.05582043 0 5269.4965 12.035665 3850 16738.471 -0.016307928 0 5269.5024 12.035302 @@ -269,7 +275,7 @@ Step Temp E_pair E_mol TotEng Press 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -290,37 +296,37 @@ Step Temp E_pair E_mol TotEng Press 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 + 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 9600 16738.549 -0.026814371 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589894 0 5269.4979 12.062708 - 9750 16738.013 0.13550109 0 5269.5101 11.407246 - 9800 16738.512 -0.011620327 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 + 9700 16735.041 1.0589893 0 5269.4979 12.062708 + 9750 16738.013 0.13550102 0 5269.5101 11.407246 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.169479 on 4 procs for 10000 steps with 81 atoms +Loop time of 0.155936 on 1 procs for 10000 steps with 81 atoms -Performance: 509796.561 tau/day, 59004.232 timesteps/s -98.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 554075.151 tau/day, 64129.068 timesteps/s +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0024633 | 0.0031875 | 0.0039403 | 0.9 | 1.88 -Neigh | 0.010975 | 0.011817 | 0.013459 | 0.9 | 6.97 -Comm | 0.072126 | 0.074024 | 0.076456 | 0.7 | 43.68 -Output | 0.0034711 | 0.0036327 | 0.0040615 | 0.4 | 2.14 -Modify | 0.069286 | 0.070574 | 0.073233 | 0.6 | 41.64 -Other | | 0.006244 | | | 3.68 +Pair | 0.013007 | 0.013007 | 0.013007 | 0.0 | 8.34 +Neigh | 0.041885 | 0.041885 | 0.041885 | 0.0 | 26.86 +Comm | 0.0094752 | 0.0094752 | 0.0094752 | 0.0 | 6.08 +Output | 0.002636 | 0.002636 | 0.002636 | 0.0 | 1.69 +Modify | 0.082249 | 0.082249 | 0.082249 | 0.0 | 52.75 +Other | | 0.006683 | | | 4.29 -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.5Oct16.rigid.g++.1 b/examples/rigid/log.20Apr18.rigid.g++.4 similarity index 89% rename from examples/rigid/log.5Oct16.rigid.g++.1 rename to examples/rigid/log.20Apr18.rigid.g++.4 index 9b84f89c95e3182a0875dedd6ef0d13aa131af08..ff72c213edb53af7c1d29d67f70410453e144ca6 100644 --- a/examples/rigid/log.5Oct16.rigid.g++.1 +++ b/examples/rigid/log.20Apr18.rigid.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task # Simple rigid body system units lj @@ -8,7 +9,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid reading atoms ... 81 atoms @@ -91,13 +92,18 @@ timestep 0.0001 thermo 50 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 18 18 18 -Memory usage per processor = 3.65531 Mbytes + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -151,8 +157,8 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 - 2650 16733.017 1.7051479 0 5269.5067 14.596295 + 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 2800 16738.585 -0.046813448 0 5269.5076 14.511073 @@ -160,7 +166,7 @@ Step Temp E_pair E_mol TotEng Press 2900 16738.465 -0.0026252725 0 5269.514 14.510277 2950 16738.476 -0.0082220764 0 5269.512 14.510223 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419352 0 5269.476 14.870305 + 3050 16715.332 7.2419351 0 5269.476 14.870305 3100 16653.226 26.818761 0 5269.5009 14.496764 3150 16739.351 -0.30690375 0 5269.4886 13.643904 3200 16733.238 1.6025328 0 5269.4737 12.016934 @@ -170,7 +176,7 @@ Step Temp E_pair E_mol TotEng Press 3400 16738.543 -0.042215005 0 5269.4991 12.092809 3450 16738.591 -0.059327511 0 5269.4972 12.092536 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.8460621 0 5269.4737 12.389816 + 3550 16713.405 7.846062 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 3700 16738.602 -0.070934368 0 5269.4889 12.025288 @@ -268,8 +274,8 @@ Step Temp E_pair E_mol TotEng Press 8300 16738.471 0 0 5269.5187 12.011719 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -289,38 +295,38 @@ Step Temp E_pair E_mol TotEng Press 9350 16738.48 0 0 5269.5214 12.011744 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 - 9550 16738.493 -0.005315616 0 5269.5203 12.011611 - 9600 16738.549 -0.026814368 0 5269.5163 12.011415 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589885 0 5269.4979 12.062708 - 9750 16738.013 0.13550123 0 5269.5101 11.407245 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 + 9700 16735.041 1.0589887 0 5269.4979 12.062708 + 9750 16738.013 0.135501 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.125672 on 1 procs for 10000 steps with 81 atoms +Loop time of 0.194532 on 4 procs for 10000 steps with 81 atoms -Performance: 687503.421 tau/day, 79572.155 timesteps/s -100.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 444142.918 tau/day, 51405.430 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0097554 | 0.0097554 | 0.0097554 | 0.0 | 7.76 -Neigh | 0.038657 | 0.038657 | 0.038657 | 0.0 | 30.76 -Comm | 0.0074 | 0.0074 | 0.0074 | 0.0 | 5.89 -Output | 0.0010791 | 0.0010791 | 0.0010791 | 0.0 | 0.86 -Modify | 0.064604 | 0.064604 | 0.064604 | 0.0 | 51.41 -Other | | 0.004176 | | | 3.32 +Pair | 0.0025368 | 0.003831 | 0.0045376 | 1.2 | 1.97 +Neigh | 0.011299 | 0.012014 | 0.013005 | 0.6 | 6.18 +Comm | 0.081939 | 0.084112 | 0.087817 | 0.8 | 43.24 +Output | 0.0044608 | 0.0047221 | 0.0053811 | 0.6 | 2.43 +Modify | 0.078212 | 0.080219 | 0.082467 | 0.7 | 41.24 +Other | | 0.009634 | | | 4.95 -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.1 b/examples/rigid/log.20Apr18.rigid.nve.early.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..7e92b4e6ef4efd96d7d3e1077f54cfc42e36a93c --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.nve.early.g++.1 @@ -0,0 +1,337 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 + 3450 16738.489 -0.021623738 0 5269.5026 13.308001 + 3500 16737.78 0.19719043 0 5269.4983 13.325999 + 3550 16658.578 25.116206 0 5269.4834 13.778249 + 3600 16738.51 -0.032864725 0 5269.4981 12.392389 + 3650 16738.899 -0.15952703 0 5269.4938 12.383503 + 3700 16738.879 -0.16025994 0 5269.487 12.382575 + 3750 16738.878 -0.16608251 0 5269.4806 12.382765 + 3800 16738.591 -0.078679341 0 5269.4776 12.383227 + 3850 16738.429 -0.024729409 0 5269.4807 12.382942 + 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 + 3950 16738.428 -0.002521266 0 5269.5027 12.383324 + 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 + 4050 16738.488 0 0 5269.5241 12.383531 + 4100 16738.468 0 0 5269.5178 12.383482 + 4150 16738.422 0 0 5269.5033 12.383369 + 4200 16738.387 0 0 5269.4921 12.383281 + 4250 16738.383 0 0 5269.4908 12.38327 + 4300 16738.4 0 0 5269.4964 12.383314 + 4350 16738.423 0 0 5269.5036 12.38337 + 4400 16738.441 0 0 5269.5092 12.383414 + 4450 16738.45 0 0 5269.5121 12.383437 + 4500 16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.048521421 0 5269.4761 12.385777 + 4800 16735.057 1.0347219 0 5269.4786 12.43543 + 4850 16735.441 0.92650928 0 5269.4913 12.418653 + 4900 16723.839 4.5908971 0 5269.5033 13.410103 + 4950 16738.531 -0.021537669 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589693 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692474 0 5269.4987 13.090038 + 5100 16738.404 0 0 5269.4976 13.090032 + 5150 16738.421 0 0 5269.5029 13.090073 + 5200 16738.44 0 0 5269.5087 13.090119 + 5250 16738.448 -0.0012793921 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376397 0 5269.5075 13.090026 + 5350 16738.479 -0.020383842 0 5269.5007 13.089898 + 5400 16735.845 0.79889481 0 5269.4909 13.136244 + 5450 16735.558 0.87619898 0 5269.4778 12.324482 + 5500 16711.494 8.47243 0 5269.4984 12.65658 + 5550 16454.525 89.074845 0 5269.2031 16.996503 + 5600 16713.084 7.9801091 0 5269.5065 13.774971 + 5650 16738.676 -0.079987812 0 5269.5033 13.168292 + 5700 16446.281 91.866085 0 5269.399 23.764658 + 5750 16738.549 -0.039869082 0 5269.5034 13.378117 + 5800 16738.487 -0.014994464 0 5269.5086 13.378394 + 5850 16738.466 -0.0051267378 0 5269.512 13.378555 + 5900 16738.462 -0.0043689966 0 5269.5113 13.378568 + 5950 16738.528 -0.032727396 0 5269.5039 13.378192 + 6000 16702.774 10.969422 0 5269.2502 13.788847 + 6050 16682.271 17.483217 0 5269.3092 13.353098 + 6100 16738.508 -0.028838289 0 5269.5016 12.521077 + 6150 16738.425 -0.0067595568 0 5269.4974 12.521216 + 6200 16738.401 -0.0011499904 0 5269.4955 12.521247 + 6250 16738.455 0 0 5269.5136 12.521403 + 6300 16738.523 0 0 5269.5352 12.521573 + 6350 16738.503 0 0 5269.5287 12.521525 + 6400 16738.427 0 0 5269.5047 12.521337 + 6450 16738.399 0 0 5269.496 12.521268 + 6500 16738.425 0 0 5269.5042 12.521331 + 6550 16738.441 0 0 5269.5093 12.521372 + 6600 16738.42 0 0 5269.5025 12.521319 + 6650 16738.398 0 0 5269.4957 12.521266 + 6700 16738.435 0 0 5269.5074 12.521355 + 6750 16738.505 0 0 5269.5293 12.521527 + 6800 16738.508 0 0 5269.5303 12.521536 + 6850 16738.446 0 0 5269.5108 12.521384 + 6900 16738.414 0 0 5269.5009 12.521306 + 6950 16738.432 0 0 5269.5063 12.521348 + 7000 16738.444 0 0 5269.5102 12.521378 + 7050 16738.421 0 0 5269.5029 12.521322 + 7100 16738.393 0 0 5269.4941 12.521253 + 7150 16738.419 0 0 5269.5022 12.521315 + 7200 16738.489 0 0 5269.5244 12.521489 + 7250 16738.505 0 0 5269.5293 12.521528 + 7300 16738.443 0 0 5269.5098 12.521376 + 7350 16738.404 0 0 5269.4976 12.521281 + 7400 16738.43 0 0 5269.5058 12.521343 + 7450 16738.461 0 0 5269.5156 12.521421 + 7500 16738.447 0 0 5269.5109 12.521385 + 7550 16738.407 0 0 5269.4986 12.521288 + 7600 16738.412 0 0 5269.5002 12.5213 + 7650 16738.478 0 0 5269.5208 12.52146 + 7700 16738.51 0 0 5269.5309 12.521541 + 7750 16738.454 0 0 5269.5135 12.521405 + 7800 16738.398 0 0 5269.4958 12.521267 + 7850 16738.407 -0.0002118068 0 5269.4982 12.521283 + 7900 16738.441 -0.00021679441 0 5269.509 12.521366 + 7950 16738.446 -0.00023847865 0 5269.5107 12.52138 + 8000 16738.423 0 0 5269.5035 12.521326 + 8050 16738.423 0 0 5269.5034 12.521325 + 8100 16738.478 -0.00069624411 0 5269.52 12.521447 + 8150 16738.523 -0.0040058094 0 5269.531 12.521494 + 8200 16738.486 -0.0092298399 0 5269.5142 12.521327 + 8250 16738.458 -0.023189572 0 5269.4914 12.521008 + 8300 16738.513 -0.045847775 0 5269.4861 12.520773 + 8350 16723.734 4.5722877 0 5269.4516 12.849562 + 8400 16738.466 -0.020202622 0 5269.497 12.835807 + 8450 16738.437 -0.012822209 0 5269.4952 12.829975 + 8500 16738.408 -0.001683355 0 5269.4972 12.8301 + 8550 16738.464 -0.00097382251 0 5269.5155 12.830254 + 8600 16738.669 -0.050581166 0 5269.5304 12.829973 + 8650 15918.256 250.07455 0 5261.3774 24.539208 + 8700 16738.446 0.00084613367 0 5269.5116 10.591358 + 8750 16738.472 -0.010145611 0 5269.5089 10.590277 + 8800 16738.468 0 0 5269.5176 10.590497 + 8850 16738.508 0 0 5269.5303 10.590596 + 8900 16738.509 0 0 5269.5306 10.590599 + 8950 16738.496 0 0 5269.5266 10.590568 + 9000 16738.477 0 0 5269.5204 10.59052 + 9050 16738.455 0 0 5269.5135 10.590465 + 9100 16738.477 0 0 5269.5205 10.590519 + 9150 16738.512 0 0 5269.5315 10.590606 + 9200 16738.502 0 0 5269.5285 10.590583 + 9250 16738.493 0 0 5269.5254 10.590559 + 9300 16738.482 0 0 5269.522 10.590532 + 9350 16738.46 0 0 5269.5151 10.590478 + 9400 16738.48 0 0 5269.5216 10.590528 + 9450 16738.509 0 0 5269.5306 10.590599 + 9500 16738.49 0 0 5269.5247 10.590554 + 9550 16738.484 0 0 5269.5226 10.590536 + 9600 16738.483 0 0 5269.5223 10.590534 + 9650 16738.464 0 0 5269.5165 10.590489 + 9700 16738.484 0 0 5269.5228 10.590537 + 9750 16738.507 0 0 5269.53 10.590595 + 9800 16738.482 0 0 5269.522 10.590532 + 9850 16738.478 0 0 5269.5207 10.590521 + 9900 16738.487 -0.00030979882 0 5269.5233 10.590538 + 9950 16738.476 -0.00095967357 0 5269.5193 10.590496 + 10000 16738.494 -0.00062714625 0 5269.5253 10.590548 +Loop time of 0.166298 on 1 procs for 10000 steps with 81 atoms + +Performance: 519549.516 tau/day, 60133.046 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.011685 | 0.011685 | 0.011685 | 0.0 | 7.03 +Neigh | 0.038539 | 0.038539 | 0.038539 | 0.0 | 23.17 +Comm | 0.0086315 | 0.0086315 | 0.0086315 | 0.0 | 5.19 +Output | 0.0026531 | 0.0026531 | 0.0026531 | 0.0 | 1.60 +Modify | 0.098759 | 0.098759 | 0.098759 | 0.0 | 59.39 +Other | | 0.00603 | | | 3.63 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 49 ave 49 max 49 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.4 b/examples/rigid/log.20Apr18.rigid.nve.early.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..1c3592990bbae7b9871d3557490358b33bd2dcb9 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.nve.early.g++.4 @@ -0,0 +1,337 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +fix_modify 1 bodyforces early + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 + 3450 16738.489 -0.021623738 0 5269.5026 13.308001 + 3500 16737.78 0.19719043 0 5269.4983 13.325999 + 3550 16658.578 25.116206 0 5269.4834 13.778249 + 3600 16738.51 -0.032864725 0 5269.4981 12.392389 + 3650 16738.899 -0.15952703 0 5269.4938 12.383503 + 3700 16738.879 -0.16025994 0 5269.487 12.382575 + 3750 16738.878 -0.16608251 0 5269.4806 12.382765 + 3800 16738.591 -0.078679341 0 5269.4776 12.383227 + 3850 16738.429 -0.024729409 0 5269.4807 12.382942 + 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 + 3950 16738.428 -0.002521266 0 5269.5027 12.383324 + 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 + 4050 16738.488 0 0 5269.5241 12.383531 + 4100 16738.468 0 0 5269.5178 12.383482 + 4150 16738.422 0 0 5269.5033 12.383369 + 4200 16738.387 0 0 5269.4921 12.383281 + 4250 16738.383 0 0 5269.4908 12.38327 + 4300 16738.4 0 0 5269.4964 12.383314 + 4350 16738.423 0 0 5269.5036 12.38337 + 4400 16738.441 0 0 5269.5092 12.383414 + 4450 16738.45 0 0 5269.5121 12.383437 + 4500 16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.048521424 0 5269.4761 12.385777 + 4800 16735.057 1.0347218 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908973 0 5269.5033 13.410103 + 4950 16738.531 -0.021537669 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589693 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692474 0 5269.4987 13.090038 + 5100 16738.404 0 0 5269.4976 13.090032 + 5150 16738.421 0 0 5269.5029 13.090073 + 5200 16738.44 0 0 5269.5087 13.090119 + 5250 16738.448 -0.0012793921 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376396 0 5269.5075 13.090026 + 5350 16738.479 -0.020383843 0 5269.5007 13.089898 + 5400 16735.845 0.79889489 0 5269.4909 13.136244 + 5450 16735.558 0.87619907 0 5269.4778 12.324482 + 5500 16711.494 8.4724273 0 5269.4984 12.656579 + 5550 16454.525 89.074821 0 5269.2031 16.996502 + 5600 16713.084 7.9801107 0 5269.5065 13.774972 + 5650 16738.676 -0.079987805 0 5269.5033 13.168292 + 5700 16446.281 91.866085 0 5269.399 23.764659 + 5750 16738.549 -0.039869082 0 5269.5034 13.378118 + 5800 16738.487 -0.014994465 0 5269.5086 13.378394 + 5850 16738.466 -0.0051267396 0 5269.512 13.378555 + 5900 16738.462 -0.004368998 0 5269.5113 13.378568 + 5950 16738.528 -0.032727397 0 5269.5039 13.378192 + 6000 16702.774 10.969422 0 5269.2502 13.788847 + 6050 16682.271 17.483223 0 5269.3092 13.353098 + 6100 16738.508 -0.028838294 0 5269.5016 12.521077 + 6150 16738.425 -0.0067595586 0 5269.4974 12.521216 + 6200 16738.401 -0.0011499906 0 5269.4955 12.521248 + 6250 16738.455 0 0 5269.5136 12.521404 + 6300 16738.523 0 0 5269.5352 12.521573 + 6350 16738.503 0 0 5269.5287 12.521525 + 6400 16738.427 0 0 5269.5047 12.521337 + 6450 16738.399 0 0 5269.496 12.521268 + 6500 16738.425 0 0 5269.5042 12.521331 + 6550 16738.441 0 0 5269.5093 12.521372 + 6600 16738.42 0 0 5269.5025 12.521319 + 6650 16738.398 0 0 5269.4957 12.521266 + 6700 16738.435 0 0 5269.5074 12.521355 + 6750 16738.505 0 0 5269.5293 12.521527 + 6800 16738.508 0 0 5269.5303 12.521536 + 6850 16738.446 0 0 5269.5108 12.521384 + 6900 16738.414 0 0 5269.5009 12.521306 + 6950 16738.432 0 0 5269.5063 12.521348 + 7000 16738.444 0 0 5269.5102 12.521379 + 7050 16738.421 0 0 5269.5029 12.521322 + 7100 16738.393 0 0 5269.4941 12.521253 + 7150 16738.419 0 0 5269.5022 12.521315 + 7200 16738.489 0 0 5269.5244 12.521489 + 7250 16738.505 0 0 5269.5293 12.521528 + 7300 16738.443 0 0 5269.5098 12.521377 + 7350 16738.404 0 0 5269.4976 12.521281 + 7400 16738.43 0 0 5269.5058 12.521344 + 7450 16738.461 0 0 5269.5156 12.521421 + 7500 16738.447 0 0 5269.5109 12.521385 + 7550 16738.407 0 0 5269.4986 12.521288 + 7600 16738.412 0 0 5269.5002 12.5213 + 7650 16738.478 0 0 5269.5208 12.521461 + 7700 16738.51 0 0 5269.5309 12.521541 + 7750 16738.454 0 0 5269.5135 12.521406 + 7800 16738.398 0 0 5269.4958 12.521267 + 7850 16738.407 -0.00021180715 0 5269.4982 12.521283 + 7900 16738.441 -0.0002167946 0 5269.509 12.521367 + 7950 16738.446 -0.0002384787 0 5269.5107 12.52138 + 8000 16738.423 0 0 5269.5035 12.521327 + 8050 16738.423 0 0 5269.5034 12.521325 + 8100 16738.478 -0.00069624484 0 5269.52 12.521448 + 8150 16738.523 -0.0040058183 0 5269.531 12.521494 + 8200 16738.486 -0.0092298512 0 5269.5142 12.521328 + 8250 16738.458 -0.023189661 0 5269.4914 12.521008 + 8300 16738.513 -0.045847765 0 5269.4861 12.520773 + 8350 16723.735 4.5720344 0 5269.4516 12.849543 + 8400 16738.466 -0.02019859 0 5269.497 12.835812 + 8450 16738.437 -0.012822198 0 5269.4952 12.829979 + 8500 16738.408 -0.0016833646 0 5269.4972 12.830104 + 8550 16738.464 -0.00097382606 0 5269.5155 12.830258 + 8600 16738.669 -0.050581176 0 5269.5304 12.829977 + 8650 15918.073 250.131 0 5261.3761 24.542327 + 8700 16738.446 0.00085039409 0 5269.5116 10.59114 + 8750 16738.472 -0.010146632 0 5269.5089 10.590059 + 8800 16738.468 0 0 5269.5176 10.590278 + 8850 16738.508 0 0 5269.5303 10.590378 + 8900 16738.509 0 0 5269.5306 10.590381 + 8950 16738.496 0 0 5269.5266 10.590349 + 9000 16738.477 0 0 5269.5204 10.590302 + 9050 16738.455 0 0 5269.5135 10.590247 + 9100 16738.477 0 0 5269.5205 10.590301 + 9150 16738.512 0 0 5269.5315 10.590388 + 9200 16738.502 0 0 5269.5285 10.590364 + 9250 16738.493 0 0 5269.5254 10.59034 + 9300 16738.482 0 0 5269.522 10.590314 + 9350 16738.46 0 0 5269.5151 10.59026 + 9400 16738.48 0 0 5269.5216 10.59031 + 9450 16738.509 0 0 5269.5306 10.590381 + 9500 16738.49 0 0 5269.5247 10.590335 + 9550 16738.484 0 0 5269.5226 10.590318 + 9600 16738.483 0 0 5269.5223 10.590316 + 9650 16738.464 0 0 5269.5165 10.590271 + 9700 16738.484 0 0 5269.5228 10.590319 + 9750 16738.507 0 0 5269.53 10.590376 + 9800 16738.482 0 0 5269.522 10.590314 + 9850 16738.478 0 0 5269.5207 10.590303 + 9900 16738.487 -0.00030979874 0 5269.5233 10.59032 + 9950 16738.476 -0.00095967134 0 5269.5192 10.590278 + 10000 16738.494 -0.00062714318 0 5269.5253 10.590329 +Loop time of 0.224811 on 4 procs for 10000 steps with 81 atoms + +Performance: 384323.005 tau/day, 44481.829 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0032673 | 0.0039269 | 0.0048387 | 1.1 | 1.75 +Neigh | 0.010401 | 0.012159 | 0.015022 | 1.6 | 5.41 +Comm | 0.087584 | 0.08909 | 0.090645 | 0.4 | 39.63 +Output | 0.0042956 | 0.0045624 | 0.0052695 | 0.6 | 2.03 +Modify | 0.10208 | 0.10506 | 0.10697 | 0.6 | 46.73 +Other | | 0.01001 | | | 4.45 + +Nlocal: 20.25 ave 34 max 9 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 38.5 ave 43 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0.75 ave 2 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.1 b/examples/rigid/log.20Apr18.rigid.nve.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..26fa4e7f680fb2a016cb0ea0c4ec195855ca4224 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.nve.g++.1 @@ -0,0 +1,335 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 + 3450 16738.489 -0.021623738 0 5269.5026 13.308001 + 3500 16737.78 0.19719043 0 5269.4983 13.325999 + 3550 16658.578 25.116206 0 5269.4834 13.778249 + 3600 16738.51 -0.032864725 0 5269.4981 12.392389 + 3650 16738.899 -0.15952703 0 5269.4938 12.383503 + 3700 16738.879 -0.16025994 0 5269.487 12.382575 + 3750 16738.878 -0.16608251 0 5269.4806 12.382765 + 3800 16738.591 -0.078679341 0 5269.4776 12.383227 + 3850 16738.429 -0.024729409 0 5269.4807 12.382942 + 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 + 3950 16738.428 -0.002521266 0 5269.5027 12.383324 + 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 + 4050 16738.488 0 0 5269.5241 12.383531 + 4100 16738.468 0 0 5269.5178 12.383482 + 4150 16738.422 0 0 5269.5033 12.383369 + 4200 16738.387 0 0 5269.4921 12.383281 + 4250 16738.383 0 0 5269.4908 12.38327 + 4300 16738.4 0 0 5269.4964 12.383314 + 4350 16738.423 0 0 5269.5036 12.38337 + 4400 16738.441 0 0 5269.5092 12.383414 + 4450 16738.45 0 0 5269.5121 12.383437 + 4500 16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.048521421 0 5269.4761 12.385777 + 4800 16735.057 1.0347219 0 5269.4786 12.43543 + 4850 16735.441 0.92650928 0 5269.4913 12.418653 + 4900 16723.839 4.5908971 0 5269.5033 13.410103 + 4950 16738.531 -0.021537669 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589693 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692474 0 5269.4987 13.090038 + 5100 16738.404 0 0 5269.4976 13.090032 + 5150 16738.421 0 0 5269.5029 13.090073 + 5200 16738.44 0 0 5269.5087 13.090119 + 5250 16738.448 -0.0012793921 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376397 0 5269.5075 13.090026 + 5350 16738.479 -0.020383842 0 5269.5007 13.089898 + 5400 16735.845 0.79889481 0 5269.4909 13.136244 + 5450 16735.558 0.87619898 0 5269.4778 12.324482 + 5500 16711.494 8.47243 0 5269.4984 12.65658 + 5550 16454.525 89.074845 0 5269.2031 16.996503 + 5600 16713.084 7.9801091 0 5269.5065 13.774971 + 5650 16738.676 -0.079987812 0 5269.5033 13.168292 + 5700 16446.281 91.866085 0 5269.399 23.764658 + 5750 16738.549 -0.039869082 0 5269.5034 13.378117 + 5800 16738.487 -0.014994464 0 5269.5086 13.378394 + 5850 16738.466 -0.0051267378 0 5269.512 13.378555 + 5900 16738.462 -0.0043689966 0 5269.5113 13.378568 + 5950 16738.528 -0.032727396 0 5269.5039 13.378192 + 6000 16702.774 10.969422 0 5269.2502 13.788847 + 6050 16682.271 17.483217 0 5269.3092 13.353098 + 6100 16738.508 -0.028838289 0 5269.5016 12.521077 + 6150 16738.425 -0.0067595568 0 5269.4974 12.521216 + 6200 16738.401 -0.0011499904 0 5269.4955 12.521247 + 6250 16738.455 0 0 5269.5136 12.521403 + 6300 16738.523 0 0 5269.5352 12.521573 + 6350 16738.503 0 0 5269.5287 12.521525 + 6400 16738.427 0 0 5269.5047 12.521337 + 6450 16738.399 0 0 5269.496 12.521268 + 6500 16738.425 0 0 5269.5042 12.521331 + 6550 16738.441 0 0 5269.5093 12.521372 + 6600 16738.42 0 0 5269.5025 12.521319 + 6650 16738.398 0 0 5269.4957 12.521266 + 6700 16738.435 0 0 5269.5074 12.521355 + 6750 16738.505 0 0 5269.5293 12.521527 + 6800 16738.508 0 0 5269.5303 12.521536 + 6850 16738.446 0 0 5269.5108 12.521384 + 6900 16738.414 0 0 5269.5009 12.521306 + 6950 16738.432 0 0 5269.5063 12.521348 + 7000 16738.444 0 0 5269.5102 12.521378 + 7050 16738.421 0 0 5269.5029 12.521322 + 7100 16738.393 0 0 5269.4941 12.521253 + 7150 16738.419 0 0 5269.5022 12.521315 + 7200 16738.489 0 0 5269.5244 12.521489 + 7250 16738.505 0 0 5269.5293 12.521528 + 7300 16738.443 0 0 5269.5098 12.521376 + 7350 16738.404 0 0 5269.4976 12.521281 + 7400 16738.43 0 0 5269.5058 12.521343 + 7450 16738.461 0 0 5269.5156 12.521421 + 7500 16738.447 0 0 5269.5109 12.521385 + 7550 16738.407 0 0 5269.4986 12.521288 + 7600 16738.412 0 0 5269.5002 12.5213 + 7650 16738.478 0 0 5269.5208 12.52146 + 7700 16738.51 0 0 5269.5309 12.521541 + 7750 16738.454 0 0 5269.5135 12.521405 + 7800 16738.398 0 0 5269.4958 12.521267 + 7850 16738.407 -0.0002118068 0 5269.4982 12.521283 + 7900 16738.441 -0.00021679441 0 5269.509 12.521366 + 7950 16738.446 -0.00023847865 0 5269.5107 12.52138 + 8000 16738.423 0 0 5269.5035 12.521326 + 8050 16738.423 0 0 5269.5034 12.521325 + 8100 16738.478 -0.00069624411 0 5269.52 12.521447 + 8150 16738.523 -0.0040058094 0 5269.531 12.521494 + 8200 16738.486 -0.0092298399 0 5269.5142 12.521327 + 8250 16738.458 -0.023189572 0 5269.4914 12.521008 + 8300 16738.513 -0.045847775 0 5269.4861 12.520773 + 8350 16723.734 4.5722877 0 5269.4516 12.849562 + 8400 16738.466 -0.020202622 0 5269.497 12.835807 + 8450 16738.437 -0.012822209 0 5269.4952 12.829975 + 8500 16738.408 -0.001683355 0 5269.4972 12.8301 + 8550 16738.464 -0.00097382251 0 5269.5155 12.830254 + 8600 16738.669 -0.050581166 0 5269.5304 12.829973 + 8650 15918.256 250.07455 0 5261.3774 24.539208 + 8700 16738.446 0.00084613367 0 5269.5116 10.591358 + 8750 16738.472 -0.010145611 0 5269.5089 10.590277 + 8800 16738.468 0 0 5269.5176 10.590497 + 8850 16738.508 0 0 5269.5303 10.590596 + 8900 16738.509 0 0 5269.5306 10.590599 + 8950 16738.496 0 0 5269.5266 10.590568 + 9000 16738.477 0 0 5269.5204 10.59052 + 9050 16738.455 0 0 5269.5135 10.590465 + 9100 16738.477 0 0 5269.5205 10.590519 + 9150 16738.512 0 0 5269.5315 10.590606 + 9200 16738.502 0 0 5269.5285 10.590583 + 9250 16738.493 0 0 5269.5254 10.590559 + 9300 16738.482 0 0 5269.522 10.590532 + 9350 16738.46 0 0 5269.5151 10.590478 + 9400 16738.48 0 0 5269.5216 10.590528 + 9450 16738.509 0 0 5269.5306 10.590599 + 9500 16738.49 0 0 5269.5247 10.590554 + 9550 16738.484 0 0 5269.5226 10.590536 + 9600 16738.483 0 0 5269.5223 10.590534 + 9650 16738.464 0 0 5269.5165 10.590489 + 9700 16738.484 0 0 5269.5228 10.590537 + 9750 16738.507 0 0 5269.53 10.590595 + 9800 16738.482 0 0 5269.522 10.590532 + 9850 16738.478 0 0 5269.5207 10.590521 + 9900 16738.487 -0.00030979882 0 5269.5233 10.590538 + 9950 16738.476 -0.00095967357 0 5269.5193 10.590496 + 10000 16738.494 -0.00062714625 0 5269.5253 10.590548 +Loop time of 0.166547 on 1 procs for 10000 steps with 81 atoms + +Performance: 518773.777 tau/day, 60043.261 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.011439 | 0.011439 | 0.011439 | 0.0 | 6.87 +Neigh | 0.038572 | 0.038572 | 0.038572 | 0.0 | 23.16 +Comm | 0.0085464 | 0.0085464 | 0.0085464 | 0.0 | 5.13 +Output | 0.0025046 | 0.0025046 | 0.0025046 | 0.0 | 1.50 +Modify | 0.099479 | 0.099479 | 0.099479 | 0.0 | 59.73 +Other | | 0.006005 | | | 3.61 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 49 ave 49 max 49 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.4 b/examples/rigid/log.20Apr18.rigid.nve.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..782457b42795a959c6a2dfbfcd003226e40bba24 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.nve.g++.4 @@ -0,0 +1,335 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.69 571.70921 0 5265.8153 32.005816 + 100 16298.128 136.75661 0 5267.6488 16.449029 + 150 16682.532 17.504156 0 5269.4124 14.901186 + 200 16733.906 1.3755079 0 5269.4571 14.571305 + 250 16738.861 -0.15272039 0 5269.4886 14.498342 + 300 16738.608 -0.055216883 0 5269.5066 14.498 + 350 16738.5 -0.017457072 0 5269.5104 14.498392 + 400 16738.451 -0.0060161309 0 5269.5063 14.49851 + 450 16738.435 -0.001271965 0 5269.5059 14.498571 + 500 16738.443 -0.00081074175 0 5269.509 14.498598 + 550 16738.452 -0.00083208965 0 5269.5118 14.498618 + 600 16738.45 -0.00058358431 0 5269.5116 14.498617 + 650 16738.443 -0.00047228525 0 5269.5093 14.4986 + 700 16738.444 0 0 5269.5102 14.498612 + 750 16738.461 0 0 5269.5157 14.498654 + 800 16738.479 0 0 5269.521 14.498697 + 850 16738.473 0 0 5269.5192 14.498683 + 900 16738.449 0 0 5269.5116 14.498624 + 950 16738.438 -0.0035324203 0 5269.5046 14.498537 + 1000 16738.562 -0.051134242 0 5269.4963 14.498093 + 1050 16737.343 0.32970192 0 5269.4934 14.527634 + 1100 16737.878 0.16213235 0 5269.4941 14.533864 + 1150 16738.682 -0.089236256 0 5269.4959 14.511765 + 1200 16738.444 -0.0075446558 0 5269.5025 14.512479 + 1250 16738.45 0 0 5269.5119 14.512611 + 1300 16738.475 0 0 5269.5199 14.512673 + 1350 16738.484 0 0 5269.5228 14.512696 + 1400 16738.469 -0.00044683992 0 5269.5175 14.512651 + 1450 16738.45 -0.0010933363 0 5269.511 14.512595 + 1500 16738.445 -0.00057484239 0 5269.51 14.512591 + 1550 16738.451 0 0 5269.5123 14.512615 + 1600 16738.452 0 0 5269.5127 14.512618 + 1650 16738.443 0 0 5269.5099 14.512596 + 1700 16738.433 0 0 5269.5068 14.512572 + 1750 16738.438 0 0 5269.5084 14.512584 + 1800 16738.459 0 0 5269.5149 14.512635 + 1850 16738.473 0 0 5269.5193 14.51267 + 1900 16738.462 0 0 5269.5159 14.512644 + 1950 16738.446 -0.0032069962 0 5269.5076 14.512539 + 2000 16738.463 -0.013425408 0 5269.5027 14.512382 + 2050 16738.535 -0.036964311 0 5269.5017 14.512152 + 2100 16738.621 -0.063490509 0 5269.5023 14.512108 + 2150 16738.594 -0.056143934 0 5269.5012 14.512117 + 2200 16738.536 -0.038486645 0 5269.5007 14.512277 + 2250 16738.496 -0.023712406 0 5269.503 14.51242 + 2300 16738.488 -0.013209094 0 5269.5109 14.51255 + 2350 16738.486 -0.0045244524 0 5269.519 14.512693 + 2400 16738.475 -0.00051678325 0 5269.5194 14.512743 + 2450 16738.456 -0.0023209272 0 5269.5115 14.512659 + 2500 16738.442 -0.0052101787 0 5269.5042 14.512594 + 2550 16738.552 -0.04420046 0 5269.4998 14.512177 + 2600 16738.42 -0.004347531 0 5269.4982 14.512783 + 2650 16734.241 1.3131302 0 5269.5 14.577195 + 2700 16738.737 -0.10612056 0 5269.4961 14.503874 + 2750 16732.705 1.7939719 0 5269.4974 14.629294 + 2800 16738.558 -0.042867033 0 5269.5032 14.519893 + 2850 16738.499 -0.01271227 0 5269.5146 14.518524 + 2900 16738.486 -0.0032778045 0 5269.52 14.518712 + 2950 16738.482 -0.0089544631 0 5269.5133 14.518629 + 3000 16738.647 -0.070862542 0 5269.5031 14.51803 + 3050 16678.313 18.829038 0 5269.409 15.533426 + 3100 16632.312 33.399217 0 5269.4975 14.588597 + 3150 16739.318 -0.31388148 0 5269.4715 13.520782 + 3200 16727.951 3.26736 0 5269.4741 12.288358 + 3250 16686.364 16.353793 0 5269.4682 14.152517 + 3300 16738.532 -0.031574462 0 5269.5064 13.310615 + 3350 16738.454 -0.0062292918 0 5269.5071 13.308187 + 3400 16738.445 -0.0049349125 0 5269.5055 13.308178 + 3450 16738.489 -0.021623738 0 5269.5026 13.308001 + 3500 16737.78 0.19719043 0 5269.4983 13.325999 + 3550 16658.578 25.116206 0 5269.4834 13.778249 + 3600 16738.51 -0.032864725 0 5269.4981 12.392389 + 3650 16738.899 -0.15952703 0 5269.4938 12.383503 + 3700 16738.879 -0.16025994 0 5269.487 12.382575 + 3750 16738.878 -0.16608251 0 5269.4806 12.382765 + 3800 16738.591 -0.078679341 0 5269.4776 12.383227 + 3850 16738.429 -0.024729409 0 5269.4807 12.382942 + 3900 16738.399 -0.0062729967 0 5269.4897 12.383192 + 3950 16738.428 -0.002521266 0 5269.5027 12.383324 + 4000 16738.467 -0.0002068506 0 5269.5173 12.383474 + 4050 16738.488 0 0 5269.5241 12.383531 + 4100 16738.468 0 0 5269.5178 12.383482 + 4150 16738.422 0 0 5269.5033 12.383369 + 4200 16738.387 0 0 5269.4921 12.383281 + 4250 16738.383 0 0 5269.4908 12.38327 + 4300 16738.4 0 0 5269.4964 12.383314 + 4350 16738.423 0 0 5269.5036 12.38337 + 4400 16738.441 0 0 5269.5092 12.383414 + 4450 16738.45 0 0 5269.5121 12.383437 + 4500 16738.45 0 0 5269.5122 12.383438 + 4550 16738.442 0 0 5269.5095 12.383417 + 4600 16738.425 0 0 5269.5042 12.383376 + 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 + 4700 16738.444 -0.024020551 0 5269.4862 12.382975 + 4750 16738.49 -0.048521424 0 5269.4761 12.385777 + 4800 16735.057 1.0347218 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908973 0 5269.5033 13.410103 + 4950 16738.531 -0.021537669 0 5269.5159 13.089982 + 5000 16738.45 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10.969422 0 5269.2502 13.788847 + 6050 16682.271 17.483223 0 5269.3092 13.353098 + 6100 16738.508 -0.028838294 0 5269.5016 12.521077 + 6150 16738.425 -0.0067595586 0 5269.4974 12.521216 + 6200 16738.401 -0.0011499906 0 5269.4955 12.521248 + 6250 16738.455 0 0 5269.5136 12.521404 + 6300 16738.523 0 0 5269.5352 12.521573 + 6350 16738.503 0 0 5269.5287 12.521525 + 6400 16738.427 0 0 5269.5047 12.521337 + 6450 16738.399 0 0 5269.496 12.521268 + 6500 16738.425 0 0 5269.5042 12.521331 + 6550 16738.441 0 0 5269.5093 12.521372 + 6600 16738.42 0 0 5269.5025 12.521319 + 6650 16738.398 0 0 5269.4957 12.521266 + 6700 16738.435 0 0 5269.5074 12.521355 + 6750 16738.505 0 0 5269.5293 12.521527 + 6800 16738.508 0 0 5269.5303 12.521536 + 6850 16738.446 0 0 5269.5108 12.521384 + 6900 16738.414 0 0 5269.5009 12.521306 + 6950 16738.432 0 0 5269.5063 12.521348 + 7000 16738.444 0 0 5269.5102 12.521379 + 7050 16738.421 0 0 5269.5029 12.521322 + 7100 16738.393 0 0 5269.4941 12.521253 + 7150 16738.419 0 0 5269.5022 12.521315 + 7200 16738.489 0 0 5269.5244 12.521489 + 7250 16738.505 0 0 5269.5293 12.521528 + 7300 16738.443 0 0 5269.5098 12.521377 + 7350 16738.404 0 0 5269.4976 12.521281 + 7400 16738.43 0 0 5269.5058 12.521344 + 7450 16738.461 0 0 5269.5156 12.521421 + 7500 16738.447 0 0 5269.5109 12.521385 + 7550 16738.407 0 0 5269.4986 12.521288 + 7600 16738.412 0 0 5269.5002 12.5213 + 7650 16738.478 0 0 5269.5208 12.521461 + 7700 16738.51 0 0 5269.5309 12.521541 + 7750 16738.454 0 0 5269.5135 12.521406 + 7800 16738.398 0 0 5269.4958 12.521267 + 7850 16738.407 -0.00021180715 0 5269.4982 12.521283 + 7900 16738.441 -0.0002167946 0 5269.509 12.521367 + 7950 16738.446 -0.0002384787 0 5269.5107 12.52138 + 8000 16738.423 0 0 5269.5035 12.521327 + 8050 16738.423 0 0 5269.5034 12.521325 + 8100 16738.478 -0.00069624484 0 5269.52 12.521448 + 8150 16738.523 -0.0040058183 0 5269.531 12.521494 + 8200 16738.486 -0.0092298512 0 5269.5142 12.521328 + 8250 16738.458 -0.023189661 0 5269.4914 12.521008 + 8300 16738.513 -0.045847765 0 5269.4861 12.520773 + 8350 16723.735 4.5720344 0 5269.4516 12.849543 + 8400 16738.466 -0.02019859 0 5269.497 12.835812 + 8450 16738.437 -0.012822198 0 5269.4952 12.829979 + 8500 16738.408 -0.0016833646 0 5269.4972 12.830104 + 8550 16738.464 -0.00097382606 0 5269.5155 12.830258 + 8600 16738.669 -0.050581176 0 5269.5304 12.829977 + 8650 15918.073 250.131 0 5261.3761 24.542327 + 8700 16738.446 0.00085039409 0 5269.5116 10.59114 + 8750 16738.472 -0.010146632 0 5269.5089 10.590059 + 8800 16738.468 0 0 5269.5176 10.590278 + 8850 16738.508 0 0 5269.5303 10.590378 + 8900 16738.509 0 0 5269.5306 10.590381 + 8950 16738.496 0 0 5269.5266 10.590349 + 9000 16738.477 0 0 5269.5204 10.590302 + 9050 16738.455 0 0 5269.5135 10.590247 + 9100 16738.477 0 0 5269.5205 10.590301 + 9150 16738.512 0 0 5269.5315 10.590388 + 9200 16738.502 0 0 5269.5285 10.590364 + 9250 16738.493 0 0 5269.5254 10.59034 + 9300 16738.482 0 0 5269.522 10.590314 + 9350 16738.46 0 0 5269.5151 10.59026 + 9400 16738.48 0 0 5269.5216 10.59031 + 9450 16738.509 0 0 5269.5306 10.590381 + 9500 16738.49 0 0 5269.5247 10.590335 + 9550 16738.484 0 0 5269.5226 10.590318 + 9600 16738.483 0 0 5269.5223 10.590316 + 9650 16738.464 0 0 5269.5165 10.590271 + 9700 16738.484 0 0 5269.5228 10.590319 + 9750 16738.507 0 0 5269.53 10.590376 + 9800 16738.482 0 0 5269.522 10.590314 + 9850 16738.478 0 0 5269.5207 10.590303 + 9900 16738.487 -0.00030979874 0 5269.5233 10.59032 + 9950 16738.476 -0.00095967134 0 5269.5192 10.590278 + 10000 16738.494 -0.00062714318 0 5269.5253 10.590329 +Loop time of 0.22441 on 4 procs for 10000 steps with 81 atoms + +Performance: 385008.767 tau/day, 44561.200 timesteps/s +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0032785 | 0.0039999 | 0.0052714 | 1.3 | 1.78 +Neigh | 0.010548 | 0.012524 | 0.016082 | 1.9 | 5.58 +Comm | 0.082771 | 0.087847 | 0.091037 | 1.1 | 39.15 +Output | 0.0042846 | 0.0045864 | 0.0054133 | 0.7 | 2.04 +Modify | 0.10401 | 0.10533 | 0.10736 | 0.4 | 46.94 +Other | | 0.01013 | | | 4.51 + +Nlocal: 20.25 ave 34 max 9 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 38.5 ave 43 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 0.75 ave 2 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 3 +Ave neighs/atom = 0.037037 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.1 b/examples/rigid/log.20Apr18.rigid.poems.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..0cba72a2dd681d8b47f54984e93b6e8b280bbcd3 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.poems.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384277 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184717 + 1150 20849.582 206.01695 0 3680.9472 -0.86699146 + 1200 21815.003 45.317414 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064078 + 1300 20780.781 217.36506 0 3680.8286 6.0538615 + 1350 20558.971 254.36482 0 3680.8601 -3.6773954 + 1400 21485.029 99.812918 0 3680.6511 -16.185473 + 1450 21771.107 52.159607 0 3680.6775 -2.4756675 + 1500 21520.948 93.503927 0 3680.3286 2.1023577 + 1550 21351.418 121.68138 0 3680.2511 5.515995 + 1600 20778.805 216.92177 0 3680.0559 15.089187 + 1650 21477.638 100.21836 0 3679.8247 -1.1045739 + 1700 18501.339 596.47922 0 3680.0357 -15.679682 + 1750 18563.642 587.3479 0 3681.2882 33.532211 + 1800 19110.186 494.82336 0 3679.8543 18.024046 + 1850 21364.191 119.23543 0 3679.9339 2.5291075 + 1900 20146.627 322.14849 0 3679.9197 5.7313175 + 1950 20692.671 231.25345 0 3680.0319 4.297772 + 2000 20943.905 189.11218 0 3679.7629 -22.64509 + 2050 19668.055 401.83025 0 3679.8394 3.6251438 + 2100 20280.434 299.76289 0 3679.8353 7.4807805 + 2150 19181.835 483.52621 0 3680.4987 22.62081 + 2200 21300.18 130.7021 0 3680.7322 4.710193 + 2250 20486.914 266.64414 0 3681.1299 -8.6458025 + 2300 18653.082 572.25481 0 3681.1017 -5.2636982 + 2350 21513.563 95.608298 0 3681.2021 -9.3624751 + 2400 21466.205 103.57569 0 3681.2765 -29.559707 + 2450 20100.204 332.25468 0 3682.2886 35.739592 + 2500 20764.513 221.64794 0 3682.4001 -12.46688 + 2550 20436.771 276.13128 0 3682.2598 -22.419404 + 2600 21466.252 104.57185 0 3682.2806 -10.080362 + 2650 20817.269 212.81674 0 3682.3615 5.1374497 + 2700 18565.157 588.46125 0 3682.6541 22.283866 + 2750 20780.743 218.76366 0 3682.2208 -8.0046411 + 2800 21032.22 176.82368 0 3682.1936 -7.078895 + 2850 16817.729 879.49153 0 3682.4464 33.140849 + 2900 19309.511 463.89319 0 3682.145 7.9225025 + 2950 20544.978 257.86831 0 3682.0314 2.0523059 + 3000 20616.438 246.0975 0 3682.1706 -0.2824889 + 3050 18648.596 574.37266 0 3682.4721 -5.8677065 + 3100 19147.135 490.76826 0 3681.9574 -1.9922835 + 3150 18568.022 587.36965 0 3682.0399 14.694505 + 3200 19720.841 395.38315 0 3682.1899 5.9162402 + 3250 19008.557 514.50687 0 3682.5998 -3.4702895 + 3300 21708.937 64.231264 0 3682.3874 -5.4808611 + 3350 20548.477 257.62974 0 3682.3759 9.7818301 + 3400 20508.84 264.0153 0 3682.1553 -12.578182 + 3450 18736.579 559.11222 0 3681.8754 21.920437 + 3500 21444.82 107.82706 0 3681.9638 0.093050651 + 3550 20439.241 275.31015 0 3681.8503 -3.0785302 + 3600 21547.1 90.778361 0 3681.9617 -5.9189729 + 3650 15623.305 1079.996 0 3683.8802 36.064752 + 3700 19912.452 363.09483 0 3681.8368 5.4802367 + 3750 21289.7 133.2258 0 3681.5091 -10.884642 + 3800 20214.875 312.09245 0 3681.2382 8.6419893 + 3850 19853.031 372.13835 0 3680.9769 2.6229234 + 3900 17863.409 703.8716 0 3681.1064 -1.4250404 + 3950 19926.351 359.87227 0 3680.9307 -14.60997 + 4000 17595.665 747.85423 0 3680.4651 24.228859 + 4050 18408.194 611.80934 0 3679.8416 4.4236034 + 4100 17506.503 762.1286 0 3679.8792 5.0526379 + 4150 18479.134 600.76034 0 3680.6159 -6.6523095 + 4200 18475.322 601.95797 0 3681.1783 1.3292995 + 4250 18301.378 630.34119 0 3680.5709 2.5387332 + 4300 19384.541 449.98455 0 3680.7414 5.8750989 + 4350 18717.888 561.31715 0 3680.9651 3.7948584 + 4400 18893.773 532.20993 0 3681.172 10.963539 + 4450 20269.613 302.15984 0 3680.4286 -10.145642 + 4500 19151.762 489.32407 0 3681.2845 21.695364 + 4550 19914.708 361.54065 0 3680.6587 -4.2298372 + 4600 21153.44 154.99598 0 3680.5693 2.3172078 + 4650 21021.611 176.81454 0 3680.4164 1.9128023 + 4700 21707.966 62.767734 0 3680.762 -5.2080189 + 4750 16517.674 927.53839 0 3680.484 17.329608 + 4800 21654.604 71.574174 0 3680.6749 -6.0650166 + 4850 18135.978 657.28622 0 3679.9493 5.4803307 + 4900 20389.048 282.49215 0 3680.6668 -2.8570431 + 4950 17159.074 820.81472 0 3680.6604 31.273877 + 5000 20788.159 215.88415 0 3680.5773 4.6345196 + 5050 21366.767 119.68693 0 3680.8148 -9.9482889 + 5100 20668.21 236.17655 0 3680.8782 3.8118334 + 5150 20468.573 269.83696 0 3681.2657 -26.625943 + 5200 19493.142 432.49135 0 3681.3483 -7.6677112 + 5250 19626.594 410.09767 0 3681.1967 7.3622341 + 5300 20771.914 219.12484 0 3681.1105 -7.0871793 + 5350 21152.459 155.26401 0 3680.6738 5.9030557 + 5400 21376.189 117.91075 0 3680.6088 -1.2004513 + 5450 21455.06 105.15166 0 3680.995 -9.1675471 + 5500 21227.896 143.35739 0 3681.3401 -6.646305 + 5550 21149.831 156.61404 0 3681.5858 -12.953136 + 5600 21364.198 120.94695 0 3681.6466 1.0372254 + 5650 20219.777 311.34588 0 3681.3088 6.5026316 + 5700 21163.024 154.3001 0 3681.4708 -0.47587262 + 5750 19583.077 418.40745 0 3682.2535 24.609517 + 5800 18801.324 548.79742 0 3682.3515 -12.082631 + 5850 20875.4 203.07604 0 3682.3093 -8.1191161 + 5900 20737.053 226.2734 0 3682.4489 -7.6845943 + 5950 21260.028 139.21888 0 3682.5568 -2.2977046 + 6000 19823.84 378.71803 0 3682.6914 -1.1163373 + 6050 20487.214 268.03474 0 3682.5704 4.313979 + 6100 17853.211 707.10918 0 3682.6443 16.762322 + 6150 21322.705 129.06 0 3682.8441 2.7500936 + 6200 21609.008 81.580972 0 3683.0823 0.37062555 + 6250 20364.115 289.30707 0 3683.3262 13.176034 + 6300 20201.9 316.16558 0 3683.149 -1.6318339 + 6350 21151.879 157.75018 0 3683.0634 -23.337621 + 6400 21453.129 107.45563 0 3682.9772 -0.60776225 + 6450 21105.382 165.1926 0 3682.7562 4.244932 + 6500 20746.748 224.6945 0 3682.4859 0.2929158 + 6550 20913.725 197.29847 0 3682.9194 -15.792862 + 6600 17956.374 690.52623 0 3683.2552 15.445255 + 6650 20270.609 303.60078 0 3682.0357 -0.26503277 + 6700 21442.931 109.08904 0 3682.9109 -2.8409166 + 6750 20907.994 198.30695 0 3682.9726 0.91664072 + 6800 20431.208 277.98326 0 3683.1845 -1.8537161 + 6850 20312.052 297.88656 0 3683.2285 3.1028547 + 6900 19458.401 439.97157 0 3683.0385 -4.1856293 + 6950 20507.759 264.99217 0 3682.952 -1.4597973 + 7000 20782.356 219.47456 0 3683.2006 -7.1967021 + 7050 20560.324 256.07109 0 3682.7917 -10.720013 + 7100 21652.145 74.086415 0 3682.7772 -0.61455054 + 7150 20134.823 326.40272 0 3682.2065 11.689827 + 7200 20778.071 219.16459 0 3682.1765 -1.796567 + 7250 20153.065 323.13721 0 3681.9814 -0.1215538 + 7300 19524.938 427.99711 0 3682.1534 -3.1139903 + 7350 20554.595 256.63855 0 3682.4044 10.023083 + 7400 18778.53 552.29852 0 3682.0534 -1.7145222 + 7450 18972.509 520.15393 0 3682.2388 1.4489874 + 7500 17680.668 736.20139 0 3682.9794 15.096954 + 7550 19070.785 504.65403 0 3683.1182 2.2707533 + 7600 20805.541 214.54957 0 3682.1398 -3.4306308 + 7650 18473.262 604.25322 0 3683.1301 2.2083367 + 7700 19294.016 466.99211 0 3682.6615 2.2666382 + 7750 20995.664 183.47108 0 3682.7484 -13.935938 + 7800 21042.433 175.06619 0 3682.1384 0.49855811 + 7850 19343.054 459.21955 0 3683.0618 7.9049312 + 7900 18382.898 619.01969 0 3682.8361 1.7996366 + 7950 16092.435 1000.6563 0 3682.7287 29.993154 + 8000 17551.635 757.47719 0 3682.7498 8.1753011 + 8050 20309.875 298.25877 0 3683.2379 -1.9545317 + 8100 21746.174 59.002125 0 3683.3645 -2.6980678 + 8150 21478.427 103.44202 0 3683.1799 -10.930392 + 8200 20986.729 185.46995 0 3683.2581 -14.298403 + 8250 20744.064 225.47546 0 3682.8194 -6.4982356 + 8300 19887.982 368.35069 0 3683.0143 1.5899179 + 8350 21871.414 37.899202 0 3683.1348 -2.0554107 + 8400 20002.858 348.98887 0 3682.7985 8.2963084 + 8450 21553.861 90.985193 0 3683.2953 2.8575186 + 8500 21605.143 82.347635 0 3683.2048 -4.711565 + 8550 20151.76 324.4703 0 3683.097 -8.5109459 + 8600 20564.158 255.77814 0 3683.1378 -1.3815408 + 8650 19316.602 463.61706 0 3683.0507 -2.6895635 + 8700 18157.859 656.69518 0 3683.0051 19.428927 + 8750 18752.43 557.67555 0 3683.0805 1.9765973 + 8800 20903.812 199.07408 0 3683.0428 1.9011523 + 8850 20132.963 327.56826 0 3683.0621 3.0389961 + 8900 21667.171 71.80023 0 3682.9954 -2.0042246 + 8950 20346.973 292.00907 0 3683.1712 7.5582361 + 9000 17889.448 695.59406 0 3677.1688 7.5315391 + 9050 19446.144 441.90609 0 3682.9302 5.9819228 + 9100 20384.34 285.05862 0 3682.4486 9.8610378 + 9150 20023.515 344.98587 0 3682.2384 -0.40175043 + 9200 17786.795 718.76166 0 3683.2275 10.984317 + 9250 20843.023 208.42263 0 3682.2597 -7.4709344 + 9300 21670.622 70.503925 0 3682.2742 -6.2303366 + 9350 20642.313 241.21277 0 3681.5983 4.7423898 + 9400 19228.566 476.44753 0 3681.2085 10.836639 + 9450 21215.705 146.40003 0 3682.3509 -9.091421 + 9500 21543.685 91.725901 0 3682.3401 -1.0608492 + 9550 20143.22 324.98532 0 3682.1887 -5.995164 + 9600 21234.294 142.96512 0 3682.0142 0.004838125 + 9650 21025.207 177.8801 0 3682.0813 -5.4857701 + 9700 20638.235 242.46577 0 3682.1716 -1.6014085 + 9750 18374.191 620.54322 0 3682.9084 13.864712 + 9800 19730.262 393.89083 0 3682.2679 5.7601754 + 9850 21547.855 91.283379 0 3682.5926 2.1989329 + 9900 20959.935 189.28821 0 3682.6108 2.1174676 + 9950 21191.026 150.79441 0 3682.6321 8.3829825 + 10000 20776.574 220.03769 0 3682.8 -1.8404787 +Loop time of 3.0852 on 1 procs for 10000 steps with 81 atoms + +Performance: 28004.636 tau/day, 3241.277 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17336 | 0.17336 | 0.17336 | 0.0 | 5.62 +Neigh | 0.1094 | 0.1094 | 0.1094 | 0.0 | 3.55 +Comm | 0.010163 | 0.010163 | 0.010163 | 0.0 | 0.33 +Output | 0.0030687 | 0.0030687 | 0.0030687 | 0.0 | 0.10 +Modify | 2.7782 | 2.7782 | 2.7782 | 0.0 | 90.05 +Other | | 0.01105 | | | 0.36 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 82 ave 82 max 82 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 887 ave 887 max 887 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 887 +Ave neighs/atom = 10.9506 +Neighbor list builds = 992 +Dangerous builds = 939 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.4 b/examples/rigid/log.20Apr18.rigid.poems.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..e2fb6b65b6602bd72ac74b5d0719836f459cd25d --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.poems.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384277 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184717 + 1150 20849.582 206.01695 0 3680.9472 -0.86699147 + 1200 21815.003 45.317414 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064078 + 1300 20780.781 217.36506 0 3680.8286 6.0538614 + 1350 20558.971 254.36483 0 3680.8601 -3.6773951 + 1400 21485.029 99.812917 0 3680.6511 -16.185473 + 1450 21771.107 52.15961 0 3680.6775 -2.4756673 + 1500 21520.948 93.503926 0 3680.3286 2.1023576 + 1550 21351.418 121.68137 0 3680.2511 5.5159947 + 1600 20778.805 216.92177 0 3680.0559 15.089188 + 1650 21477.638 100.21836 0 3679.8247 -1.1045741 + 1700 18501.339 596.4792 0 3680.0357 -15.679682 + 1750 18563.642 587.34785 0 3681.2882 33.53221 + 1800 19110.185 494.82342 0 3679.8543 18.024046 + 1850 21364.191 119.23548 0 3679.9339 2.5291079 + 1900 20146.626 322.14873 0 3679.9197 5.7313282 + 1950 20692.672 231.2533 0 3680.0319 4.2977759 + 2000 20943.904 189.11231 0 3679.7629 -22.645089 + 2050 19668.052 401.83077 0 3679.8394 3.6251598 + 2100 20280.434 299.76292 0 3679.8353 7.4807838 + 2150 19181.841 483.52513 0 3680.4987 22.620829 + 2200 21300.185 130.70136 0 3680.7321 4.7101928 + 2250 20486.897 266.64698 0 3681.1299 -8.6459184 + 2300 18653.018 572.26538 0 3681.1017 -5.2635489 + 2350 21513.576 95.606125 0 3681.202 -9.3627078 + 2400 21466.185 103.579 0 3681.2764 -29.55912 + 2450 20100.274 332.24291 0 3682.2886 35.736349 + 2500 20764.562 221.63964 0 3682.4 -12.465656 + 2550 20437.187 276.06174 0 3682.2596 -22.421308 + 2600 21466.269 104.56898 0 3682.2805 -10.080867 + 2650 20819.865 212.38395 0 3682.3615 5.1305357 + 2700 18565.57 588.39438 0 3682.656 22.28768 + 2750 20789.153 217.36229 0 3682.2211 -8.051962 + 2800 21045.639 174.58656 0 3682.193 -7.0803377 + 2850 16845.227 874.90505 0 3682.4429 32.992098 + 2900 19319.232 462.27119 0 3682.1432 7.9276373 + 2950 20558.495 255.61185 0 3682.0277 1.9151653 + 3000 20615.868 246.18886 0 3682.1668 -0.016805532 + 3050 18695.136 566.5914 0 3682.4474 -7.3528355 + 3100 19381.554 451.57712 0 3681.8361 -2.0887636 + 3150 19080.633 502.00742 0 3682.1129 5.2518182 + 3200 20969.083 187.13559 0 3681.9828 12.156446 + 3250 20474.81 269.6876 0 3682.156 1.4067779 + 3300 18836.313 542.79266 0 3682.1781 -9.1497216 + 3350 21397.694 116.27473 0 3682.557 -6.4412585 + 3400 20886.812 201.52507 0 3682.6604 6.3038335 + 3450 21604.639 81.93055 0 3682.7038 2.3769444 + 3500 20847.621 207.85705 0 3682.4605 -2.758021 + 3550 20627.979 244.69999 0 3682.6964 -0.33497747 + 3600 19265.519 471.27582 0 3682.1956 2.3506222 + 3650 20351.848 290.65727 0 3682.6319 3.5445062 + 3700 18507.473 597.72931 0 3682.3082 -21.283074 + 3750 20344.017 291.60622 0 3682.2757 6.5366987 + 3800 20672.372 237.18966 0 3682.585 6.7310703 + 3850 21366.943 122.07461 0 3683.2318 -3.5870721 + 3900 20890.294 201.69901 0 3683.4147 -9.5644117 + 3950 20684.181 235.91733 0 3683.2809 -4.8913079 + 4000 21499.086 100.67563 0 3683.8566 1.1969651 + 4050 18549.152 590.04529 0 3681.5707 -9.1914883 + 4100 18436.457 604.2601 0 3677.003 3.6486137 + 4150 19332.655 462.03124 0 3684.1404 -11.280758 + 4200 21199.837 150.66602 0 3683.9722 0.14505208 + 4250 19088.228 501.77395 0 3683.1453 1.6869973 + 4300 16617.942 913.86736 0 3683.5244 9.1792322 + 4350 19765.761 388.52744 0 3682.821 -4.1982973 + 4400 20181.964 320.06096 0 3683.7216 5.3685715 + 4450 20132.04 328.29106 0 3683.631 6.3340995 + 4500 21026.359 179.13858 0 3683.5317 -15.365253 + 4550 19273.765 471.36221 0 3683.6564 -0.71397595 + 4600 20064.71 339.29348 0 3683.4117 -4.8121056 + 4650 19821.01 380.27685 0 3683.7784 11.857115 + 4700 18724.367 563.42963 0 3684.1575 13.250333 + 4750 20467.467 273.2046 0 3684.449 -1.8076823 + 4800 19630.315 412.48507 0 3684.2042 -9.0412254 + 4850 19483.424 437.0206 0 3684.258 11.22465 + 4900 18504.179 600.28485 0 3684.3146 -5.2345686 + 4950 21436.13 111.62139 0 3684.3098 -5.8197915 + 5000 18022.817 680.57727 0 3684.38 19.238942 + 5050 20750.212 226.15635 0 3684.525 -0.73974419 + 5100 20569.533 255.21358 0 3683.4691 -18.332775 + 5150 21447.046 109.3048 0 3683.8124 -2.5745966 + 5200 18985.753 519.77191 0 3684.0641 9.7821968 + 5250 21334.568 128.16597 0 3683.9273 -0.61310451 + 5300 18836.476 544.54018 0 3683.9528 -17.979429 + 5350 18574.391 587.20088 0 3682.9327 40.990206 + 5400 21003.047 183.40176 0 3683.9096 6.1115776 + 5450 20693.875 234.62783 0 3683.607 5.4472209 + 5500 17673.479 738.99306 0 3684.5729 -28.621738 + 5550 19265.837 472.34663 0 3683.3195 -6.609151 + 5600 20800.947 217.12409 0 3683.9486 2.6477049 + 5650 21746.371 59.453265 0 3683.8485 1.5272163 + 5700 20448.97 275.57425 0 3683.736 -7.9864104 + 5750 19776.152 387.64417 0 3683.6695 -16.604848 + 5800 15779.293 1055.4995 0 3685.3817 20.365883 + 5850 21008.009 182.52093 0 3683.8557 -6.6727217 + 5900 21566.123 89.588216 0 3683.9421 -7.8944316 + 5950 21591.695 85.284975 0 3683.9009 -2.4895203 + 6000 17737.17 726.79112 0 3682.9861 1.5643841 + 6050 16648.524 907.73295 0 3682.487 3.0853478 + 6100 19917.439 363.6324 0 3683.2056 4.358303 + 6150 21767.004 56.152017 0 3683.986 -8.8722559 + 6200 17654.098 742.15421 0 3684.5039 9.7673482 + 6250 20125.754 329.65218 0 3683.9445 5.5050658 + 6300 20160.047 323.44453 0 3683.4524 4.852504 + 6350 20509.459 264.29515 0 3682.5383 2.5335834 + 6400 17199.686 817.09171 0 3683.7061 8.3428304 + 6450 18748.366 558.82243 0 3683.5501 0.23782614 + 6500 19133.519 494.28383 0 3683.2037 8.1586096 + 6550 20311.228 297.30741 0 3682.5122 -1.7015056 + 6600 18879.49 536.62652 0 3683.2082 5.0874769 + 6650 18189.35 651.42447 0 3682.9828 -15.223564 + 6700 19925.861 361.90598 0 3682.8828 0.26811015 + 6750 19420.312 445.30915 0 3682.0278 5.5725626 + 6800 19925.024 361.87412 0 3682.7114 -3.9763013 + 6850 16196.938 985.7242 0 3685.2138 2.8265047 + 6900 19779.752 386.51634 0 3683.1416 16.798629 + 6950 21043.144 176.83133 0 3684.0221 -4.193188 + 7000 18555.362 589.47043 0 3682.0307 14.516315 + 7050 21225.883 147.54974 0 3685.1969 -13.466586 + 7100 21234.667 145.92615 0 3685.0373 -5.1951121 + 7150 21483.472 104.62556 0 3685.2042 -5.6904048 + 7200 21014.278 182.97687 0 3685.3566 1.044649 + 7250 18588.789 587.96259 0 3686.094 22.707132 + 7300 20202.932 318.14401 0 3685.2994 -10.795766 + 7350 18304.22 634.7344 0 3685.4377 -1.6801482 + 7400 20967.579 190.67822 0 3685.2747 -0.94800692 + 7450 20991.588 186.07163 0 3684.6696 -1.411476 + 7500 19056.583 507.18197 0 3683.2791 3.2026014 + 7550 18542.455 594.92944 0 3685.3386 -27.908724 + 7600 19895.73 367.08589 0 3683.0409 4.1334366 + 7650 20384.942 285.88041 0 3683.3707 -7.515362 + 7700 20683.189 235.46294 0 3682.6611 10.876437 + 7750 20729.325 228.204 0 3683.0915 3.8844308 + 7800 21667.475 71.752748 0 3682.9985 -15.457992 + 7850 19043.652 508.96807 0 3682.9101 -5.8335792 + 7900 21079.827 169.61123 0 3682.9158 -1.3216223 + 7950 20713.266 230.43917 0 3682.6502 -0.20026535 + 8000 20606.41 248.06357 0 3682.4652 4.2844844 + 8050 20284.503 302.0469 0 3682.7973 6.3402329 + 8100 21859.537 39.514865 0 3682.7711 -13.302141 + 8150 18495.181 600.26329 0 3682.7934 9.9318242 + 8200 21458.549 105.63828 0 3682.0631 -7.7419285 + 8250 18704.511 564.30958 0 3681.728 14.680489 + 8300 20689.366 233.57049 0 3681.7982 2.3067527 + 8350 20692.974 232.67005 0 3681.499 4.2743386 + 8400 20240.086 307.5395 0 3680.8872 1.9694217 + 8450 19075.969 501.34689 0 3680.6751 11.056078 + 8500 21456.727 103.36067 0 3679.4818 -3.4512371 + 8550 20393.16 279.84781 0 3678.7078 6.3282998 + 8600 20898.88 195.43751 0 3678.5842 -14.393947 + 8650 20297.482 295.3169 0 3678.2306 -0.96829147 + 8700 21079.56 164.72934 0 3677.9893 -8.339122 + 8750 21142.519 154.18527 0 3677.9384 -4.6169442 + 8800 20143.871 320.23161 0 3677.5435 6.5710426 + 8850 21030.065 172.88831 0 3677.8992 1.3973883 + 8900 19814.648 375.22097 0 3677.6624 2.6996208 + 8950 17392.382 778.87517 0 3677.6055 11.963975 + 9000 19209.163 476.44659 0 3677.9738 8.7050034 + 9050 20143.824 320.17051 0 3677.4745 -5.8044332 + 9100 21400.78 110.99404 0 3677.7908 -3.0027429 + 9150 21834.471 38.970732 0 3678.0493 -2.5838117 + 9200 21344.715 120.55831 0 3678.0108 4.8187829 + 9250 20998.277 178.31959 0 3678.0324 -1.2009012 + 9300 21141.788 154.4658 0 3678.0971 -21.693564 + 9350 21439.398 105.00432 0 3678.2374 -16.113694 + 9400 21296.282 128.83877 0 3678.2191 -2.9990284 + 9450 19050.623 503.10319 0 3678.207 15.622525 + 9500 20845.847 203.77117 0 3678.079 -1.7504827 + 9550 18808.956 543.38757 0 3678.2135 -2.6611868 + 9600 20612.559 242.57373 0 3678.0002 -0.1650541 + 9650 20522.637 257.28926 0 3677.7288 6.8876074 + 9700 20970.074 182.75754 0 3677.7699 -4.5350279 + 9750 18297.505 625.06808 0 3674.6522 32.429153 + 9800 21042.472 170.78969 0 3677.8684 5.4901963 + 9850 20444.092 270.84839 0 3678.197 6.9444494 + 9900 21597.787 78.901871 0 3678.533 2.3445932 + 9950 18376.854 616.35469 0 3679.1636 -8.55063 + 10000 21490.054 97.234379 0 3678.9101 -0.36115606 +Loop time of 3.38095 on 4 procs for 10000 steps with 81 atoms + +Performance: 25554.943 tau/day, 2957.748 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.015775 | 0.043664 | 0.1024 | 16.8 | 1.29 +Neigh | 0.012822 | 0.029038 | 0.061576 | 11.5 | 0.86 +Comm | 0.18256 | 0.2516 | 0.30898 | 10.5 | 7.44 +Output | 0.0063725 | 0.0069898 | 0.0081069 | 0.8 | 0.21 +Modify | 2.9608 | 3.0171 | 3.0947 | 2.8 | 89.24 +Other | | 0.03255 | | | 0.96 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 45.5 ave 82 max 12 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 218.75 ave 875 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 875 +Ave neighs/atom = 10.8025 +Neighbor list builds = 993 +Dangerous builds = 945 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.1 b/examples/rigid/log.20Apr18.rigid.poems2.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..9062b78def3407178b062603c2a74207cac6e611 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.poems2.g++.1 @@ -0,0 +1,342 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 +1 clusters, 4 bodies, 3 joints, 36 atoms +fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +1 clusters, 5 bodies, 4 joints, 45 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +WARNING: More than one fix poems (../fix_poems.cpp:363) +WARNING: More than one fix poems (../fix_poems.cpp:363) +WARNING: One or more atoms are time integrated more than once (../modify.cpp:279) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12167.633 1505.5478 0 3758.8133 35.125973 + 100 17556.978 512.66277 0 3763.9549 11.137534 + 150 19579.586 138.04942 0 3763.8987 -29.953971 + 200 19757.51 105.30542 0 3764.1036 -0.030645317 + 250 18218.374 390.10747 0 3763.8804 13.711001 + 300 19383.039 174.40688 0 3763.8586 5.7240693 + 350 20125.986 36.972611 0 3764.0071 1.9559205 + 400 18888.816 266.10975 0 3764.0386 9.6362168 + 450 19307.656 188.2511 0 3763.743 1.9326206 + 500 16331.197 738.56392 0 3762.8597 9.1715579 + 550 19318.722 186.16172 0 3763.7027 3.0115336 + 600 19455.268 161.20621 0 3764.0336 0.55208034 + 650 18487.011 340.03216 0 3763.5528 -8.0359122 + 700 17321.201 556.32471 0 3763.9545 -13.631751 + 750 18979.187 249.04389 0 3763.7082 -2.6072455 + 800 19342.456 181.85552 0 3763.7918 8.1918726 + 850 19070.641 232.19342 0 3763.7936 7.3148472 + 900 19478.873 156.65987 0 3763.8586 2.4284987 + 950 19912.415 76.437437 0 3763.9216 -1.4667227 + 1000 16003.749 802.39753 0 3766.0548 46.642188 + 1050 19859.583 86.64176 0 3764.3424 -2.1961943 + 1100 19229.575 203.61488 0 3764.6473 -10.632365 + 1150 18821.6 279.15861 0 3764.64 -0.89495035 + 1200 19392.695 173.59744 0 3764.8373 1.8508753 + 1250 16459.624 717.32104 0 3765.3995 33.478127 + 1300 19343.863 182.59043 0 3764.7874 0.75890736 + 1350 20019.643 57.503573 0 3764.8448 0.31444671 + 1400 18549.582 329.31436 0 3764.4221 10.738303 + 1450 15163.926 957.47585 0 3765.6103 -17.92346 + 1500 19223.688 204.15177 0 3764.0939 -1.6134528 + 1550 18147.996 404.12677 0 3764.8668 8.4194783 + 1600 18615.043 317.42469 0 3764.6548 -2.3288917 + 1650 20120.654 38.887903 0 3764.935 -8.7620301 + 1700 19450.907 162.98262 0 3765.0025 2.3254748 + 1750 19374.631 177.37975 0 3765.2744 8.9328771 + 1800 19424.404 167.93963 0 3765.0514 0.081227378 + 1850 17936.203 442.85082 0 3764.3699 6.6011902 + 1900 19982.595 64.406292 0 3764.8868 -2.95296 + 1950 16215.781 761.92636 0 3764.8487 13.995056 + 2000 18584.444 322.1163 0 3763.6801 7.1653369 + 2050 20107.965 41.025841 0 3764.723 -0.31088772 + 2100 20002.324 60.594786 0 3764.7288 -6.7919989 + 2150 16949.875 626.57523 0 3765.4409 3.50855 + 2200 20010.954 58.808121 0 3764.5403 -10.862112 + 2250 18982.734 247.00818 0 3762.3293 -0.53817452 + 2300 18401.254 354.88774 0 3762.5274 1.0921595 + 2350 19390.545 172.93755 0 3763.7793 -3.3523777 + 2400 16080.137 786.51156 0 3764.3147 -16.202632 + 2450 18870.17 268.79443 0 3763.2704 11.201845 + 2500 19688.736 117.49945 0 3763.5616 4.3786781 + 2550 18869.811 268.97474 0 3763.3842 -5.6659314 + 2600 17021.088 611.38597 0 3763.4393 6.3051835 + 2650 18743.998 292.7827 0 3763.8934 2.4233167 + 2700 19745.629 106.63088 0 3763.2289 -0.34816161 + 2750 19527.584 147.21131 0 3763.4306 -1.6219417 + 2800 18195.354 392.99533 0 3762.5053 24.376674 + 2850 18550.094 327.77867 0 3762.9812 4.2654596 + 2900 20174.105 27.269108 0 3763.2144 1.7109311 + 2950 17744.679 476.70478 0 3762.7564 0.46336417 + 3000 19161.715 214.56545 0 3763.0311 2.3774967 + 3050 18357.87 363.54089 0 3763.1465 7.5885138 + 3100 18851.02 272.19735 0 3763.1269 8.0560784 + 3150 19586.208 136.32381 0 3763.3995 -10.118566 + 3200 19300.444 189.2076 0 3763.3639 -12.590066 + 3250 18680.955 303.88073 0 3763.3168 -1.0138975 + 3300 18444.612 347.49752 0 3763.1664 8.9271155 + 3350 19006.554 243.54359 0 3763.2757 4.7398999 + 3400 17842.797 459.11352 0 3763.3351 28.63048 + 3450 19801.317 96.103613 0 3763.0141 4.0933253 + 3500 18599.338 318.61343 0 3762.9353 6.3657111 + 3550 19737.266 107.84071 0 3762.89 1.3861757 + 3600 19002.648 244.0525 0 3763.0613 8.7615304 + 3650 19154.418 215.94396 0 3763.0584 -2.6243193 + 3700 19036.117 237.84014 0 3763.047 -5.6841944 + 3750 20045.863 50.759281 0 3762.9562 -2.1930939 + 3800 19331.877 182.69303 0 3762.6703 0.57474959 + 3850 18193.947 393.70074 0 3762.9502 -4.1144639 + 3900 19675.638 119.2295 0 3762.8663 0.46172332 + 3950 19506.743 150.36614 0 3762.7259 5.8020668 + 4000 17985.008 431.80897 0 3762.366 10.755615 + 4050 19947.208 68.962683 0 3762.8902 -2.0041629 + 4100 19936.06 70.997196 0 3762.8602 -6.6295574 + 4150 19011.006 242.10402 0 3762.6608 -12.682711 + 4200 18108.183 409.44214 0 3762.8094 -0.42654932 + 4250 18734.162 293.70086 0 3762.9901 8.8549986 + 4300 16619.218 686.30953 0 3763.9426 43.405681 + 4350 18818.184 277.95188 0 3762.8007 20.953883 + 4400 18649.616 307.93211 0 3761.5647 -3.6011031 + 4450 18626.995 313.23564 0 3762.6792 -2.5430627 + 4500 18133.284 405.27778 0 3763.2934 3.057056 + 4550 19985.929 61.792735 0 3762.8908 1.9540846 + 4600 18664.305 306.02805 0 3762.3809 1.2395242 + 4650 19822.408 92.030223 0 3762.8466 -1.0496216 + 4700 19218.014 203.93895 0 3762.8305 0.74203538 + 4750 19425.781 165.36374 0 3762.7306 4.0113982 + 4800 18604.891 317.55244 0 3762.9026 16.671366 + 4850 19648.156 124.29963 0 3762.8471 4.1073 + 4900 18928.508 257.76023 0 3763.0394 -4.3547566 + 4950 19795.841 97.135231 0 3763.0317 -10.401888 + 5000 20150.671 31.452661 0 3763.0584 -3.352706 + 5050 18694.789 300.8954 0 3762.8933 11.690808 + 5100 16936.745 627.00902 0 3763.4434 -0.56880353 + 5150 18446.99 346.49004 0 3762.5992 8.409244 + 5200 18532.691 330.61677 0 3762.5966 10.358529 + 5250 18342.743 366.3264 0 3763.1306 -9.5622676 + 5300 20038.203 52.234825 0 3763.0131 -3.6974868 + 5350 19337.092 182.06755 0 3763.0106 -0.045248915 + 5400 19561.005 140.5518 0 3762.9602 1.3850963 + 5450 19415.557 167.29181 0 3762.7654 2.6966013 + 5500 18646.823 309.81657 0 3762.9319 7.4858844 + 5550 19165.312 214.07271 0 3763.2046 1.4335924 + 5600 18879.507 266.90953 0 3763.1146 7.8746695 + 5650 19824.482 91.786842 0 3762.9872 -2.4395467 + 5700 19699.85 114.8239 0 3762.9442 4.2779932 + 5750 19535.697 145.24886 0 3762.9706 5.9452722 + 5800 18275.446 378.66191 0 3763.0038 11.965062 + 5850 19931.992 71.873259 0 3762.9828 -2.3097575 + 5900 18528.705 331.64793 0 3762.8897 -18.312104 + 5950 16535.446 701.02536 0 3763.1451 -14.797902 + 6000 18678.807 303.76763 0 3762.806 -3.2732626 + 6050 16661.525 677.73561 0 3763.2031 17.862761 + 6100 18100.317 410.39139 0 3762.3019 -4.9765779 + 6150 16487.861 707.08907 0 3760.3967 32.53899 + 6200 16823.279 647.56578 0 3762.9878 -9.8237219 + 6250 18418.096 351.89624 0 3762.6548 -2.0149855 + 6300 18822.067 277.01314 0 3762.5811 5.3782716 + 6350 19300.198 188.57243 0 3762.6832 -1.9316023 + 6400 18425.789 350.70367 0 3762.8868 2.6884393 + 6450 18708.506 297.50643 0 3762.0447 -13.808707 + 6500 19528.099 146.10805 0 3762.4226 -1.5991505 + 6550 19701.841 114.01327 0 3762.5023 4.4322487 + 6600 18892.934 262.83827 0 3761.5297 10.689265 + 6650 19041.669 235.52692 0 3761.7619 -1.1425512 + 6700 19352.162 178.40501 0 3762.1388 -0.55130997 + 6750 16177.653 765.61942 0 3761.481 4.6526477 + 6800 19007.323 242.63753 0 3762.5122 3.6202242 + 6850 14255.206 1125.4974 0 3765.3503 -31.10433 + 6900 18481.408 340.4703 0 3762.9532 0.53246054 + 6950 19227.569 202.33363 0 3762.9946 -0.94126626 + 7000 18771.85 286.70279 0 3762.9714 3.151759 + 7050 18689.51 301.95602 0 3762.9765 8.0511724 + 7100 18599.258 318.83229 0 3763.1394 -0.86222116 + 7150 17739.189 478.35458 0 3763.3896 11.976827 + 7200 19492.829 153.62536 0 3763.4084 -8.6815909 + 7250 18797.718 282.17319 0 3763.232 -19.897633 + 7300 18353.871 364.09362 0 3762.9585 5.4538454 + 7350 19040.053 237.34144 0 3763.2772 6.5600248 + 7400 19452.586 160.98629 0 3763.317 -9.0542585 + 7450 19033.845 238.45033 0 3763.2365 3.2654681 + 7500 18137.358 404.80969 0 3763.5796 -7.2639486 + 7550 16863.391 642.47654 0 3765.3267 31.248679 + 7600 16374.538 731.74039 0 3764.0622 29.566291 + 7650 19837.917 89.823014 0 3763.5114 -2.6605403 + 7700 15593.154 876.08807 0 3763.7093 -9.7668717 + 7750 16609.929 687.32679 0 3763.2396 1.0775966 + 7800 17513.384 519.87756 0 3763.0968 3.4979836 + 7850 20022.015 56.036771 0 3763.8173 -4.316185 + 7900 17681.324 489.71547 0 3764.0347 5.1978443 + 7950 18320.382 371.17872 0 3763.8421 6.1860655 + 8000 20014.059 57.688322 0 3763.9956 -9.0623854 + 8050 16203.013 762.61545 0 3763.1735 31.662714 + 8100 18749.745 291.57889 0 3763.7538 -14.015057 + 8150 19411.326 169.05845 0 3763.7485 -4.3392799 + 8200 17994.991 431.56932 0 3763.9751 6.8158642 + 8250 19325.923 185.1137 0 3763.9883 9.4923883 + 8300 17354.302 550.33316 0 3764.0927 6.1636399 + 8350 19900.895 78.431831 0 3763.7828 -4.5224196 + 8400 17775.757 471.62915 0 3763.4361 12.949899 + 8450 19909.324 76.935162 0 3763.8471 -2.950115 + 8500 18601.933 318.79405 0 3763.5965 6.0173542 + 8550 18685.758 303.59497 0 3763.9205 2.7277487 + 8600 19297.521 190.12606 0 3763.741 4.8998933 + 8650 17396.37 542.14326 0 3763.6932 39.937715 + 8700 17134.714 590.99465 0 3764.0898 10.37328 + 8750 14348.104 1106.7544 0 3763.8106 -3.8604659 + 8800 19830.924 90.929138 0 3763.3225 0.26603444 + 8850 18551.537 326.53747 0 3762.0072 -1.5369982 + 8900 20040.322 52.066026 0 3763.2367 -12.667979 + 8950 19314.585 186.54793 0 3763.3228 -0.64755555 + 9000 19117.66 222.84553 0 3763.153 5.2990011 + 9050 19072.016 231.26038 0 3763.1152 -1.6513695 + 9100 19284.933 191.73976 0 3763.0237 -3.932358 + 9150 17356.576 548.61808 0 3762.7988 1.3659056 + 9200 18939.549 255.43703 0 3762.761 3.3037106 + 9250 19621.961 129.5012 0 3763.1976 1.667 + 9300 16898.033 633.79921 0 3763.0647 7.5941845 + 9350 19662.75 122.10836 0 3763.3584 -3.3144828 + 9400 16118.338 778.70243 0 3763.5799 9.8684537 + 9450 17362.374 548.18847 0 3763.443 6.8117548 + 9500 17873.057 453.37389 0 3763.1993 9.5651746 + 9550 19282.305 192.593 0 3763.3901 -4.987757 + 9600 18236.48 386.36263 0 3763.4886 8.8658343 + 9650 17695.571 486.6517 0 3763.6093 12.471421 + 9700 19044.003 237.04652 0 3763.7138 0.84430497 + 9750 17937.299 442.4372 0 3764.1592 3.981475 + 9800 18179.761 396.86987 0 3763.4923 -11.397273 + 9850 19157.292 215.8937 0 3763.5404 -7.7648682 + 9900 19719.066 111.98124 0 3763.6602 5.5378968 + 9950 18103.235 410.65473 0 3763.1056 28.201374 + 10000 18479.903 341.32548 0 3763.5297 -5.0581298 +Loop time of 3.14341 on 1 procs for 10000 steps with 81 atoms + +Performance: 27486.104 tau/day, 3181.262 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12201 | 0.12201 | 0.12201 | 0.0 | 3.88 +Neigh | 0.077269 | 0.077269 | 0.077269 | 0.0 | 2.46 +Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.39 +Output | 0.0032048 | 0.0032048 | 0.0032048 | 0.0 | 0.10 +Modify | 2.9172 | 2.9172 | 2.9172 | 0.0 | 92.80 +Other | | 0.01151 | | | 0.37 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 67 ave 67 max 67 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 599 ave 599 max 599 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 599 +Ave neighs/atom = 7.39506 +Neighbor list builds = 993 +Dangerous builds = 945 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.4 b/examples/rigid/log.20Apr18.rigid.poems2.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..812b101841c6a9260eb4fad1a39b26a07c2dd64a --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.poems2.g++.4 @@ -0,0 +1,342 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 +1 clusters, 4 bodies, 3 joints, 36 atoms +fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +1 clusters, 5 bodies, 4 joints, 45 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +WARNING: More than one fix poems (../fix_poems.cpp:363) +WARNING: More than one fix poems (../fix_poems.cpp:363) +WARNING: One or more atoms are time integrated more than once (../modify.cpp:279) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12167.633 1505.5478 0 3758.8133 35.125973 + 100 17556.978 512.66277 0 3763.9549 11.137534 + 150 19579.586 138.04942 0 3763.8987 -29.953971 + 200 19757.51 105.30542 0 3764.1036 -0.030645317 + 250 18218.374 390.10747 0 3763.8804 13.711001 + 300 19383.039 174.40688 0 3763.8586 5.7240693 + 350 20125.986 36.972611 0 3764.0071 1.9559205 + 400 18888.816 266.10975 0 3764.0386 9.6362168 + 450 19307.656 188.2511 0 3763.743 1.9326206 + 500 16331.197 738.56392 0 3762.8597 9.1715579 + 550 19318.722 186.16172 0 3763.7027 3.0115336 + 600 19455.268 161.20621 0 3764.0336 0.55208034 + 650 18487.011 340.03216 0 3763.5528 -8.0359122 + 700 17321.201 556.32471 0 3763.9545 -13.631751 + 750 18979.187 249.04389 0 3763.7082 -2.6072455 + 800 19342.456 181.85552 0 3763.7918 8.1918726 + 850 19070.641 232.19342 0 3763.7936 7.3148472 + 900 19478.873 156.65987 0 3763.8586 2.4284987 + 950 19912.415 76.437437 0 3763.9216 -1.4667227 + 1000 16003.749 802.39753 0 3766.0548 46.642188 + 1050 19859.583 86.64176 0 3764.3424 -2.1961943 + 1100 19229.575 203.61488 0 3764.6473 -10.632365 + 1150 18821.6 279.15861 0 3764.64 -0.89495035 + 1200 19392.695 173.59744 0 3764.8373 1.8508753 + 1250 16459.624 717.32104 0 3765.3995 33.478127 + 1300 19343.863 182.59043 0 3764.7874 0.75890736 + 1350 20019.643 57.503573 0 3764.8448 0.31444671 + 1400 18549.582 329.31436 0 3764.4221 10.738303 + 1450 15163.926 957.47584 0 3765.6103 -17.923459 + 1500 19223.688 204.15172 0 3764.0939 -1.6134536 + 1550 18147.996 404.12676 0 3764.8668 8.4194774 + 1600 18615.043 317.42466 0 3764.6548 -2.3288957 + 1650 20120.654 38.887927 0 3764.935 -8.7620244 + 1700 19450.906 162.98284 0 3765.0025 2.3254707 + 1750 19374.632 177.37954 0 3765.2744 8.9328778 + 1800 19424.403 167.93971 0 3765.0514 0.081234023 + 1850 17936.311 442.83087 0 3764.3699 6.600894 + 1900 19982.596 64.40607 0 3764.8868 -2.9530102 + 1950 16215.95 761.89459 0 3764.8482 13.994238 + 2000 18584.39 322.12621 0 3763.68 7.1654863 + 2050 20107.966 41.025634 0 3764.723 -0.31093298 + 2100 20002.346 60.590652 0 3764.7288 -6.7919499 + 2150 16949.612 626.62391 0 3765.441 3.5094585 + 2200 20010.952 58.808492 0 3764.5403 -10.862255 + 2250 18982.727 247.00941 0 3762.3292 -0.53796622 + 2300 18401.351 354.86992 0 3762.5275 1.0919209 + 2350 19390.5 172.94589 0 3763.7793 -3.3526281 + 2400 16081.648 786.23133 0 3764.3143 -16.197875 + 2450 18870.722 268.69249 0 3763.2707 11.192419 + 2500 19687.71 117.6898 0 3763.562 4.387789 + 2550 18872.129 268.54506 0 3763.3838 -5.6577428 + 2600 17017.179 612.11028 0 3763.4397 6.3187623 + 2650 18766.343 288.63699 0 3763.8856 2.3968008 + 2700 19737.998 108.02069 0 3763.2054 -0.30752024 + 2750 19508.797 150.69812 0 3763.4384 -1.6171126 + 2800 18394.822 355.73011 0 3762.1787 21.193311 + 2850 18561.108 325.76417 0 3763.0065 3.9331499 + 2900 20124.042 36.554163 0 3763.2286 0.54133121 + 2950 15727.607 849.90471 0 3762.4245 13.885323 + 3000 17991.206 431.32693 0 3763.0317 9.9953567 + 3050 18834.86 275.34241 0 3763.2795 9.1519305 + 3100 18986.272 247.38123 0 3763.3575 -1.8754521 + 3150 19979.145 63.575968 0 3763.4177 -11.800026 + 3200 19953.846 68.376593 0 3763.5332 -6.7719573 + 3250 15646.02 867.19502 0 3764.6062 16.433911 + 3300 16946.252 625.14854 0 3763.3433 4.3975456 + 3350 19006.567 243.97026 0 3763.7048 5.3392405 + 3400 18082.133 414.87059 0 3763.4138 15.143954 + 3450 18273.719 379.36162 0 3763.3836 5.4465204 + 3500 19783.17 100.06678 0 3763.6167 1.9588505 + 3550 19794.99 97.904519 0 3763.6435 -3.0349395 + 3600 18357.708 363.98291 0 3763.5585 -2.1229788 + 3650 19647.179 125.48949 0 3763.8559 1.2967845 + 3700 18806.632 281.78709 0 3764.4967 5.125718 + 3750 18982.747 248.97053 0 3764.294 -0.72036085 + 3800 19597.926 135.04805 0 3764.2935 -3.2129291 + 3850 18914.042 261.7133 0 3764.3136 -12.163282 + 3900 18646.326 311.16482 0 3764.1881 5.1808943 + 3950 18589.554 321.36256 0 3763.8726 4.9554103 + 4000 17877.615 453.02456 0 3763.694 9.8457113 + 4050 19440.059 164.15739 0 3764.1684 -5.4054486 + 4100 18505.545 337.36023 0 3764.313 4.8468985 + 4150 19220.307 204.85944 0 3764.1755 -6.5040818 + 4200 19058.915 234.79578 0 3764.2245 3.1852011 + 4250 19867.025 85.136186 0 3764.2149 5.6156236 + 4300 16989.857 616.86564 0 3763.1355 -3.4041875 + 4350 19782.09 100.85847 0 3764.2085 3.2531098 + 4400 19879.56 82.559198 0 3763.9593 1.6340828 + 4450 19409.95 169.46676 0 3763.9019 -1.824265 + 4500 19742.977 107.72786 0 3763.8347 -0.72711698 + 4550 17166.529 585.04113 0 3764.028 -0.38806102 + 4600 19604.596 133.61426 0 3764.0949 -5.2712214 + 4650 18865.608 270.23956 0 3763.8707 1.5751363 + 4700 20190.139 25.270932 0 3764.1855 -10.159924 + 4750 20043.487 52.56327 0 3764.3201 -4.713579 + 4800 19361.931 178.70311 0 3764.246 4.2460799 + 4850 19460.365 160.29083 0 3764.0621 3.5079181 + 4900 18252.89 384.16194 0 3764.3268 4.1870604 + 4950 19516.947 150.07365 0 3764.3231 4.0238527 + 5000 19041.145 238.27335 0 3764.4113 8.2280019 + 5050 19519.408 149.66793 0 3764.3731 -0.088904966 + 5100 18087.848 415.34004 0 3764.9416 8.9482852 + 5150 19392.463 173.43121 0 3764.628 -6.6722716 + 5200 19683.968 119.46663 0 3764.6458 -2.0330852 + 5250 19675.404 121.09497 0 3764.6884 3.0627309 + 5300 18627.53 314.96107 0 3764.5038 5.2692141 + 5350 20022.616 56.725346 0 3764.6172 -7.7034469 + 5400 19353.4 180.6482 0 3764.6112 -2.3897589 + 5450 16966.649 622.29693 0 3764.2689 6.3601638 + 5500 17584.292 508.42495 0 3764.7753 5.949219 + 5550 19169.69 214.76864 0 3764.7113 3.3778997 + 5600 19491.814 155.19149 0 3764.7866 -0.20031164 + 5650 19079.585 231.70394 0 3764.9605 7.3017226 + 5700 19686.564 119.34 0 3765 0.98980357 + 5750 19639.909 127.89886 0 3764.919 2.3982612 + 5800 19474.109 158.55418 0 3764.8706 3.4940447 + 5850 16957.663 624.72623 0 3765.0342 10.739819 + 5900 19950.579 70.027987 0 3764.5796 4.6925057 + 5950 19759.601 105.38621 0 3764.5716 3.0958319 + 6000 19129.749 221.96406 0 3764.5102 -1.0612997 + 6050 16087.951 785.36134 0 3764.6115 -15.255986 + 6100 18851.976 272.98306 0 3764.0896 4.9341766 + 6150 19532.23 147.4113 0 3764.4909 1.3206073 + 6200 18051.604 421.79367 0 3764.6833 2.587863 + 6250 18922.77 259.81211 0 3764.0287 10.363589 + 6300 18402.504 356.81518 0 3764.6864 8.3589218 + 6350 19315.369 187.64457 0 3764.5647 1.0716382 + 6400 19700.59 116.50438 0 3764.7618 2.165408 + 6450 19596.362 135.79675 0 3764.7527 1.6466783 + 6500 20217.677 20.884953 0 3764.8993 -3.5893732 + 6550 18278.991 379.95981 0 3764.9582 7.0433091 + 6600 20142.999 34.761283 0 3764.9462 1.7083655 + 6650 20185.488 26.899017 0 3764.9524 -0.65741058 + 6700 17942.962 441.72909 0 3764.4999 -3.691039 + 6750 16435.681 720.9581 0 3764.6028 -9.4583249 + 6800 17825.95 463.58979 0 3764.6916 6.1557503 + 6850 19440.75 164.52796 0 3764.6669 -11.921703 + 6900 18824.905 278.4897 0 3764.5832 -1.4668322 + 6950 19069.14 233.25502 0 3764.5772 6.8149838 + 7000 18983.209 249.29193 0 3764.701 15.140158 + 7050 15623.103 872.33684 0 3765.5041 7.3268767 + 7100 20090.283 44.006184 0 3764.429 2.6959947 + 7150 15535.27 888.39683 0 3765.2987 -4.1285644 + 7200 19425.575 167.19079 0 3764.5195 4.9190857 + 7250 18684.497 304.24754 0 3764.3396 7.3927682 + 7300 17632.518 498.82765 0 3764.1087 5.1101854 + 7350 18969.793 251.66375 0 3764.5884 -3.7865508 + 7400 17700.626 486.89931 0 3764.7931 -8.8531288 + 7450 17897.361 450.31562 0 3764.6417 -3.6095062 + 7500 18795.228 284.03842 0 3764.6361 8.3567203 + 7550 18658.285 309.34015 0 3764.5781 0.4306691 + 7600 19230.039 203.5385 0 3764.6567 0.80253549 + 7650 19513.551 150.86999 0 3764.4906 0.32848159 + 7700 19494.849 154.28788 0 3764.4452 -4.2498631 + 7750 20011.058 58.832118 0 3764.5835 0.54896615 + 7800 19241.055 201.57548 0 3764.7338 -0.26200786 + 7850 19512.742 151.11436 0 3764.5851 2.7308876 + 7900 19688.007 118.68023 0 3764.6075 0.80454178 + 7950 16891.645 636.56823 0 3764.6507 -25.839253 + 8000 19425.572 167.33746 0 3764.6657 -2.8744687 + 8050 19444.916 163.57779 0 3764.4882 8.5388183 + 8100 19540.338 145.77731 0 3764.3585 5.5606379 + 8150 17997.991 429.85951 0 3762.8208 20.179487 + 8200 19463.886 159.50302 0 3763.9264 0.19577123 + 8250 19517.733 149.53457 0 3763.9295 2.3294314 + 8300 19236.221 201.66041 0 3763.9236 5.8204747 + 8350 18662.608 308.25544 0 3764.2939 5.4422482 + 8400 19030.046 239.38211 0 3763.4647 3.7940188 + 8450 18058.148 419.70672 0 3763.8081 4.4010713 + 8500 16866.001 641.00564 0 3764.3392 -19.894815 + 8550 19484.364 155.35821 0 3763.5737 4.2635496 + 8600 18562.912 326.16323 0 3763.7395 11.288271 + 8650 19256.188 197.67578 0 3763.6365 -4.1872666 + 8700 19653.945 124.27148 0 3763.8909 -7.4888761 + 8750 19590.834 136.12748 0 3764.0596 1.0605539 + 8800 19065.424 233.46882 0 3764.1029 1.8432113 + 8850 18961.297 252.69734 0 3764.0486 6.7414134 + 8900 19879.711 82.777822 0 3764.2058 0.12631864 + 8950 18689.712 302.80546 0 3763.8632 5.1584036 + 9000 19114.403 224.23511 0 3763.9393 -4.5856366 + 9050 17626.3 500.49518 0 3764.6248 -3.9436947 + 9100 18552.501 328.86032 0 3764.5087 -0.32810034 + 9150 15039.846 979.12961 0 3764.2862 16.571104 + 9200 19146.923 218.64681 0 3764.3733 -4.6264398 + 9250 17606.161 503.14852 0 3763.5487 13.13675 + 9300 18002.328 430.47362 0 3764.2381 4.9326117 + 9350 19980.452 64.168644 0 3764.2524 -5.6111349 + 9400 18953.798 254.44926 0 3764.4118 2.3662302 + 9450 17151.075 588.59472 0 3764.7197 4.3116983 + 9500 19128.858 221.38199 0 3763.763 3.6641306 + 9550 18217.322 390.53199 0 3764.1101 1.8537154 + 9600 19094.478 227.98925 0 3764.0038 3.972665 + 9650 19577.649 138.55507 0 3764.0456 4.0408247 + 9700 19331.361 184.31942 0 3764.2011 -4.7996733 + 9750 18999.798 245.87295 0 3764.3541 -0.26741334 + 9800 18987.181 248.37105 0 3764.5157 6.1717595 + 9850 20094.73 43.013036 0 3764.2593 -8.9770288 + 9900 18988.815 247.63984 0 3764.087 -6.3990966 + 9950 18290.808 377.34967 0 3764.5363 7.7453525 + 10000 19558.326 142.47047 0 3764.3828 3.4110829 +Loop time of 3.53831 on 4 procs for 10000 steps with 81 atoms + +Performance: 24418.438 tau/day, 2826.208 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0096724 | 0.035349 | 0.063574 | 10.3 | 1.00 +Neigh | 0.0091243 | 0.022333 | 0.037608 | 6.9 | 0.63 +Comm | 0.18063 | 0.2494 | 0.33202 | 12.6 | 7.05 +Output | 0.0060797 | 0.0065744 | 0.0074706 | 0.7 | 0.19 +Modify | 3.0943 | 3.1895 | 3.2828 | 4.0 | 90.14 +Other | | 0.0352 | | | 0.99 + +Nlocal: 20.25 ave 36 max 0 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 17.5 ave 37 max 1 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 154.25 ave 393 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 617 +Ave neighs/atom = 7.61728 +Neighbor list builds = 993 +Dangerous builds = 948 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.1 b/examples/rigid/log.20Apr18.rigid.property.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..76ef36825b00775073409ad7d4c97c9e9261e4c3 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.property.g++.1 @@ -0,0 +1,340 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +fix 0 all property/atom i_bodies + +read_data data.rigid-property fix 0 NULL Bodies + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +# assemble bodies from per-atom custom integer property bodies +fix 1 all rigid custom i_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3750 16737.731 0.20706557 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.00022115871 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9600 16738.549 -0.026814371 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589893 0 5269.4979 12.062708 + 9750 16738.013 0.13550102 0 5269.5101 11.407246 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.140719 on 1 procs for 10000 steps with 81 atoms + +Performance: 613990.898 tau/day, 71063.761 timesteps/s +97.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010882 | 0.010882 | 0.010882 | 0.0 | 7.73 +Neigh | 0.037245 | 0.037245 | 0.037245 | 0.0 | 26.47 +Comm | 0.0092154 | 0.0092154 | 0.0092154 | 0.0 | 6.55 +Output | 0.0024879 | 0.0024879 | 0.0024879 | 0.0 | 1.77 +Modify | 0.074702 | 0.074702 | 0.074702 | 0.0 | 53.09 +Other | | 0.006187 | | | 4.40 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.4 b/examples/rigid/log.20Apr18.rigid.property.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..c34324b19c8d5928fd0bee8e128ff88555f65d92 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.property.g++.4 @@ -0,0 +1,340 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic +atom_modify map array + +pair_style lj/cut 2.5 + +fix 0 all property/atom i_bodies + +read_data data.rigid-property fix 0 NULL Bodies + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +# assemble bodies from per-atom custom integer property bodies +fix 1 all rigid custom i_bodies +9 rigid bodies with 81 atoms + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.685 571.71558 0 5265.82 32.006171 + 100 16298.442 136.66184 0 5267.653 16.444229 + 150 16682.606 17.490511 0 5269.4219 14.900344 + 200 16733.929 1.372872 0 5269.4617 14.569267 + 250 16738.853 -0.15252816 0 5269.4864 14.496404 + 300 16738.588 -0.055171335 0 5269.5002 14.496025 + 350 16738.492 -0.017444677 0 5269.5077 14.496446 + 400 16738.464 -0.0060102023 0 5269.5104 14.496618 + 450 16738.455 -0.0012713351 0 5269.5124 14.496701 + 500 16738.455 -0.00081068621 0 5269.5128 14.496709 + 550 16738.455 -0.00083203497 0 5269.5129 14.496707 + 600 16738.455 -0.00058355356 0 5269.5131 14.496709 + 650 16738.455 -0.00047226704 0 5269.5131 14.496708 + 700 16738.455 0 0 5269.5136 14.496713 + 750 16738.455 0 0 5269.5136 14.49671 + 800 16738.455 0 0 5269.5137 14.496709 + 850 16738.455 0 0 5269.5137 14.49671 + 900 16738.456 0 0 5269.5138 14.496713 + 950 16738.462 -0.0035323872 0 5269.5122 14.496671 + 1000 16738.586 -0.051135144 0 5269.5036 14.496229 + 1050 16737.358 0.32995057 0 5269.4981 14.525763 + 1100 16737.892 0.16210246 0 5269.4984 14.531983 + 1150 16738.703 -0.089235095 0 5269.5025 14.509899 + 1200 16738.466 -0.0075446243 0 5269.5096 14.510615 + 1250 16738.456 0 0 5269.514 14.510704 + 1300 16738.457 0 0 5269.5141 14.510701 + 1350 16738.457 0 0 5269.5141 14.510699 + 1400 16738.457 -0.00044736511 0 5269.5138 14.510693 + 1450 16738.458 -0.0010971179 0 5269.5134 14.510687 + 1500 16738.458 -0.00057885428 0 5269.5139 14.510698 + 1550 16738.457 0 0 5269.5143 14.51071 + 1600 16738.457 0 0 5269.5144 14.510712 + 1650 16738.457 0 0 5269.5144 14.510712 + 1700 16738.458 0 0 5269.5144 14.51071 + 1750 16738.458 0 0 5269.5145 14.510708 + 1800 16738.458 0 0 5269.5145 14.510706 + 1850 16738.458 0 0 5269.5146 14.510705 + 1900 16738.458 0 0 5269.5146 14.510706 + 1950 16738.465 -0.0031733615 0 5269.5134 14.510659 + 2000 16738.491 -0.013255268 0 5269.5117 14.510532 + 2050 16738.556 -0.0365811 0 5269.5087 14.51029 + 2100 16738.633 -0.063209659 0 5269.5065 14.510219 + 2150 16738.607 -0.05601761 0 5269.5055 14.510231 + 2200 16738.557 -0.038423032 0 5269.5072 14.510404 + 2250 16738.515 -0.023709918 0 5269.5088 14.510539 + 2300 16738.489 -0.013249035 0 5269.5111 14.510621 + 2350 16738.468 -0.0045563719 0 5269.5131 14.510714 + 2400 16738.46 -0.00052194273 0 5269.5146 14.510771 + 2450 16738.464 -0.0023259756 0 5269.514 14.510746 + 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 + 2550 16738.581 -0.044940117 0 5269.5085 14.510315 + 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 + 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2700 16738.761 -0.10614946 0 5269.5038 14.499584 + 2750 16733.973 1.4038179 0 5269.5064 14.598107 + 2800 16738.585 -0.046813448 0 5269.5076 14.511073 + 2850 16738.487 -0.012558719 0 5269.5111 14.510111 + 2900 16738.465 -0.0026252725 0 5269.514 14.510277 + 2950 16738.476 -0.0082220764 0 5269.512 14.510223 + 3000 16738.66 -0.071284779 0 5269.507 14.509758 + 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3100 16653.226 26.818761 0 5269.5009 14.496764 + 3150 16739.351 -0.30690375 0 5269.4886 13.643904 + 3200 16733.238 1.6025328 0 5269.4737 12.016934 + 3250 16734.374 1.2554429 0 5269.4841 11.963561 + 3300 16732.156 1.9585967 0 5269.4893 12.234024 + 3350 16738.655 -0.079693236 0 5269.497 12.092757 + 3400 16738.543 -0.042215005 0 5269.4991 12.092809 + 3450 16738.591 -0.059327511 0 5269.4972 12.092536 + 3500 16738.759 -0.11761245 0 5269.4918 12.09203 + 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3600 16734.939 1.0821936 0 5269.4891 12.173591 + 3650 16738.808 -0.13663194 0 5269.4882 12.027009 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 + 3750 16737.731 0.20706558 0 5269.4927 12.061948 + 3800 16738.578 -0.05582043 0 5269.4965 12.035665 + 3850 16738.471 -0.016307928 0 5269.5024 12.035302 + 3900 16738.449 -0.0058182199 0 5269.5059 12.035401 + 3950 16738.439 -0.0012027325 0 5269.5074 12.035461 + 4000 16738.436 -0.00020698452 0 5269.5075 12.035469 + 4050 16738.437 0 0 5269.5078 12.035454 + 4100 16738.437 0 0 5269.508 12.035435 + 4150 16738.438 0 0 5269.5081 12.035426 + 4200 16738.438 0 0 5269.5083 12.035432 + 4250 16738.439 0 0 5269.5085 12.035447 + 4300 16738.439 0 0 5269.5086 12.035463 + 4350 16738.44 0 0 5269.5087 12.035474 + 4400 16738.44 0 0 5269.5088 12.035478 + 4450 16738.44 0 0 5269.5089 12.035474 + 4500 16738.44 0 0 5269.509 12.035462 + 4550 16738.441 0 0 5269.5092 12.035449 + 4600 16738.441 0 0 5269.5093 12.035445 + 4650 16738.442 0 0 5269.5095 12.035451 + 4700 16738.442 0 0 5269.5096 12.03546 + 4750 16738.443 0 0 5269.5097 12.035465 + 4800 16738.443 0 0 5269.5098 12.035466 + 4850 16738.443 0 0 5269.51 12.035463 + 4900 16738.444 0 0 5269.5101 12.035456 + 4950 16738.444 0 0 5269.5102 12.035447 + 5000 16738.445 0 0 5269.5104 12.03544 + 5050 16738.445 0 0 5269.5105 12.035442 + 5100 16738.446 0 0 5269.5107 12.035455 + 5150 16738.446 0 0 5269.5108 12.03547 + 5200 16738.446 0 0 5269.5109 12.035479 + 5250 16738.447 0 0 5269.511 12.035479 + 5300 16738.447 0 0 5269.5111 12.03547 + 5350 16738.447 0 0 5269.5112 12.035454 + 5400 16738.448 0 0 5269.5113 12.035434 + 5450 16738.448 0 0 5269.5115 12.03542 + 5500 16738.449 0 0 5269.5117 12.035422 + 5550 16738.457 -0.0030919234 0 5269.5111 12.035383 + 5600 16738.51 -0.021618357 0 5269.5092 12.035106 + 5650 16738.622 -0.059214788 0 5269.507 12.035694 + 5700 16395.28 108.06942 0 5269.5463 24.369038 + 5750 16738.544 -0.033973429 0 5269.5077 12.011261 + 5800 16738.456 -0.0037013529 0 5269.5102 12.011675 + 5850 16738.451 0 0 5269.5123 12.011709 + 5900 16738.451 -0.0002211587 0 5269.5122 12.011687 + 5950 16738.452 -0.00024253349 0 5269.5124 12.011678 + 6000 16738.452 0 0 5269.5128 12.011688 + 6050 16738.453 0 0 5269.513 12.011702 + 6100 16738.453 0 0 5269.5131 12.011716 + 6150 16738.454 0 0 5269.5132 12.011725 + 6200 16738.454 0 0 5269.5133 12.011728 + 6250 16738.454 0 0 5269.5134 12.011723 + 6300 16738.455 0 0 5269.5135 12.011712 + 6350 16738.455 0 0 5269.5137 12.0117 + 6400 16738.456 0 0 5269.5138 12.011697 + 6450 16738.456 0 0 5269.514 12.011704 + 6500 16738.456 0 0 5269.5141 12.011714 + 6550 16738.457 0 0 5269.5142 12.011719 + 6600 16738.457 0 0 5269.5143 12.011718 + 6650 16738.458 0 0 5269.5144 12.011713 + 6700 16738.458 0 0 5269.5146 12.011705 + 6750 16738.459 0 0 5269.5147 12.011696 + 6800 16738.459 0 0 5269.5149 12.01169 + 6850 16738.46 0 0 5269.515 12.011695 + 6900 16738.46 0 0 5269.5152 12.01171 + 6950 16738.46 0 0 5269.5153 12.011726 + 7000 16738.461 0 0 5269.5154 12.011736 + 7050 16738.461 0 0 5269.5155 12.011737 + 7100 16738.461 0 0 5269.5155 12.011728 + 7150 16738.461 0 0 5269.5156 12.011712 + 7200 16738.462 0 0 5269.5158 12.011691 + 7250 16738.463 0 0 5269.516 12.011676 + 7300 16738.463 0 0 5269.5162 12.011677 + 7350 16738.464 0 0 5269.5164 12.011693 + 7400 16738.464 0 0 5269.5165 12.011713 + 7450 16738.465 0 0 5269.5166 12.011729 + 7500 16738.465 0 0 5269.5167 12.011736 + 7550 16738.465 0 0 5269.5168 12.011734 + 7600 16738.465 0 0 5269.5168 12.011722 + 7650 16738.466 0 0 5269.517 12.011704 + 7700 16738.466 0 0 5269.5171 12.011687 + 7750 16738.467 0 0 5269.5173 12.011681 + 7800 16738.467 0 0 5269.5175 12.011687 + 7850 16738.468 0 0 5269.5176 12.0117 + 7900 16738.468 0 0 5269.5178 12.011712 + 7950 16738.469 0 0 5269.5179 12.011721 + 8000 16738.469 0 0 5269.518 12.011724 + 8050 16738.469 0 0 5269.5181 12.01172 + 8100 16738.47 0 0 5269.5182 12.011709 + 8150 16738.47 0 0 5269.5183 12.0117 + 8200 16738.47 0 0 5269.5185 12.0117 + 8250 16738.471 0 0 5269.5186 12.011709 + 8300 16738.471 0 0 5269.5187 12.011719 + 8350 16738.472 0 0 5269.5189 12.011723 + 8400 16738.472 0 0 5269.519 12.01172 + 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 + 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 + 8650 16738.474 0 0 5269.5197 12.011699 + 8700 16738.475 0 0 5269.5199 12.011715 + 8750 16738.475 0 0 5269.52 12.011732 + 8800 16738.475 0 0 5269.52 12.011743 + 8850 16738.476 0 0 5269.5201 12.011744 + 8900 16738.476 0 0 5269.5202 12.011735 + 8950 16738.476 0 0 5269.5203 12.011719 + 9000 16738.477 0 0 5269.5205 12.011698 + 9050 16738.477 0 0 5269.5206 12.011683 + 9100 16738.478 0 0 5269.5208 12.011684 + 9150 16738.479 0 0 5269.521 12.011701 + 9200 16738.479 0 0 5269.5212 12.011722 + 9250 16738.479 0 0 5269.5213 12.011738 + 9300 16738.48 0 0 5269.5214 12.011746 + 9350 16738.48 0 0 5269.5214 12.011744 + 9400 16738.48 0 0 5269.5215 12.011732 + 9450 16738.48 0 0 5269.5216 12.011715 + 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 + 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 + 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9650 16738.765 -0.10191523 0 5269.5092 12.011013 + 9700 16735.041 1.0589887 0 5269.4979 12.062708 + 9750 16738.013 0.135501 0 5269.5101 11.407245 + 9800 16738.512 -0.011620329 0 5269.5201 11.394973 + 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9950 16738.49 0 0 5269.5245 11.395076 + 10000 16738.49 0 0 5269.5246 11.395075 +Loop time of 0.206235 on 4 procs for 10000 steps with 81 atoms + +Performance: 418940.303 tau/day, 48488.461 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0026572 | 0.004187 | 0.0050838 | 1.5 | 2.03 +Neigh | 0.012115 | 0.012789 | 0.013634 | 0.5 | 6.20 +Comm | 0.084275 | 0.089969 | 0.095318 | 1.5 | 43.62 +Output | 0.0048559 | 0.0051559 | 0.0059836 | 0.7 | 2.50 +Modify | 0.077074 | 0.083586 | 0.088022 | 1.5 | 40.53 +Other | | 0.01055 | | | 5.11 + +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:00 diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.1 b/examples/rigid/log.20Apr18.rigid.tnr.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..097fd132aa7c352d4ceac0735d1f9b455ec8e002 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.tnr.g++.1 @@ -0,0 +1,458 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule +800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 + 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 + 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 + 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 + 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 + 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 + 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 + 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 + 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 + 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 + 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 + 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 + 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 + 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 + 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 + 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 + 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 + 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 + 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 + 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 + 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 + 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216998 -0.0032636911 + 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 + 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738261 0.0090537939 0.013165402 + 2500 1.4153808 5.9421661 7.0538718 0.00015906308 7.0607216 62.244 62.244 62.244 0.0023516211 -0.0019814987 0.00010706678 + 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 + 2700 1.4138077 5.9369067 7.047377 0.0024268843 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960354 0.00049277379 + 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113032 0.0047214106 + 2900 1.3938659 5.921023 7.01583 0.0053751201 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566097 0.0064197134 + 3000 1.390221 5.9205014 7.0124455 -0.0010750973 6.9661486 62.244 62.244 62.244 0.0019519817 -0.0041878875 -0.0009893861 + 3100 1.4205722 5.9178284 7.0336117 0.0098735467 7.4587964 62.244 62.244 62.244 0.0040973349 0.012167268 0.013356037 + 3200 1.398418 5.9150349 7.0134173 0.0061541837 7.278435 62.244 62.244 62.244 0.0067621825 0.011952562 -0.00025219321 + 3300 1.4269859 5.9148727 7.0356937 0.006062387 7.2967584 62.244 62.244 62.244 0.012956233 -2.480748e-05 0.005255736 + 3400 1.434286 5.9356705 7.0622253 0.0002731615 7.0739885 62.244 62.244 62.244 -0.00054959543 0.0052526331 -0.0038835532 + 3500 1.4416808 5.9228153 7.0551783 0.0083383068 7.414251 62.244 62.244 62.244 0.0073994017 0.0030328023 0.014582716 + 3600 1.4136063 5.9039442 7.0142562 0.0019711852 7.0991414 62.244 62.244 62.244 -0.00032317688 0.0035029725 0.0027337599 + 3700 1.433382 5.91201 7.0378548 0.0071286927 7.3448378 62.244 62.244 62.244 0.0064768108 0.0046765006 0.010232767 + 3800 1.3659481 5.9032872 6.9761663 -0.0054034056 6.7434793 62.244 62.244 62.244 -0.007394357 -0.0082833116 -0.00053254832 + 3900 1.396322 5.9043001 7.0010362 0.005331024 7.2306062 62.244 62.244 62.244 0.0081855301 0.0048806234 0.0029269184 + 4000 1.412548 5.906066 7.0155468 0.0028450132 7.1380616 62.244 62.244 62.244 0.0052588387 0.00072412871 0.0025520721 + 4100 1.3943949 5.9040868 6.9993093 0.0058053193 7.2493039 62.244 62.244 62.244 0.0060583148 0.0024781972 0.0088794459 + 4200 1.4249768 5.8906369 7.0098798 0.0030209006 7.1399689 62.244 62.244 62.244 0.0061742017 -0.0020795681 0.0049680681 + 4300 1.3899827 5.8966327 6.9883897 0.0057278096 7.2350464 62.244 62.244 62.244 0.0049035059 0.0021868561 0.010093067 + 4400 1.4414361 5.8986386 7.0308094 0.0050941357 7.2501783 62.244 62.244 62.244 0.0057971901 0.0037941986 0.0056910185 + 4500 1.4093099 5.8922729 6.9992103 0.0012182325 7.0516711 62.244 62.244 62.244 0.0042896986 0.0014287789 -0.00206378 + 4600 1.3779677 5.892894 6.9752138 0.002057623 7.0638213 62.244 62.244 62.244 0.0029271755 -0.0031752166 0.0064209102 + 4700 1.4086418 5.9096898 7.0161024 -0.00052853259 6.9933422 62.244 62.244 62.244 -0.001862386 -0.0018129293 0.0020897176 + 4800 1.4394 5.9146102 7.0451818 0.015326441 7.7051846 62.244 62.244 62.244 0.014754936 0.017967956 0.013256431 + 4900 1.4496219 5.9074613 7.0460616 0.0075297868 7.370317 62.244 62.244 62.244 0.0092907193 0.0079794674 0.0053191736 + 5000 1.4280291 5.9106136 7.032254 -0.0013249587 6.9751972 62.244 62.244 62.244 -0.0044875103 0.0020723667 -0.0015597324 +Loop time of 6.73744 on 1 procs for 5000 steps with 5600 atoms + +Performance: 320596.735 tau/day, 742.122 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.52635 | 0.52635 | 0.52635 | 0.0 | 7.81 +Bond | 0.26628 | 0.26628 | 0.26628 | 0.0 | 3.95 +Neigh | 1.5927 | 1.5927 | 1.5927 | 0.0 | 23.64 +Comm | 0.16011 | 0.16011 | 0.16011 | 0.0 | 2.38 +Output | 0.0040634 | 0.0040634 | 0.0040634 | 0.0 | 0.06 +Modify | 4.0145 | 4.0145 | 4.0145 | 0.0 | 59.58 +Other | | 0.1735 | | | 2.57 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1352 ave 1352 max 1352 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5257 ave 5257 max 5257 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5257 +Ave neighs/atom = 0.93875 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 766 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule +800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4280291 5.9106136 7.032254 0.02814128 8.2441024 62.244 62.244 62.244 0.019873502 0.039656784 0.024893554 + 5100 1.4435659 5.8998386 7.0336823 0.0063929319 7.3089813 62.244 62.244 62.244 0.0089837757 0.0052773116 0.0049177085 + 5200 1.3970069 5.9117164 7.0089904 0.0065245686 7.289958 62.244 62.244 62.244 0.008502047 0.0043872479 0.0066844108 + 5300 1.433167 5.8796669 7.0053428 0.0076478538 7.3346825 62.244 62.244 62.244 0.0061384889 0.0070193789 0.0097856935 + 5400 1.4191626 5.8830864 6.9977626 0.0026371359 7.1113257 62.244 62.244 62.244 0.0024097043 -0.00082200506 0.0063237084 + 5500 1.409376 5.8753367 6.982326 0.010180815 7.4207427 62.244 62.244 62.244 0.010429709 0.0081711083 0.011941628 + 5600 1.4005678 5.882485 6.9825559 0.00036705268 6.9983623 62.244 62.244 62.244 -0.0034485466 0.0031079204 0.0014417843 + 5700 1.4116833 5.8842566 6.9930582 0.00053413233 7.0160595 62.244 62.244 62.244 0.0016669624 -0.0030741941 0.0030096286 + 5800 1.409035 5.894902 7.0016235 4.7080816e-05 7.003651 62.244 62.244 62.244 0.0018596854 -5.3937508e-05 -0.0016645054 + 5900 1.4150353 5.8928576 7.004292 0.0063467985 7.2776043 62.244 62.244 62.244 0.0055755751 0.0090839847 0.0043808358 + 6000 1.4374163 5.8778036 7.0068171 0.0031890481 7.1441472 62.244 62.244 62.244 0.0067647375 0.0015458579 0.0012565488 +Loop time of 1.41082 on 1 procs for 1000 steps with 5600 atoms + +Performance: 306205.780 tau/day, 708.810 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.149 | 0.149 | 0.149 | 0.0 | 10.56 +Bond | 0.053873 | 0.053873 | 0.053873 | 0.0 | 3.82 +Neigh | 0.35532 | 0.35532 | 0.35532 | 0.0 | 25.19 +Comm | 0.032433 | 0.032433 | 0.032433 | 0.0 | 2.30 +Output | 0.00080752 | 0.00080752 | 0.00080752 | 0.0 | 0.06 +Modify | 0.78447 | 0.78447 | 0.78447 | 0.0 | 55.60 +Other | | 0.03491 | | | 2.47 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1347 ave 1347 max 1347 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5592 ave 5592 max 5592 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5592 +Ave neighs/atom = 0.998571 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 153 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 +800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.4374163 5.8778036 7.0068171 -0.0020672233 6.9177963 62.244 62.244 62.244 0.034504923 -0.030001164 -0.010705429 + 6100 1.4393824 5.8852696 7.0158274 0.0055792227 7.2560855 62.244 62.244 62.244 0.0072602759 0.0074870643 0.0019903278 + 6200 1.4265711 5.8853532 7.0058484 0.0019366613 7.0892468 62.244 62.244 62.244 -0.0035411799 0.0047319741 0.0046191897 + 6300 1.4030198 5.8824874 6.9844843 0.0055760353 7.2246052 62.244 62.244 62.244 0.0031273033 0.0080002386 0.005600564 + 6400 1.3592064 5.8924876 6.9600714 0.0051450348 7.1816321 62.244 62.244 62.244 0.0042848197 0.0044005693 0.0067497155 + 6500 1.3946028 5.8798014 6.9751872 0.0051168754 7.1955353 62.244 62.244 62.244 0.0020473208 0.0038175566 0.0094857487 + 6600 1.3652122 5.8985637 6.9708648 0.0065480579 7.2528439 62.244 62.244 62.244 0.0056940621 0.0062242398 0.0077258719 + 6700 1.3808929 5.9047739 6.9893913 0.0074053719 7.308289 62.244 62.244 62.244 0.0049554161 0.012378296 0.0048824031 + 6800 1.4140879 5.891133 7.0018233 0.001592636 7.070407 62.244 62.244 62.244 -9.4421917e-05 -0.00029455229 0.0051668821 + 6900 1.4364121 5.8904988 7.0187235 0.00647853 7.2977086 62.244 62.244 62.244 0.0024458531 0.0073279625 0.0096617742 + 7000 1.4370567 5.8900758 7.0188069 0.00098705898 7.0613127 62.244 62.244 62.244 0.0024436343 -0.0011032284 0.001620771 +Loop time of 1.44111 on 1 procs for 1000 steps with 5600 atoms + +Performance: 299769.942 tau/day, 693.912 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14928 | 0.14928 | 0.14928 | 0.0 | 10.36 +Bond | 0.053511 | 0.053511 | 0.053511 | 0.0 | 3.71 +Neigh | 0.35946 | 0.35946 | 0.35946 | 0.0 | 24.94 +Comm | 0.033026 | 0.033026 | 0.033026 | 0.0 | 2.29 +Output | 0.00081658 | 0.00081658 | 0.00081658 | 0.0 | 0.06 +Modify | 0.80995 | 0.80995 | 0.80995 | 0.0 | 56.20 +Other | | 0.03506 | | | 2.43 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1351 ave 1351 max 1351 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5541 ave 5541 max 5541 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5541 +Ave neighs/atom = 0.989464 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 153 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.4370567 5.8900758 7.0188069 -0.0033603557 6.8740999 62.244 62.244 62.244 -0.094745193 0.10894465 -0.024280521 + 7100 1.485379 5.864626 7.0313116 0.018625962 7.6475425 57.008236 57.008236 57.008236 0.023222208 0.015549704 0.017105973 + 7200 1.5367991 5.8157585 7.0228319 0.019179143 7.4580039 50.273593 50.273593 50.273593 0.019479917 0.008906575 0.029150938 + 7300 1.5692285 5.785208 7.0177529 0.026450106 7.4560147 45.27218 45.27218 45.27218 0.029705272 0.019989987 0.029655059 + 7400 1.5961415 5.7633541 7.0170377 0.049085262 7.6510208 41.665015 41.665015 41.665015 0.045248259 0.047932005 0.054075524 + 7500 1.5805951 5.7223115 6.9637843 0.022024393 7.1962354 38.952791 38.952791 38.952791 0.017398546 0.0097043058 0.038970326 + 7600 1.5679583 5.6928914 6.9244386 0.05023237 7.3717858 36.808633 36.808633 36.808633 0.029561593 0.080716323 0.040419195 + 7700 1.5214637 5.661404 6.8564322 0.038992847 7.1614257 35.25044 35.25044 35.25044 0.013961981 0.064676103 0.038340457 + 7800 1.5313649 5.6185256 6.8213307 0.053950562 7.1990319 33.971403 33.971403 33.971403 0.036690654 0.066107903 0.059053129 + 7900 1.5272701 5.5732963 6.7728851 0.067896988 7.2131774 33.115109 33.115109 33.115109 0.046486851 0.073976177 0.083227936 + 8000 1.4754162 5.5525858 6.7114461 0.036458901 6.9347086 32.48878 32.48878 32.48878 0.066065978 0.031260775 0.01204995 +Loop time of 3.09124 on 1 procs for 1000 steps with 5600 atoms + +Performance: 139749.554 tau/day, 323.494 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.38334 | 0.38334 | 0.38334 | 0.0 | 12.40 +Bond | 0.079063 | 0.079063 | 0.079063 | 0.0 | 2.56 +Neigh | 1.3711 | 1.3711 | 1.3711 | 0.0 | 44.35 +Comm | 0.07249 | 0.07249 | 0.07249 | 0.0 | 2.35 +Output | 0.00079656 | 0.00079656 | 0.00079656 | 0.0 | 0.03 +Modify | 1.1412 | 1.1412 | 1.1412 | 0.0 | 36.92 +Other | | 0.04324 | | | 1.40 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2922 ave 2922 max 2922 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24639 ave 24639 max 24639 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 24639 +Ave neighs/atom = 4.39982 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 335 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.784 | 7.784 | 7.784 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.4754162 5.5525858 6.7114461 -0.036273091 6.4893215 32.48878 32.48878 32.48878 -0.12886524 -0.13731772 0.15736368 + 8100 1.4842494 5.5359706 6.701769 0.040754696 6.9494736 32.246136 32.48878 32.48878 0.0098547221 0.069850343 0.042559024 + 8200 1.4385513 5.5252007 6.6551057 -0.0053954052 6.6228379 31.729684 32.48878 32.48878 0.029251386 -0.023427626 -0.022009975 + 8300 1.4426011 5.5073818 6.6404676 0.034683453 6.8437384 31.093797 32.48878 32.48878 0.028287259 0.027455229 0.048307871 + 8400 1.4194517 5.5015592 6.6164624 0.015869651 6.7074209 30.408624 32.48878 32.48878 0.020129982 0.00586219 0.021616782 + 8500 1.4584335 5.4424151 6.5879365 0.025786252 6.7324275 29.728548 32.48878 32.48878 0.051564744 0.0046756434 0.021118368 + 8600 1.4578973 5.4266016 6.5717019 0.061244725 6.9097759 29.286286 32.48878 32.48878 0.08652905 0.052448352 0.044756773 + 8700 1.4158345 5.4199695 6.5320317 0.076133238 6.9466617 28.894001 32.48878 32.48878 0.078560655 0.077921379 0.071917679 + 8800 1.4360707 5.3986549 6.5266116 0.05106059 6.7993343 28.337182 32.48878 32.48878 0.030158729 0.080651224 0.042371819 + 8900 1.424778 5.386975 6.5060619 0.0023828771 6.5185272 27.75397 32.48878 32.48878 -0.026562751 0.0076340254 0.026077357 + 9000 1.4273004 5.369067 6.490135 0.077698761 6.8879525 27.163833 32.48878 32.48878 0.056923916 0.050917329 0.12525504 +Loop time of 3.05599 on 1 procs for 1000 steps with 5600 atoms + +Performance: 141361.930 tau/day, 327.227 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.60397 | 0.60397 | 0.60397 | 0.0 | 19.76 +Bond | 0.080384 | 0.080384 | 0.080384 | 0.0 | 2.63 +Neigh | 1.1078 | 1.1078 | 1.1078 | 0.0 | 36.25 +Comm | 0.057267 | 0.057267 | 0.057267 | 0.0 | 1.87 +Output | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.03 +Modify | 1.1674 | 1.1674 | 1.1674 | 0.0 | 38.20 +Other | | 0.03837 | | | 1.26 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3326 ave 3326 max 3326 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31301 ave 31301 max 31301 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31301 +Ave neighs/atom = 5.58946 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 168 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.787 | 7.787 | 7.787 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.4273004 5.369067 6.490135 0.075024718 6.8742614 27.163833 32.48878 32.48878 0.020257355 0.083191009 0.12162579 + 9100 1.425834 5.3711961 6.4911123 0.045582762 6.7236289 27.13015 32.448495 32.448495 0.047970965 0.045448278 0.043329042 + 9200 1.4609827 5.3288319 6.4763555 0.072880923 6.8414166 26.96611 32.252298 32.252298 0.053774659 0.093193782 0.071674329 + 9300 1.448717 5.3331013 6.4709909 0.048446002 6.7095138 26.811748 32.067676 32.067676 0.053340258 0.056657855 0.035339893 + 9400 1.441683 5.326611 6.4589758 0.014571871 6.5288665 26.578822 31.789089 31.789089 0.043939432 -0.038654064 0.038430244 + 9500 1.4651641 5.2943716 6.4451796 0.079668782 6.8205296 26.421077 31.600422 31.600422 0.10411792 0.075090335 0.059798087 + 9600 1.4617024 5.2886327 6.4367216 0.01137432 6.4894218 26.274239 31.424799 31.424799 0.023318055 0.015516795 -0.0047118896 + 9700 1.4381296 5.2798198 6.4093935 0.030371415 6.5484925 26.173039 31.303761 31.303761 0.05231569 0.025227191 0.013571362 + 9800 1.4412744 5.2674085 6.3994523 0.076731911 6.7476559 26.092768 31.207754 31.207754 0.05712947 0.077029719 0.096036545 + 9900 1.4427959 5.2666411 6.39988 0.034570225 6.5551479 26.003248 31.100686 31.100686 0.020955217 0.019879252 0.062876207 + 10000 1.4337411 5.258442 6.3845688 0.011619021 6.4367617 26.004486 31.102166 31.102166 0.018666906 0.01076669 0.005423467 +Loop time of 3.23963 on 1 procs for 1000 steps with 5600 atoms + +Performance: 133348.758 tau/day, 308.678 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.71266 | 0.71266 | 0.71266 | 0.0 | 22.00 +Bond | 0.0805 | 0.0805 | 0.0805 | 0.0 | 2.48 +Neigh | 1.2019 | 1.2019 | 1.2019 | 0.0 | 37.10 +Comm | 0.061646 | 0.061646 | 0.061646 | 0.0 | 1.90 +Output | 0.00080585 | 0.00080585 | 0.00080585 | 0.0 | 0.02 +Modify | 1.1436 | 1.1436 | 1.1436 | 0.0 | 35.30 +Other | | 0.03849 | | | 1.19 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3617 ave 3617 max 3617 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 35834 ave 35834 max 35834 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 35834 +Ave neighs/atom = 6.39893 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 162 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.793 | 7.793 | 7.793 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.4337411 5.258442 6.3845688 0.26156311 7.559515 26.004486 31.102166 31.102166 0.31569183 0.56043401 -0.091436513 + 10100 1.4450694 5.2429626 6.3779872 0.026397674 6.4966895 26.018016 31.118349 31.102166 0.012890725 0.035887426 0.030414871 + 10200 1.4603735 5.2471262 6.3941713 0.041496848 6.5804213 25.993694 31.089259 31.102166 0.043043384 0.031851909 0.04959525 + 10300 1.4434562 5.2268279 6.3605855 0.073867581 6.6874051 25.808018 30.867184 31.102166 0.049265569 0.084151743 0.08818543 + 10400 1.4391471 5.209772 6.3401449 0.010656841 6.3865593 25.605881 30.625422 31.102166 -0.012411333 -0.014743822 0.059125677 + 10500 1.4239127 5.2146206 6.3330277 0.08346505 6.689122 25.342982 30.310987 31.102166 0.15420896 0.040839126 0.055347067 + 10600 1.4524651 5.1794989 6.3203324 -0.025909515 6.2120807 25.079294 29.995608 31.102166 -0.014573849 -0.056558124 -0.0065965719 + 10700 1.4455577 5.1721256 6.3075337 0.084888991 6.6555495 24.842844 29.712806 31.102166 0.10063515 0.067972312 0.08605951 + 10800 1.4598996 5.15251 6.2991829 0.11430526 6.7624231 24.700034 29.542001 31.102166 0.12408423 0.12316195 0.095669606 + 10900 1.4149128 5.1641212 6.2754594 0.045495923 6.4584246 24.605124 29.428485 31.102166 0.10001213 0.053235051 -0.016759411 + 11000 1.3909637 5.1566933 6.2492208 0.046382806 6.433354 24.446408 29.238657 31.102166 0.091440494 0.0046064525 0.043101472 +Loop time of 3.41971 on 1 procs for 1000 steps with 5600 atoms + +Performance: 126326.531 tau/day, 292.423 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.78521 | 0.78521 | 0.78521 | 0.0 | 22.96 +Bond | 0.080655 | 0.080655 | 0.080655 | 0.0 | 2.36 +Neigh | 1.2846 | 1.2846 | 1.2846 | 0.0 | 37.57 +Comm | 0.064334 | 0.064334 | 0.064334 | 0.0 | 1.88 +Output | 0.00080228 | 0.00080228 | 0.00080228 | 0.0 | 0.02 +Modify | 1.1651 | 1.1651 | 1.1651 | 0.0 | 34.07 +Other | | 0.03903 | | | 1.14 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3805 ave 3805 max 3805 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40038 ave 40038 max 40038 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 40038 +Ave neighs/atom = 7.14964 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 162 +Dangerous builds = 0 + +Total wall time: 0:00:22 diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.4 b/examples/rigid/log.20Apr18.rigid.tnr.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..28457f51ee4fef7fbc8db5d263e0abfa27bf8e61 --- /dev/null +++ b/examples/rigid/log.20Apr18.rigid.tnr.g++.4 @@ -0,0 +1,458 @@ +LAMMPS (20 Apr 2018) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule +800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 + 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 + 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 + 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 + 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 + 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 + 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 + 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 + 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 + 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 + 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 + 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 + 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 + 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 + 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278431 + 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 + 1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 + 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 + 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 + 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119435 -0.0036279901 + 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 + 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 + 2300 1.4048926 5.9444129 7.0478808 0.0062444035 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 + 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825028 + 2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539 + 2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112 + 2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357 + 2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412 + 2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892 + 3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658 + 3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485 + 3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783 + 3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048 + 3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724 + 3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433 + 3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225 + 3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455 + 3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624 + 3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689 + 4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626 + 4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172 + 4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746 + 4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924 + 4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638 + 4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334 + 4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263 + 4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225 + 4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449 + 4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056 + 5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771 +Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms + +Performance: 624133.913 tau/day, 1444.754 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85 +Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91 +Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76 +Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58 +Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10 +Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02 +Other | | 0.2 | | | 5.78 + +Nlocal: 1400 ave 1844 max 907 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 642 ave 714 max 581 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 1307.25 ave 1883 max 682 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 5229 +Ave neighs/atom = 0.93375 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 762 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule +800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215 + 5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298 + 5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911 + 5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068 + 5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373 + 5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707 + 5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387 + 5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341 + 5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223 + 5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198 + 6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689 +Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms + +Performance: 544612.641 tau/day, 1260.677 timesteps/s +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55 +Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66 +Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30 +Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11 +Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09 +Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66 +Other | | 0.04459 | | | 5.62 + +Nlocal: 1400 ave 1844 max 884 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 713.5 ave 818 max 656 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Neighs: 1315 ave 1956 max 573 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 5260 +Ave neighs/atom = 0.939286 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 156 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 +800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779 + 6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027 + 6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881 + 6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499 + 6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801 + 6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659 + 6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155 + 6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075 + 6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066 + 6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381 + 7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375 +Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms + +Performance: 531376.713 tau/day, 1230.039 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74 +Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62 +Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33 +Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10 +Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09 +Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04 +Other | | 0.04134 | | | 5.09 + +Nlocal: 1400 ave 1861 max 953 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 732.5 ave 799 max 634 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 1478.5 ave 2087 max 852 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 5914 +Ave neighs/atom = 1.05607 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 154 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619 + 7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475 + 7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823 + 7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808 + 7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154 + 7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934 + 7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266 + 7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104 + 7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242 + 7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921 + 8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435 +Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms + +Performance: 292430.022 tau/day, 676.921 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82 +Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35 +Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30 +Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68 +Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03 +Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73 +Other | | 0.04563 | | | 3.09 + +Nlocal: 1400 ave 1711 max 1074 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1617 ave 1748 max 1514 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 6221.75 ave 8875 max 3829 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 24887 +Ave neighs/atom = 4.44411 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 340 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.408 | 7.596 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531 + 8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895 + 8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249 + 8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714 + 8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747 + 8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867 + 8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873 + 8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702 + 8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987 + 8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801 + 9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686 +Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms + +Performance: 304989.819 tau/day, 705.995 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25 +Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42 +Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36 +Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21 +Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04 +Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92 +Other | | 0.03963 | | | 2.80 + +Nlocal: 1400 ave 1641 max 1120 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 1593.5 ave 1674 max 1480 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 7766.25 ave 10004 max 5618 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 31065 +Ave neighs/atom = 5.54732 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 168 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.409 | 7.596 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595 + 9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716 + 9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967 + 9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325 + 9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319 + 9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422 + 9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125 + 9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226 + 9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283 + 9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026 + 10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892 +Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms + +Performance: 293069.938 tau/day, 678.403 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07 +Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37 +Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66 +Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03 +Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04 +Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18 +Other | | 0.0391 | | | 2.65 + +Nlocal: 1400 ave 1629 max 1159 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 1760.25 ave 1871 max 1635 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Neighs: 9467.75 ave 11967 max 6712 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 37871 +Ave neighs/atom = 6.76268 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 163 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506 + 10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812 + 10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461 + 10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255 + 10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884 + 10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428 + 10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401 + 10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703 + 10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507 + 10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896 + 11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759 +Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms + +Performance: 287222.965 tau/day, 664.868 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15 +Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36 +Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36 +Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19 +Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03 +Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41 +Other | | 0.0375 | | | 2.49 + +Nlocal: 1400 ave 1605 max 1229 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Nghost: 1859 ave 1964 max 1718 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 10208.2 ave 13091 max 7670 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 40833 +Ave neighs/atom = 7.29161 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 160 +Dangerous builds = 0 + +Total wall time: 0:00:10 diff --git a/examples/rigid/log.5Oct16.rigid.poems.g++.1 b/examples/rigid/log.5Oct16.rigid.poems.g++.1 deleted file mode 100644 index 8b5e47c00a078b92f4a66c0fb0a4cf30229c1949..0000000000000000000000000000000000000000 --- a/examples/rigid/log.5Oct16.rigid.poems.g++.1 +++ /dev/null @@ -1,332 +0,0 @@ -LAMMPS (5 Oct 2016) -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 18 18 18 -Memory usage per processor = 2.96781 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384277 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184717 - 1150 20849.582 206.01695 0 3680.9472 -0.86699149 - 1200 21815.003 45.317414 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064078 - 1300 20780.781 217.36506 0 3680.8286 6.0538616 - 1350 20558.971 254.36482 0 3680.8601 -3.6773952 - 1400 21485.029 99.812921 0 3680.6511 -16.185473 - 1450 21771.107 52.15961 0 3680.6775 -2.4756673 - 1500 21520.948 93.503927 0 3680.3286 2.1023576 - 1550 21351.418 121.68137 0 3680.2511 5.5159947 - 1600 20778.805 216.92177 0 3680.0559 15.089188 - 1650 21477.638 100.21836 0 3679.8247 -1.1045746 - 1700 18501.339 596.47914 0 3680.0357 -15.679679 - 1750 18563.642 587.34785 0 3681.2882 33.532209 - 1800 19110.185 494.8234 0 3679.8543 18.024046 - 1850 21364.191 119.23545 0 3679.9339 2.5291103 - 1900 20146.626 322.14867 0 3679.9197 5.7313218 - 1950 20692.672 231.25325 0 3680.0319 4.2977763 - 2000 20943.904 189.11235 0 3679.7629 -22.645121 - 2050 19668.057 401.82994 0 3679.8394 3.6251916 - 2100 20280.442 299.76155 0 3679.8353 7.4807949 - 2150 19181.86 483.522 0 3680.4987 22.620507 - 2200 21300.161 130.70534 0 3680.7322 4.7102665 - 2250 20486.943 266.63931 0 3681.1299 -8.6456512 - 2300 18653.122 572.24819 0 3681.1018 -5.2637122 - 2350 21513.523 95.614901 0 3681.2021 -9.3621767 - 2400 21466.272 103.56446 0 3681.2765 -29.561368 - 2450 20100.105 332.27123 0 3682.2887 35.744287 - 2500 20764.395 221.6677 0 3682.4001 -12.468906 - 2550 20435.699 276.31055 0 3682.2603 -22.413697 - 2600 21466.467 104.53618 0 3682.2807 -10.078508 - 2650 20814.737 213.23892 0 3682.3617 5.1390411 - 2700 18565.761 588.3578 0 3682.6513 22.27664 - 2750 20772.36 220.1607 0 3682.2206 -7.9448198 - 2800 21018.563 179.10058 0 3682.1945 -7.0717829 - 2850 16789.412 884.21472 0 3682.4501 33.279015 - 2900 19304.363 464.75282 0 3682.1466 7.947554 - 2950 20513.758 263.07578 0 3682.0355 2.2361434 - 3000 20617.309 245.95251 0 3682.1706 -0.75213689 - 3050 18567.52 587.90473 0 3682.4914 -4.0112006 - 3100 18696.577 566.20617 0 3682.3023 -1.4814167 - 3150 19864.606 371.56078 0 3682.3284 8.9362836 - 3200 18902.643 532.04614 0 3682.4867 0.76630303 - 3250 21110.454 163.86212 0 3682.271 -1.6253894 - 3300 19369.939 454.05833 0 3682.3816 4.9066544 - 3350 19082.603 501.69905 0 3682.133 3.5982292 - 3400 19527.779 426.918 0 3681.5478 6.9612143 - 3450 19892.953 366.19989 0 3681.6921 3.0050426 - 3500 19708.981 396.84552 0 3681.6756 7.0757635 - 3550 20256.096 306.23937 0 3682.2554 -1.752138 - 3600 21289.889 133.93823 0 3682.253 -3.7462615 - 3650 18333.877 627.18028 0 3682.8264 -15.276791 - 3700 19829.133 377.33753 0 3682.1931 -6.269648 - 3750 20771.635 220.07171 0 3682.0109 -28.479036 - 3800 18373.813 619.79253 0 3682.0947 29.594781 - 3850 19320.99 461.92786 0 3682.0928 -5.3212101 - 3900 16119.825 995.68064 0 3682.3182 -8.4683118 - 3950 15556.948 1091.3655 0 3684.1902 20.98273 - 4000 20000.464 348.24891 0 3681.6596 7.1589745 - 4050 18870.219 536.59924 0 3681.6358 -3.7997025 - 4100 19889.518 367.49253 0 3682.4122 -14.091266 - 4150 15789.623 1051.3399 0 3682.9438 -4.4152389 - 4200 20548.889 256.83493 0 3681.6498 0.92234153 - 4250 20681.925 235.46113 0 3682.4487 -11.515773 - 4300 19330.404 460.80975 0 3682.5437 -22.351775 - 4350 19369.443 453.35405 0 3681.5945 29.418242 - 4400 20762.165 222.24133 0 3682.6021 2.6627047 - 4450 19984.657 350.71294 0 3681.4891 28.88731 - 4500 21167.58 154.25344 0 3682.1834 -3.0784322 - 4550 18133.576 660.73671 0 3682.9995 2.5305835 - 4600 19935.069 360.36826 0 3682.8798 2.4575034 - 4650 21413.76 113.86464 0 3682.8246 -5.1271547 - 4700 21716.333 63.609419 0 3682.9982 -2.4708049 - 4750 21352.947 124.36961 0 3683.1941 -0.29026265 - 4800 19043.788 508.8617 0 3682.8264 14.797006 - 4850 20516.121 263.78758 0 3683.1411 7.1348281 - 4900 20624.5 245.81827 0 3683.235 0.34708051 - 4950 20317.197 296.68937 0 3682.8889 -0.55065946 - 5000 18346.865 625.37246 0 3683.1832 7.3371413 - 5050 18867.53 538.49153 0 3683.0799 1.9249866 - 5100 18790.276 551.17224 0 3682.885 2.2333017 - 5150 20241.365 311.84683 0 3685.4076 -3.998004 - 5200 17685.058 739.76418 0 3687.2739 3.2835025 - 5250 18496.626 604.58166 0 3687.3526 -10.185776 - 5300 18420.042 617.82026 0 3687.8273 -16.392458 - 5350 18767.338 559.0349 0 3686.9246 4.5320767 - 5400 20423.245 284.90517 0 3688.7794 -8.6356656 - 5450 21080.398 176.18494 0 3689.5846 -16.450038 - 5500 16684.424 909.12643 0 3689.8637 49.94555 - 5550 20132.31 335.03663 0 3690.4216 -16.018038 - 5600 20430.923 285.17562 0 3690.3295 -5.0773675 - 5650 20479.943 276.55962 0 3689.8834 5.4334564 - 5700 20061.532 345.95553 0 3689.5441 -16.230658 - 5750 20523.759 268.92217 0 3689.5487 -4.4128812 - 5800 18900.356 537.65462 0 3687.7139 13.605549 - 5850 20280.502 310.27193 0 3690.3556 -4.7884959 - 5900 19050.26 515.66087 0 3690.7042 7.8864722 - 5950 19566.917 430.2997 0 3691.4525 31.715268 - 6000 18878.118 544.75449 0 3691.1076 -4.2415329 - 6050 19308.682 471.70734 0 3689.821 -10.561614 - 6100 18776.194 560.04764 0 3689.4133 -7.7286747 - 6150 21475.064 110.1508 0 3689.3281 -3.6506391 - 6200 19975 360.82675 0 3689.9934 10.282021 - 6250 21396.341 123.5341 0 3689.5909 -5.7215163 - 6300 18533.423 600.87422 0 3689.778 15.408027 - 6350 20653.152 247.19253 0 3689.3846 8.5607784 - 6400 19716.537 403.41487 0 3689.5044 13.165575 - 6450 21120.66 168.79838 0 3688.9084 -0.50382728 - 6500 19700.345 404.7155 0 3688.1064 13.941375 - 6550 10818.393 1892.037 0 3695.1025 38.423155 - 6600 18684.478 574.84755 0 3688.9273 5.9176985 - 6650 19219.732 486.04269 0 3689.3314 18.287659 - 6700 20058.587 344.88255 0 3687.9804 6.5372086 - 6750 21279.318 142.77333 0 3689.3264 2.498188 - 6800 20671.545 244.25024 0 3689.5078 -4.1356416 - 6850 21203.598 155.82001 0 3689.753 -0.0083061182 - 6900 21699.344 73.301497 0 3689.8588 -8.0309898 - 6950 20951.212 197.19403 0 3689.0627 0.76668303 - 7000 20166.275 329.02869 0 3690.0746 2.0083318 - 7050 21554.944 97.465792 0 3689.9564 -3.2420086 - 7100 20817.494 220.25476 0 3689.8372 0.17206182 - 7150 21481.11 109.84029 0 3690.0253 -3.6814741 - 7200 21266.824 145.53099 0 3690.0016 -2.060543 - 7250 19434.684 450.81331 0 3689.9273 9.4822765 - 7300 21246.525 148.96573 0 3690.0532 3.3208839 - 7350 19749.269 398.60049 0 3690.1454 1.0929662 - 7400 20354.792 297.70261 0 3690.168 1.547159 - 7450 19996.859 357.16723 0 3689.977 -0.68412025 - 7500 20179.628 326.53243 0 3689.8038 -2.4805507 - 7550 18765.184 561.65039 0 3689.1811 -1.7976428 - 7600 19457.496 447.04428 0 3689.9603 -1.9055522 - 7650 18206.823 655.57276 0 3690.0433 1.2797964 - 7700 19152.344 497.77422 0 3689.8315 18.145069 - 7750 21387.484 125.48654 0 3690.0673 -2.9915772 - 7800 18127.052 668.61425 0 3689.7896 9.044869 - 7850 21419.557 120.08889 0 3690.015 6.2651717 - 7900 21817.182 53.739819 0 3689.9368 -4.2387416 - 7950 18215.195 654.15494 0 3690.0208 -54.628049 - 8000 21523.503 102.58018 0 3689.8307 -4.84236 - 8050 20720.799 236.28689 0 3689.7535 -9.3725225 - 8100 21196.483 157.3232 0 3690.0704 -7.7222497 - 8150 20869.667 211.65308 0 3689.9309 -6.8438295 - 8200 17790.052 725.72497 0 3690.7336 -25.697688 - 8250 19634.94 417.71929 0 3690.2094 8.861604 - 8300 19135.784 500.92443 0 3690.2218 -3.1245167 - 8350 20191.718 324.93312 0 3690.2195 6.5736107 - 8400 20695.239 241.02378 0 3690.2302 -14.592221 - 8450 21793.857 57.609525 0 3689.9191 -11.509747 - 8500 21271.088 144.43102 0 3689.6124 -0.091587085 - 8550 20064.337 345.21754 0 3689.2737 9.5058471 - 8600 20282.86 308.2307 0 3688.7074 2.265529 - 8650 21223.055 151.24306 0 3688.419 1.7296834 - 8700 18875.342 542.42055 0 3688.3108 6.367148 - 8750 20922.65 201.55122 0 3688.6595 3.4208578 - 8800 21406.54 120.8539 0 3688.6106 1.8253729 - 8850 19868.524 377.05623 0 3688.477 16.327796 - 8900 20025.322 348.94892 0 3686.5025 17.063406 - 8950 21224.374 151.3567 0 3688.7524 -0.11028753 - 9000 21318.309 135.862 0 3688.9135 -0.50826819 - 9050 17538.618 768.00136 0 3691.1043 37.978645 - 9100 21247.861 147.84641 0 3689.1566 -6.7773259 - 9150 18455.677 613.08767 0 3689.0339 -3.4844751 - 9200 19486.859 441.03829 0 3688.8482 -18.602827 - 9250 21774.926 59.710446 0 3688.8648 -13.379919 - 9300 17628.877 750.72321 0 3688.8694 27.797974 - 9350 19827.334 383.85708 0 3688.4128 6.5459021 - 9400 20020.126 351.61742 0 3688.3051 -14.332562 - 9450 21596.338 88.904175 0 3688.2939 1.5779716 - 9500 18981.418 524.60141 0 3688.1711 5.4352409 - 9550 18652.616 579.05144 0 3687.8208 25.600729 - 9600 21198.037 155.23097 0 3688.2371 -3.3586596 - 9650 19958.317 361.32544 0 3687.7115 4.2910178 - 9700 19129.101 499.5993 0 3687.7828 13.267102 - 9750 21913.967 35.689587 0 3688.0174 -7.3222905 - 9800 21314.694 135.43794 0 3687.8869 -9.5613518 - 9850 20899.743 204.82802 0 3688.1185 -2.6321428 - 9900 20288.244 306.5013 0 3687.8753 3.6196618 - 9950 19271.015 475.88527 0 3687.7211 -1.8196764 - 10000 21122.24 167.82714 0 3688.2005 -3.8464842 -Loop time of 3.6648 on 1 procs for 10000 steps with 81 atoms - -Performance: 23575.670 tau/day, 2728.665 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.15599 | 0.15599 | 0.15599 | 0.0 | 4.26 -Neigh | 0.099093 | 0.099093 | 0.099093 | 0.0 | 2.70 -Comm | 0.0088665 | 0.0088665 | 0.0088665 | 0.0 | 0.24 -Output | 0.0016377 | 0.0016377 | 0.0016377 | 0.0 | 0.04 -Modify | 3.392 | 3.392 | 3.392 | 0.0 | 92.56 -Other | | 0.007194 | | | 0.20 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 95 ave 95 max 95 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 744 ave 744 max 744 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 744 -Ave neighs/atom = 9.18519 -Neighbor list builds = 992 -Dangerous builds = 941 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.5Oct16.rigid.poems.g++.4 b/examples/rigid/log.5Oct16.rigid.poems.g++.4 deleted file mode 100644 index 06610ea5c8e9ece3f154dc4c9d1730e592c7bc69..0000000000000000000000000000000000000000 --- a/examples/rigid/log.5Oct16.rigid.poems.g++.4 +++ /dev/null @@ -1,332 +0,0 @@ -LAMMPS (5 Oct 2016) -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 18 18 18 -Memory usage per processor = 2.94053 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384276 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184718 - 1150 20849.582 206.01695 0 3680.9472 -0.8669916 - 1200 21815.003 45.317417 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064076 - 1300 20780.781 217.36504 0 3680.8286 6.0538619 - 1350 20558.972 254.3648 0 3680.8601 -3.6773987 - 1400 21485.029 99.812949 0 3680.6511 -16.185471 - 1450 21771.108 52.15959 0 3680.6775 -2.4756681 - 1500 21520.948 93.503949 0 3680.3286 2.1023578 - 1550 21351.418 121.6814 0 3680.2511 5.5159978 - 1600 20778.805 216.92171 0 3680.0559 15.089182 - 1650 21477.639 100.2182 0 3679.8247 -1.1045944 - 1700 18501.343 596.47853 0 3680.0357 -15.67963 - 1750 18563.643 587.34767 0 3681.2882 33.532167 - 1800 19110.19 494.82264 0 3679.8543 18.024034 - 1850 21364.196 119.23454 0 3679.9339 2.5291491 - 1900 20146.643 322.14595 0 3679.9197 5.731152 - 1950 20692.67 231.25357 0 3680.0319 4.2977641 - 2000 20943.904 189.11223 0 3679.763 -22.645645 - 2050 19668.152 401.81407 0 3679.8394 3.6255896 - 2100 20280.572 299.73976 0 3679.8351 7.4809355 - 2150 19182.121 483.47905 0 3680.4992 22.615309 - 2200 21299.76 130.77281 0 3680.7327 4.7114154 - 2250 20487.784 266.4995 0 3681.1302 -8.6406776 - 2300 18655.125 571.91487 0 3681.1023 -5.2671669 - 2350 21512.614 95.766913 0 3681.2025 -9.3523428 - 2400 21467.773 103.31519 0 3681.2773 -29.600307 - 2450 20096.937 332.80159 0 3682.2911 35.890912 - 2500 20761.446 222.16118 0 3682.4022 -12.528127 - 2550 20409.6 280.67234 0 3682.2723 -22.277373 - 2600 21469.964 103.95529 0 3682.2826 -10.038267 - 2650 20708.138 231.00516 0 3682.3615 5.3659502 - 2700 18584.743 585.07862 0 3682.5357 21.785261 - 2750 20503.019 264.91491 0 3682.0847 -4.5583917 - 2800 20584.075 251.44664 0 3682.1258 -6.5084595 - 2850 17277.076 802.33356 0 3681.8462 15.519513 - 2900 19392.956 449.92915 0 3682.0885 -4.3829957 - 2950 18371.786 620.29835 0 3682.2626 7.2117592 - 3000 20412.015 280.25302 0 3682.2555 0.32492606 - 3050 20858.248 205.65269 0 3682.0273 4.5055715 - 3100 21561.094 88.438447 0 3681.9541 -3.7523733 - 3150 15471.278 1103.4497 0 3681.9961 -14.576367 - 3200 15386.973 1117.8815 0 3682.377 15.051163 - 3250 19741.037 392.04755 0 3682.2204 -2.6610995 - 3300 20870.191 203.58229 0 3681.9475 -4.7795545 - 3350 16648.228 907.66571 0 3682.3704 -8.9242511 - 3400 20104.016 331.58603 0 3682.2554 6.4783858 - 3450 21421.316 112.28228 0 3682.5015 -8.3484987 - 3500 19284.533 467.80739 0 3681.8962 -12.835452 - 3550 20160.125 322.4476 0 3682.4684 1.6574827 - 3600 16682.415 902.73752 0 3683.14 22.383296 - 3650 16762.19 890.14636 0 3683.8446 16.119412 - 3700 17858.568 707.37212 0 3683.8 -1.6582504 - 3750 20029.881 345.15986 0 3683.4733 -3.1415889 - 3800 20734 227.99158 0 3683.6582 -7.9580418 - 3850 20741.089 226.39408 0 3683.2423 8.3055765 - 3900 18671.251 571.42296 0 3683.2981 -3.7468858 - 3950 19547.209 423.14256 0 3681.0108 5.8312279 - 4000 19739.799 393.58799 0 3683.5544 18.604884 - 4050 20014.121 347.8176 0 3683.5044 9.93387 - 4100 20503.654 266.08691 0 3683.3626 8.1304118 - 4150 18309.702 632.29807 0 3683.9151 -0.0021480359 - 4200 20509.423 265.60353 0 3683.8408 -2.1658857 - 4250 21805.541 50.325935 0 3684.5828 1.082842 - 4300 21420.551 114.90431 0 3684.9962 -1.7985998 - 4350 20256.928 308.74187 0 3684.8966 -11.669472 - 4400 21633.488 79.629274 0 3685.2106 -0.96131785 - 4450 20793.327 219.66955 0 3685.2241 1.3752349 - 4500 18719.484 564.86754 0 3684.7816 2.6308699 - 4550 20966.335 190.68308 0 3685.0722 -18.587627 - 4600 19428.962 446.59618 0 3684.7565 -4.4051672 - 4650 18408.956 616.85009 0 3685.0095 2.777272 - 4700 19215.779 482.57562 0 3685.2054 19.441016 - 4750 20155.927 326.13401 0 3685.4553 6.1734993 - 4800 20918.085 199.31832 0 3685.6659 3.4407437 - 4850 20236.958 312.07276 0 3684.899 3.2612893 - 4900 21419.89 115.36879 0 3685.3505 -4.675951 - 4950 19707.901 401.14828 0 3685.7985 -10.730734 - 5000 19407.201 450.64394 0 3685.1775 17.518981 - 5050 21527.598 97.655186 0 3685.5882 -9.2294707 - 5100 21581.933 88.595517 0 3685.5843 -20.669485 - 5150 21161.214 158.48503 0 3685.3541 -2.7587502 - 5200 21166.679 157.24762 0 3685.0275 -18.180044 - 5250 20909.576 200.23507 0 3685.1644 -16.617303 - 5300 21911.746 33.236563 0 3685.1942 -5.8313967 - 5350 20857.303 208.87453 0 3685.0916 12.176312 - 5400 20958.96 191.96694 0 3685.1269 3.6116429 - 5450 20433.179 279.61178 0 3685.1415 13.324529 - 5500 19604.675 416.88499 0 3684.3308 21.536484 - 5550 18171.145 655.92915 0 3684.4534 -9.2269804 - 5600 19799.907 385.12116 0 3685.1056 22.202165 - 5650 19711.882 399.30581 0 3684.6194 15.93063 - 5700 17908.833 699.52405 0 3684.3295 0.35530356 - 5750 18606.518 583.538 0 3684.6243 -4.4540843 - 5800 21814.053 48.974627 0 3684.6501 -1.5206358 - 5850 18029.107 679.9357 0 3684.7868 12.137677 - 5900 21090.739 169.64502 0 3684.7682 -1.5051545 - 5950 21086.26 170.29075 0 3684.6674 -2.8164474 - 6000 21285.771 136.95608 0 3684.5846 -26.582739 - 6050 21203.994 150.87822 0 3684.8772 -2.6617226 - 6100 21481.553 104.57796 0 3684.8368 -16.524974 - 6150 20354.4 292.57675 0 3684.9767 2.7960207 - 6200 21326.591 130.75243 0 3685.1843 -1.5929194 - 6250 21505.087 101.07817 0 3685.2593 -3.7821931 - 6300 21296.273 135.6593 0 3685.0382 -0.55635908 - 6350 21295.389 135.86485 0 3685.0964 5.6614093 - 6400 16552.242 926.02655 0 3684.7336 14.177218 - 6450 20148.951 327.1151 0 3685.2736 7.4561085 - 6500 20962.151 191.79415 0 3685.486 -4.5436711 - 6550 21710.328 67.433972 0 3685.8219 -5.7678572 - 6600 20698.571 234.79099 0 3684.5528 -2.1984068 - 6650 17892.287 704.05484 0 3686.1026 11.525836 - 6700 21272.999 141.26589 0 3686.7657 0.44088069 - 6750 19558.993 426.46448 0 3686.2966 -16.907401 - 6800 20350.247 295.23951 0 3686.9474 1.1284348 - 6850 18665.05 573.5326 0 3684.3742 17.088712 - 6900 19769.199 392.1551 0 3687.0216 6.7562425 - 6950 19439.159 446.99138 0 3686.8512 -6.0105763 - 7000 19379.907 456.53471 0 3686.5192 -9.0505095 - 7050 19983.754 356.02523 0 3686.651 -5.6274314 - 7100 19867.737 375.47627 0 3686.7658 17.315482 - 7150 19258.794 477.47344 0 3687.2724 14.316676 - 7200 21282.428 139.96051 0 3687.0318 -0.77043459 - 7250 19828.603 381.98919 0 3686.7564 6.5142869 - 7300 20574.582 257.8245 0 3686.9215 -3.6547118 - 7350 21613.467 84.771568 0 3687.0161 -7.5188826 - 7400 21817.009 50.844944 0 3687.0131 -14.888864 - 7450 14937.538 1197.4257 0 3687.0154 1.7540499 - 7500 18326.914 632.40374 0 3686.8894 8.3397357 - 7550 13611.007 1418.4727 0 3686.9739 -19.379482 - 7600 19173.985 491.9482 0 3687.6123 17.229001 - 7650 16911.504 867.33649 0 3685.9204 -21.042834 - 7700 21752.116 61.143705 0 3686.4963 -10.344487 - 7750 20208.337 318.26355 0 3686.3197 13.385814 - 7800 21649.909 77.950987 0 3686.2692 -1.7911084 - 7850 20139.64 329.50319 0 3686.1098 -5.5805093 - 7900 21355.026 126.7642 0 3685.9352 -7.7062172 - 7950 21336.178 129.88925 0 3685.9188 -2.059298 - 8000 21047.596 177.71546 0 3685.6482 0.37963466 - 8050 19217.351 482.62331 0 3685.5152 6.5582595 - 8100 20499.057 268.7173 0 3685.2268 -1.1959737 - 8150 21494.301 102.83829 0 3685.2219 -1.6427647 - 8200 20074.928 339.19817 0 3685.0195 6.285123 - 8250 17335.157 793.47566 0 3682.6685 22.877381 - 8300 17340.544 794.62619 0 3684.7168 3.9147755 - 8350 20529.345 262.51162 0 3684.0691 4.031768 - 8400 18884.747 537.47827 0 3684.9361 22.853404 - 8450 20341.86 293.10484 0 3683.4148 0.33856656 - 8500 19300.282 467.58127 0 3684.2949 12.35507 - 8550 21631.936 78.254534 0 3683.5772 -10.992959 - 8600 20204.913 316.83233 0 3684.3178 20.74228 - 8650 21018.189 181.32054 0 3684.352 1.8412068 - 8700 20161.304 323.97907 0 3684.1964 -2.646629 - 8750 19081.79 504.00155 0 3684.2998 -10.088053 - 8800 20834.489 211.76247 0 3684.1773 14.896336 - 8850 20929.355 196.18335 0 3684.4092 -1.2602398 - 8900 21491.074 102.47788 0 3684.3235 -1.4696758 - 8950 20474.735 271.69461 0 3684.1504 -6.9489258 - 9000 21128.641 162.40732 0 3683.8474 -7.7928168 - 9050 18421.801 614.46442 0 3684.7646 24.40313 - 9100 19301.292 466.98873 0 3683.8707 4.4687046 - 9150 21575.705 88.213763 0 3684.1646 -0.94696984 - 9200 20004.776 350.05448 0 3684.1838 -7.3466605 - 9250 21384.079 120.14472 0 3684.1578 -8.3773844 - 9300 21980.599 20.702393 0 3684.1356 -12.666293 - 9350 21686.606 69.517984 0 3683.9524 -8.8366533 - 9400 20732.704 228.46247 0 3683.9131 -6.4080307 - 9450 19798.859 384.34696 0 3684.1568 7.6198484 - 9500 20270.695 305.22664 0 3683.6758 1.5862486 - 9550 16496.156 935.28481 0 3684.6441 15.001468 - 9600 20642.429 241.08853 0 3681.4934 -9.2159382 - 9650 21292.587 135.4474 0 3684.2119 -0.54770976 - 9700 18888.158 536.60518 0 3684.6315 5.3236926 - 9750 18750.018 559.35922 0 3684.3623 -9.9424949 - 9800 20544.772 259.71076 0 3683.8394 8.732202 - 9850 16698.125 901.90076 0 3684.9216 9.9553329 - 9900 21450.963 109.58687 0 3684.7474 -4.8001999 - 9950 20664.461 240.66995 0 3684.7468 -3.4840781 - 10000 18951.367 526.45428 0 3685.0155 21.512727 -Loop time of 3.89095 on 4 procs for 10000 steps with 81 atoms - -Performance: 22205.346 tau/day, 2570.063 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.012426 | 0.039516 | 0.089301 | 15.3 | 1.02 -Neigh | 0.012618 | 0.027118 | 0.055113 | 10.4 | 0.70 -Comm | 0.16629 | 0.21469 | 0.26329 | 8.2 | 5.52 -Output | 0.0051188 | 0.0053029 | 0.0055087 | 0.2 | 0.14 -Modify | 3.5241 | 3.5783 | 3.6729 | 3.0 | 91.96 -Other | | 0.02605 | | | 0.67 - -Nlocal: 20.25 ave 81 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 46.25 ave 95 max 14 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 249.25 ave 997 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 997 -Ave neighs/atom = 12.3086 -Neighbor list builds = 993 -Dangerous builds = 943 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.5Oct16.rigid.poems2.g++.1 b/examples/rigid/log.5Oct16.rigid.poems2.g++.1 deleted file mode 100644 index edbef2d5b691d05bff1f665704301a72079aadc0..0000000000000000000000000000000000000000 --- a/examples/rigid/log.5Oct16.rigid.poems2.g++.1 +++ /dev/null @@ -1,336 +0,0 @@ -LAMMPS (5 Oct 2016) -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 -1 clusters, 4 bodies, 3 joints, 36 atoms -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -1 clusters, 5 bodies, 4 joints, 45 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -WARNING: More than one fix poems (../fix_poems.cpp:352) -WARNING: More than one fix poems (../fix_poems.cpp:352) -WARNING: One or more atoms are time integrated more than once (../modify.cpp:269) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 18 18 18 -Memory usage per processor = 3.53031 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12167.633 1505.5478 0 3758.8133 35.125973 - 100 17556.978 512.66277 0 3763.9549 11.137534 - 150 19579.586 138.04942 0 3763.8987 -29.953971 - 200 19757.51 105.30542 0 3764.1036 -0.030645317 - 250 18218.374 390.10747 0 3763.8804 13.711001 - 300 19383.039 174.40688 0 3763.8586 5.7240693 - 350 20125.986 36.972611 0 3764.0071 1.9559205 - 400 18888.816 266.10975 0 3764.0386 9.6362168 - 450 19307.656 188.2511 0 3763.743 1.9326206 - 500 16331.197 738.56392 0 3762.8597 9.1715579 - 550 19318.722 186.16172 0 3763.7027 3.0115336 - 600 19455.268 161.20621 0 3764.0336 0.55208034 - 650 18487.011 340.03216 0 3763.5528 -8.0359122 - 700 17321.201 556.32471 0 3763.9545 -13.631751 - 750 18979.187 249.04389 0 3763.7082 -2.6072455 - 800 19342.456 181.85552 0 3763.7918 8.1918726 - 850 19070.641 232.19342 0 3763.7936 7.3148472 - 900 19478.873 156.65987 0 3763.8586 2.4284987 - 950 19912.415 76.437437 0 3763.9216 -1.4667227 - 1000 16003.749 802.39753 0 3766.0548 46.642188 - 1050 19859.583 86.64176 0 3764.3424 -2.1961943 - 1100 19229.575 203.61488 0 3764.6473 -10.632365 - 1150 18821.6 279.15861 0 3764.64 -0.89495035 - 1200 19392.695 173.59744 0 3764.8373 1.8508753 - 1250 16459.624 717.32104 0 3765.3995 33.478127 - 1300 19343.863 182.59043 0 3764.7874 0.75890736 - 1350 20019.643 57.503573 0 3764.8448 0.31444671 - 1400 18549.582 329.31436 0 3764.4221 10.738303 - 1450 15163.926 957.47585 0 3765.6103 -17.923459 - 1500 19223.688 204.15175 0 3764.0939 -1.6134531 - 1550 18147.996 404.12677 0 3764.8668 8.4194779 - 1600 18615.043 317.42467 0 3764.6548 -2.3288934 - 1650 20120.654 38.887913 0 3764.935 -8.7620277 - 1700 19450.907 162.98272 0 3765.0025 2.3254731 - 1750 19374.632 177.37966 0 3765.2744 8.9328774 - 1800 19424.404 167.93966 0 3765.0514 0.081230261 - 1850 17936.249 442.84231 0 3764.3699 6.6010636 - 1900 19982.595 64.406198 0 3764.8868 -2.9529813 - 1950 16215.852 761.91287 0 3764.8485 13.994708 - 2000 18584.422 322.12049 0 3763.68 7.1654003 - 2050 20107.965 41.025754 0 3764.723 -0.3109069 - 2100 20002.333 60.593017 0 3764.7288 -6.7919784 - 2150 16949.762 626.59623 0 3765.441 3.508941 - 2200 20010.953 58.808279 0 3764.5403 -10.862172 - 2250 18982.73 247.00892 0 3762.3292 -0.53807815 - 2300 18401.298 354.87973 0 3762.5274 1.0920554 - 2350 19390.524 172.9415 0 3763.7793 -3.3524932 - 2400 16080.801 786.38838 0 3764.3146 -16.200514 - 2450 18870.412 268.74976 0 3763.2705 11.197736 - 2500 19688.29 117.58223 0 3763.5618 4.382644 - 2550 18870.825 268.78678 0 3763.384 -5.6623656 - 2600 17019.35 611.70808 0 3763.4395 6.3109641 - 2650 18753.285 291.0596 0 3763.8902 2.4120296 - 2700 19742.456 107.20901 0 3763.2193 -0.33061303 - 2750 19522.438 148.16759 0 3763.4339 -1.6254851 - 2800 18304.801 372.55152 0 3762.3295 22.6368 - 2850 18465.36 343.48495 0 3762.9961 4.4169272 - 2900 20151.999 31.372926 0 3763.2245 1.2013699 - 2950 15498.143 892.80071 0 3762.8272 13.263724 - 3000 18728.301 294.65113 0 3762.855 8.1897838 - 3050 18538.466 330.25223 0 3763.3015 8.5865739 - 3100 19081.409 229.5907 0 3763.1849 -4.8573813 - 3150 18498.802 337.11548 0 3762.8195 1.0555321 - 3200 19925.897 73.358029 0 3763.339 -7.7325108 - 3250 19780.108 100.23785 0 3763.2209 -5.5974972 - 3300 19221.043 203.82387 0 3763.2763 4.2703251 - 3350 19025.292 240.11329 0 3763.3156 5.7708328 - 3400 18153.696 401.52086 0 3763.3164 21.076943 - 3450 18611.375 316.50396 0 3763.0548 -3.5484945 - 3500 19931.319 71.969274 0 3762.9543 1.8764978 - 3550 19747.562 106.05439 0 3763.0103 -2.5506186 - 3600 18491.39 338.4134 0 3762.7449 -4.0527808 - 3650 19757.998 104.19207 0 3763.0806 1.4865598 - 3700 20108.003 39.345514 0 3763.0498 0.062827129 - 3750 19222.505 203.28065 0 3763.0039 0.33719277 - 3800 19286.383 191.08831 0 3762.6406 -0.1826802 - 3850 19450.083 161.09138 0 3762.9587 -0.2708263 - 3900 18002.304 429.25655 0 3763.0166 -4.6832439 - 3950 17186.829 582.26502 0 3765.0111 55.816834 - 4000 16826.434 645.84974 0 3761.856 19.675962 - 4050 19227.526 202.18151 0 3762.8344 -0.2596098 - 4100 19908.792 76.084531 0 3762.8978 -2.796813 - 4150 17821.329 462.63065 0 3762.8768 13.069155 - 4200 19917.133 74.574998 0 3762.9329 -6.4181155 - 4250 19012.618 241.96787 0 3762.823 4.0847974 - 4300 19077.34 229.98133 0 3762.8221 4.324323 - 4350 19361.128 177.47406 0 3762.8681 -7.377974 - 4400 18565.044 324.95107 0 3762.9223 2.5229032 - 4450 19352.406 178.98756 0 3762.7665 0.10862717 - 4500 18482.218 340.15496 0 3762.788 12.518301 - 4550 18359.732 362.83749 0 3762.7879 3.7500902 - 4600 19623.618 128.71624 0 3762.7196 -1.1328521 - 4650 17565.707 509.99904 0 3762.9078 1.7135935 - 4700 19876.052 81.892814 0 3762.6431 0.32476108 - 4750 19022.676 239.92262 0 3762.6403 -0.24613022 - 4800 18862.685 269.24248 0 3762.3324 6.2733979 - 4850 19899.174 77.426145 0 3762.4584 0.42535238 - 4900 18250.865 382.72867 0 3762.5185 23.308462 - 4950 18895.847 263.22651 0 3762.4575 8.0634675 - 5000 19096.705 225.69358 0 3762.1204 3.6816481 - 5050 16546.294 698.91312 0 3763.0416 17.453618 - 5100 19501.208 151.20999 0 3762.5449 -1.1231291 - 5150 19479.879 155.00669 0 3762.3917 -3.983378 - 5200 17397.818 541.23039 0 3763.0485 6.1109992 - 5250 18564.869 324.10557 0 3762.0442 9.2244762 - 5300 16271.663 747.52374 0 3760.7947 -6.5256602 - 5350 19831.418 89.851887 0 3762.3367 -2.3453958 - 5400 18723.697 294.67435 0 3762.0256 4.6822081 - 5450 19547.28 142.21934 0 3762.086 -5.5243408 - 5500 19415.447 166.68729 0 3762.1404 -9.5658991 - 5550 18492.721 337.54773 0 3762.1256 6.5184903 - 5600 19391.389 171.14375 0 3762.1416 -0.53835361 - 5650 18503.465 334.62751 0 3761.1951 4.6580363 - 5700 18153.344 399.91064 0 3761.6409 12.851587 - 5750 18342.297 365.14769 0 3761.8694 2.7148176 - 5800 19583.241 135.64969 0 3762.1758 -1.089608 - 5850 15967.283 804.18382 0 3761.088 11.278762 - 5900 19040.271 235.35509 0 3761.3312 5.1352158 - 5950 17920.962 443.17951 0 3761.8762 4.9621366 - 6000 19100.92 224.3946 0 3761.602 -9.537589 - 6050 17982.119 432.3251 0 3762.3472 -2.851617 - 6100 16233.096 755.46191 0 3761.5908 25.113316 - 6150 18316.543 370.01118 0 3761.9635 -1.7445703 - 6200 18483.464 339.13282 0 3761.9966 -2.0857447 - 6250 18609.406 315.56032 0 3761.7467 -12.289208 - 6300 17167.919 582.68212 0 3761.9264 -3.8263397 - 6350 17870.329 452.58116 0 3761.9013 -3.3843134 - 6400 19309.717 186.11786 0 3761.9913 -4.9462739 - 6450 17964.073 435.39924 0 3762.0794 12.272972 - 6500 18772.847 285.61959 0 3762.0727 6.7928648 - 6550 18915.116 259.41365 0 3762.213 -4.1449761 - 6600 19446.628 161.18763 0 3762.415 -2.1906581 - 6650 16348.787 734.99282 0 3762.546 -9.9624546 - 6700 19066.684 231.43863 0 3762.3061 -5.362833 - 6750 14890.323 1004.547 0 3762.0143 37.373013 - 6800 18235.19 385.253 0 3762.1401 0.21012662 - 6850 16447.997 716.11276 0 3762.0382 -9.2095411 - 6900 18343.362 364.81902 0 3761.7379 10.417932 - 6950 16014.084 797.13348 0 3762.7046 6.7906777 - 7000 19120.393 221.29236 0 3762.1059 -1.3461375 - 7050 18055.409 418.30136 0 3761.8957 1.5772317 - 7100 18407.231 353.41868 0 3762.1652 0.61071769 - 7150 18728.136 293.64021 0 3761.8136 5.1649654 - 7200 17706.628 483.07628 0 3762.0815 18.000708 - 7250 19349.505 178.89673 0 3762.1385 2.540201 - 7300 20016.293 55.389159 0 3762.1101 -1.5793163 - 7350 19398.573 169.86661 0 3762.1949 -5.060123 - 7400 19466.526 157.37407 0 3762.2862 1.7158273 - 7450 18440.348 347.09196 0 3761.9712 12.781963 - 7500 19989.907 60.555934 0 3762.3906 -1.5033319 - 7550 19667.28 120.27403 0 3762.363 -3.3502366 - 7600 18497.707 336.15863 0 3761.66 1.7887539 - 7650 17901.957 447.17282 0 3762.3501 0.016725252 - 7700 19758.725 103.3129 0 3762.3361 -23.534448 - 7750 19443.957 161.6532 0 3762.386 -10.323924 - 7800 19776.178 100.1773 0 3762.4324 6.0854422 - 7850 19242.512 198.86705 0 3762.2952 5.2823659 - 7900 19499.929 151.30366 0 3762.4017 12.299911 - 7950 19630.317 127.19541 0 3762.4393 8.0799632 - 8000 19872.384 82.421129 0 3762.4923 2.2126691 - 8050 17747.038 476.27982 0 3762.7683 -7.7042786 - 8100 18832.654 274.78106 0 3762.3095 13.882157 - 8150 19949.814 68.09711 0 3762.5072 -0.54410896 - 8200 17555.866 511.02517 0 3762.1115 6.2471175 - 8250 17800.1 465.9992 0 3762.314 13.583485 - 8300 19755.224 103.89732 0 3762.2721 -1.487243 - 8350 17583.61 506.17539 0 3762.3995 -9.7819128 - 8400 18529.003 330.75623 0 3762.0532 14.731228 - 8450 20155.902 29.797078 0 3762.3716 -8.5711085 - 8500 18047.548 420.54645 0 3762.685 7.3875118 - 8550 19790.794 97.493375 0 3762.4553 -3.3427911 - 8600 19997.902 59.172074 0 3762.4874 3.3479688 - 8650 19987.319 61.148363 0 3762.5037 -1.889232 - 8700 19363.91 176.41833 0 3762.3276 -9.4291288 - 8750 18712.689 296.3979 0 3761.7107 5.9221369 - 8800 19783.17 98.860518 0 3762.4105 -3.5262066 - 8850 18796.049 281.60057 0 3762.3504 -8.2913002 - 8900 16738.277 662.62261 0 3762.3035 8.5838631 - 8950 17869.613 452.25006 0 3761.4377 11.561101 - 9000 18682.512 302.27997 0 3762.0043 3.8878724 - 9050 17513.759 518.50265 0 3761.7914 23.05778 - 9100 17500.686 521.57944 0 3762.4473 -2.8435751 - 9150 19645.683 124.43597 0 3762.5254 -3.0193092 - 9200 18898.897 262.76552 0 3762.5612 3.5891701 - 9250 20114.279 37.614866 0 3762.4813 -0.58120871 - 9300 19562.613 139.54073 0 3762.2468 -3.2630158 - 9350 19679.811 118.05865 0 3762.468 -3.4644363 - 9400 19297.384 188.84527 0 3762.4349 0.40498037 - 9450 18267.029 379.52581 0 3762.309 -0.13762867 - 9500 19951.072 67.63844 0 3762.2814 -7.575539 - 9550 19134.562 218.46835 0 3761.9057 -1.9626244 - 9600 19089.093 227.29178 0 3762.3089 -1.94158 - 9650 16964.603 620.71289 0 3762.3061 16.987042 - 9700 18846.881 271.3129 0 3761.4761 3.4458802 - 9750 19309.225 186.0142 0 3761.7966 9.4048627 - 9800 16359.704 733.51007 0 3763.0849 15.870164 - 9850 19958.532 66.203725 0 3762.2282 6.0043645 - 9900 19864.564 83.502384 0 3762.1253 -0.65360617 - 9950 18996.789 244.25101 0 3762.1749 -2.4961826 - 10000 17933.494 441.33587 0 3762.3532 -6.0731708 -Loop time of 3.80061 on 1 procs for 10000 steps with 81 atoms - -Performance: 22733.175 tau/day, 2631.155 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11276 | 0.11276 | 0.11276 | 0.0 | 2.97 -Neigh | 0.075881 | 0.075881 | 0.075881 | 0.0 | 2.00 -Comm | 0.011113 | 0.011113 | 0.011113 | 0.0 | 0.29 -Output | 0.0016332 | 0.0016332 | 0.0016332 | 0.0 | 0.04 -Modify | 3.5918 | 3.5918 | 3.5918 | 0.0 | 94.51 -Other | | 0.007383 | | | 0.19 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 71 ave 71 max 71 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 612 ave 612 max 612 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 612 -Ave neighs/atom = 7.55556 -Neighbor list builds = 989 -Dangerous builds = 906 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.5Oct16.rigid.poems2.g++.4 b/examples/rigid/log.5Oct16.rigid.poems2.g++.4 deleted file mode 100644 index b408fb6f098ec6b74d06d4b9f44cf19efdbf47fc..0000000000000000000000000000000000000000 --- a/examples/rigid/log.5Oct16.rigid.poems2.g++.4 +++ /dev/null @@ -1,336 +0,0 @@ -LAMMPS (5 Oct 2016) -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 -1 clusters, 4 bodies, 3 joints, 36 atoms -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -1 clusters, 5 bodies, 4 joints, 45 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -WARNING: More than one fix poems (../fix_poems.cpp:352) -WARNING: More than one fix poems (../fix_poems.cpp:352) -WARNING: One or more atoms are time integrated more than once (../modify.cpp:269) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 18 18 18 -Memory usage per processor = 3.50303 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12167.633 1505.5478 0 3758.8133 35.125973 - 100 17556.978 512.66277 0 3763.9549 11.137534 - 150 19579.586 138.04942 0 3763.8987 -29.953971 - 200 19757.51 105.30542 0 3764.1036 -0.030645317 - 250 18218.374 390.10747 0 3763.8804 13.711001 - 300 19383.039 174.40688 0 3763.8586 5.7240693 - 350 20125.986 36.972611 0 3764.0071 1.9559205 - 400 18888.816 266.10975 0 3764.0386 9.6362168 - 450 19307.656 188.2511 0 3763.743 1.9326206 - 500 16331.197 738.56392 0 3762.8597 9.1715579 - 550 19318.722 186.16172 0 3763.7027 3.0115336 - 600 19455.268 161.20621 0 3764.0336 0.55208034 - 650 18487.011 340.03216 0 3763.5528 -8.0359122 - 700 17321.201 556.32471 0 3763.9545 -13.631751 - 750 18979.187 249.04389 0 3763.7082 -2.6072455 - 800 19342.456 181.85552 0 3763.7918 8.1918726 - 850 19070.641 232.19342 0 3763.7936 7.3148472 - 900 19478.873 156.65987 0 3763.8586 2.4284987 - 950 19912.415 76.437437 0 3763.9216 -1.4667227 - 1000 16003.749 802.39753 0 3766.0548 46.642188 - 1050 19859.583 86.64176 0 3764.3424 -2.1961943 - 1100 19229.575 203.61488 0 3764.6473 -10.632365 - 1150 18821.6 279.15861 0 3764.64 -0.89495035 - 1200 19392.695 173.59744 0 3764.8373 1.8508753 - 1250 16459.624 717.32104 0 3765.3995 33.478127 - 1300 19343.863 182.59043 0 3764.7874 0.75890736 - 1350 20019.643 57.503573 0 3764.8448 0.31444671 - 1400 18549.582 329.31436 0 3764.4221 10.738303 - 1450 15163.926 957.47585 0 3765.6103 -17.923459 - 1500 19223.688 204.15176 0 3764.0939 -1.6134529 - 1550 18147.996 404.12677 0 3764.8668 8.4194781 - 1600 18615.043 317.42468 0 3764.6548 -2.3288926 - 1650 20120.654 38.887908 0 3764.935 -8.7620288 - 1700 19450.907 162.98267 0 3765.0025 2.3254739 - 1750 19374.631 177.3797 0 3765.2744 8.9328773 - 1800 19424.404 167.93965 0 3765.0514 0.081228843 - 1850 17936.227 442.84645 0 3764.3699 6.6011251 - 1900 19982.595 64.406244 0 3764.8868 -2.952971 - 1950 16215.818 761.91942 0 3764.8486 13.994877 - 2000 18584.433 322.11846 0 3763.6801 7.1653695 - 2050 20107.965 41.025796 0 3764.723 -0.31089763 - 2100 20002.329 60.593879 0 3764.7288 -6.7919882 - 2150 16949.817 626.58598 0 3765.4409 3.5087505 - 2200 20010.954 58.8082 0 3764.5403 -10.862143 - 2250 18982.732 247.00854 0 3762.3293 -0.53812607 - 2300 18401.276 354.88369 0 3762.5274 1.0921058 - 2350 19390.535 172.93951 0 3763.7793 -3.3524354 - 2400 16080.475 786.44896 0 3764.3146 -16.201558 - 2450 18870.293 268.77171 0 3763.2704 11.199749 - 2500 19688.508 117.54164 0 3763.5617 4.3806994 - 2550 18870.328 268.87896 0 3763.3841 -5.6641099 - 2600 17020.211 611.54841 0 3763.4394 6.3081434 - 2650 18748.838 291.88478 0 3763.8917 2.4175163 - 2700 19743.991 106.92945 0 3763.224 -0.33916964 - 2750 19525.446 147.60906 0 3763.4324 -1.6251174 - 2800 18257.411 381.40184 0 3762.4038 23.39495 - 2850 18496.796 337.65425 0 3762.9868 4.3657735 - 2900 20163.418 29.253902 0 3763.2203 1.4431917 - 2950 16823.317 646.69817 0 3762.1273 4.9041552 - 3000 19223.007 203.2529 0 3763.069 4.0414458 - 3050 17391.02 542.93746 0 3763.4968 15.139863 - 3100 19205.6 206.57791 0 3763.1705 4.8519241 - 3150 19835.659 90.247763 0 3763.5179 -14.900053 - 3200 18962.776 251.5838 0 3763.2089 -13.706561 - 3250 19418.837 167.29058 0 3763.3716 -2.0866468 - 3300 18628.291 313.69067 0 3763.3742 5.9919715 - 3350 17465.974 529.14439 0 3763.5841 14.122593 - 3400 18488.661 339.6186 0 3763.4448 21.526798 - 3450 19163.152 214.26098 0 3762.9928 4.1888096 - 3500 18000.27 429.81789 0 3763.2011 5.4734485 - 3550 19582.423 136.71887 0 3763.0935 -2.5335675 - 3600 19634.325 127.2219 0 3763.208 -1.9728322 - 3650 19428.114 165.40707 0 3763.2059 -2.3318779 - 3700 19861.116 85.356944 0 3763.3414 -3.9097609 - 3750 19337.239 182.43992 0 3763.4102 -3.3559651 - 3800 19493.146 153.40349 0 3763.2453 -0.71089657 - 3850 18607.616 317.74889 0 3763.6037 3.475832 - 3900 19719.59 111.5553 0 3763.3313 0.58876668 - 3950 19756.661 104.5522 0 3763.1931 3.7526698 - 4000 17904.708 447.1673 0 3762.854 12.270654 - 4050 19588.087 135.80435 0 3763.2279 0.94578945 - 4100 19065.901 232.38235 0 3763.1048 -2.7495195 - 4150 18775.075 286.2257 0 3763.0915 -3.7039858 - 4200 18800.725 281.46601 0 3763.0817 0.15619543 - 4250 19732.687 108.90618 0 3763.1075 3.0865861 - 4300 18278.151 377.63653 0 3762.4794 1.5768601 - 4350 17915.757 445.4804 0 3763.2133 -3.7040484 - 4400 15987.794 802.41575 0 3763.1183 22.252078 - 4450 19302.37 188.69495 0 3763.2079 0.91081327 - 4500 20039.32 52.304099 0 3763.2893 -2.0828905 - 4550 19535.953 145.4374 0 3763.2064 -3.3804255 - 4600 19700.723 114.79823 0 3763.0803 -1.1761163 - 4650 17804.641 465.85788 0 3763.0136 7.5947192 - 4700 19913.881 75.240289 0 3762.996 -2.1100557 - 4750 19982.484 62.535995 0 3762.996 -4.5821237 - 4800 17400.76 540.21707 0 3762.58 -5.8418778 - 4850 19199.88 206.90989 0 3762.4433 3.4536341 - 4900 19173.92 212.11327 0 3762.8392 5.0387071 - 4950 19236.635 200.57537 0 3762.9152 -1.4932783 - 5000 19077.616 230.04967 0 3762.9415 4.3742655 - 5050 19893.763 78.909747 0 3762.94 -1.5796711 - 5100 18884.746 265.68301 0 3762.8583 2.2767949 - 5150 17417.096 537.54036 0 3762.9286 -2.8632555 - 5200 18247.844 383.60092 0 3762.8312 10.384179 - 5250 19494.107 152.60532 0 3762.6251 -4.7617287 - 5300 18739.781 292.46206 0 3762.7919 23.210048 - 5350 19310.938 186.62363 0 3762.7232 14.895327 - 5400 19540.39 144.14287 0 3762.7336 6.094624 - 5450 20074.459 45.247888 0 3762.7403 -2.0871835 - 5500 19986.377 61.668045 0 3762.849 -2.4551918 - 5550 19038.904 237.07578 0 3762.7987 5.4250813 - 5600 19439.124 163.1438 0 3762.9816 4.1291468 - 5650 19480.321 155.58325 0 3763.0501 -3.5308058 - 5700 19869.291 83.651379 0 3763.1497 -7.8661592 - 5750 19991.447 61.068554 0 3763.1884 -6.8473586 - 5800 19454.072 160.36805 0 3762.9739 1.527662 - 5850 17994.409 430.95597 0 3763.2539 -5.6078082 - 5900 19209.794 205.74997 0 3763.1193 8.4113055 - 5950 19046.427 236.06321 0 3763.1793 10.463356 - 6000 19409.899 168.95271 0 3763.3785 2.542067 - 6050 18068.174 417.35443 0 3763.3125 10.498199 - 6100 19549.253 143.21885 0 3763.4509 2.3075797 - 6150 18464.719 344.0303 0 3763.4228 0.46469762 - 6200 19811.205 94.62725 0 3763.3689 1.2382763 - 6250 18715.36 297.26445 0 3763.0718 -3.4541762 - 6300 17115.664 594.09913 0 3763.6666 4.2065564 - 6350 18155.927 400.71764 0 3762.9264 1.1521258 - 6400 19873.093 83.169067 0 3763.3716 0.16383592 - 6450 19991.88 61.13218 0 3763.3321 -1.3008128 - 6500 19434.416 164.40698 0 3763.3728 -13.593422 - 6550 19855.253 86.645329 0 3763.544 -0.85704037 - 6600 19251.141 198.41152 0 3763.4376 4.3027745 - 6650 19741.815 107.69047 0 3763.582 4.994835 - 6700 19633.466 127.69333 0 3763.5203 6.3677145 - 6750 16231.353 757.83705 0 3763.6431 -1.5978692 - 6800 18863.396 270.1114 0 3763.3329 -11.915909 - 6850 19644.779 125.29421 0 3763.2163 -1.151217 - 6900 18883.642 266.06889 0 3763.0397 -4.3950749 - 6950 19042.364 236.54144 0 3762.9052 5.5718878 - 7000 18351.868 364.38028 0 3762.8743 7.8958273 - 7050 19981.031 62.840667 0 3763.0316 -5.8572298 - 7100 19796.372 97.073665 0 3763.0685 -3.5178361 - 7150 19805.385 95.235221 0 3762.899 -2.5481726 - 7200 18722.055 295.86113 0 3762.9084 13.826356 - 7250 19537.304 144.54234 0 3762.5616 1.2288666 - 7300 18787.328 283.49504 0 3762.6299 9.0044469 - 7350 18886.005 265.52121 0 3762.9295 6.6791881 - 7400 19891.864 79.239278 0 3762.9178 -2.3882842 - 7450 18164.752 399.07065 0 3762.9137 3.9400481 - 7500 18702.612 299.582 0 3763.0286 4.7987316 - 7550 19884.986 80.231665 0 3762.6365 -0.75016515 - 7600 19549.059 142.16243 0 3762.3586 -2.1035756 - 7650 18223.668 387.9047 0 3762.658 -17.064339 - 7700 19428.4 164.79531 0 3762.6473 -2.8342541 - 7750 19239.584 199.93029 0 3762.8163 3.1746033 - 7800 19458.005 159.46176 0 3762.7961 1.714515 - 7850 18320.308 369.77051 0 3762.4202 2.1422976 - 7900 18817.415 278.04812 0 3762.7546 0.94492621 - 7950 19892.761 79.115928 0 3762.9606 1.4948501 - 8000 19592.344 134.7639 0 3762.9758 -1.8520224 - 8050 19316.109 185.70579 0 3762.7631 -4.8061205 - 8100 19867.017 83.850395 0 3762.9277 -3.496391 - 8150 19129.936 220.29802 0 3762.8789 -2.8357376 - 8200 18449.554 346.30415 0 3762.8883 1.4417837 - 8250 18405.197 354.49049 0 3762.8602 6.7020283 - 8300 18310.437 372.25376 0 3763.0755 3.9043508 - 8350 18842.702 273.55075 0 3762.94 -10.987272 - 8400 18574.308 323.33378 0 3763.0204 12.008785 - 8450 15368.628 918.21692 0 3764.2591 34.80292 - 8500 18432.887 349.54013 0 3763.0378 0.00064258465 - 8550 15777.73 841.79263 0 3763.5945 15.473699 - 8600 17205.381 576.4515 0 3762.6331 2.3985544 - 8650 19773.742 101.48276 0 3763.2869 2.3978892 - 8700 19059.824 232.99716 0 3762.5941 5.2611349 - 8750 19006.086 243.41125 0 3763.0568 4.7880403 - 8800 19492.691 153.0188 0 3762.7763 1.9118755 - 8850 19625.883 128.44474 0 3762.8675 3.4157389 - 8900 19916.97 74.635094 0 3762.9629 -10.157254 - 8950 16012.956 798.16801 0 3763.5302 16.904998 - 9000 19364.051 177.00354 0 3762.9389 -13.373346 - 9050 19133.929 219.61882 0 3762.9389 -7.3824392 - 9100 18657.168 307.85939 0 3762.8905 9.3071421 - 9150 17975.904 434.21548 0 3763.0867 6.9609506 - 9200 19075.282 230.41699 0 3762.8767 7.0961232 - 9250 20115.276 37.578674 0 3762.6298 1.8678552 - 9300 18195.486 393.20682 0 3762.7413 13.272552 - 9350 19617.155 129.85893 0 3762.6653 -2.0849447 - 9400 19276.325 193.03425 0 3762.724 -2.8963555 - 9450 18642.803 310.4759 0 3762.8467 3.407984 - 9500 19175.951 211.72785 0 3762.8298 -0.39025564 - 9550 17669.191 490.85942 0 3762.9319 5.3867954 - 9600 18481.199 340.29485 0 3762.7391 8.9004886 - 9650 20091.442 42.504743 0 3763.1422 -1.3206133 - 9700 19651.405 124.04835 0 3763.1975 1.4000525 - 9750 19138.245 219.03637 0 3763.1558 5.8352794 - 9800 19189.146 209.67958 0 3763.2251 6.214691 - 9850 19899.376 78.096337 0 3763.166 -0.75102404 - 9900 19447.247 161.27279 0 3762.6149 -6.4166376 - 9950 19807.083 95.152663 0 3763.1309 -0.88933698 - 10000 18972.157 249.56342 0 3762.9258 1.9189241 -Loop time of 3.99472 on 4 procs for 10000 steps with 81 atoms - -Performance: 21628.565 tau/day, 2503.306 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0090363 | 0.029554 | 0.05092 | 8.8 | 0.74 -Neigh | 0.0090437 | 0.021045 | 0.034359 | 6.3 | 0.53 -Comm | 0.1326 | 0.17829 | 0.2132 | 7.3 | 4.46 -Output | 0.0044832 | 0.0048217 | 0.0053875 | 0.5 | 0.12 -Modify | 3.6632 | 3.7381 | 3.8211 | 2.9 | 93.58 -Other | | 0.02291 | | | 0.57 - -Nlocal: 20.25 ave 37 max 0 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 17.75 ave 33 max 4 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 144.75 ave 356 max 0 min -Histogram: 2 0 0 0 0 0 1 0 0 1 - -Total # of neighbors = 579 -Ave neighs/atom = 7.14815 -Neighbor list builds = 994 -Dangerous builds = 958 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.5Oct16.rigid.tnr.g++.1 b/examples/rigid/log.5Oct16.rigid.tnr.g++.1 deleted file mode 100644 index 935b7eaf073db00214c230a128fc1e43153dad2e..0000000000000000000000000000000000000000 --- a/examples/rigid/log.5Oct16.rigid.tnr.g++.1 +++ /dev/null @@ -1,452 +0,0 @@ -LAMMPS (5 Oct 2016) -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule -800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 45 45 45 -Memory usage per processor = 7.32042 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 - 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 - 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 - 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 - 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 - 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 - 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 - 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 - 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 - 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 - 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 - 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 - 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 - 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 - 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 - 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 - 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 - 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 - 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 - 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 - 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 - 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911 - 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 - 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402 - 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677 - 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 - 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371 - 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106 - 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713 - 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611 - 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039 - 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251 - 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362 - 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524 - 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699 - 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752 - 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797 - 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772 - 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034 - 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065 - 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387 - 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557 - 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574 - 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421 - 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711 - 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462 - 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986 - 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278 - 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891 - 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248 -Loop time of 6.51777 on 1 procs for 5000 steps with 5600 atoms - -Performance: 331401.531 tau/day, 767.133 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.51894 | 0.51894 | 0.51894 | 0.0 | 7.96 -Bond | 0.24096 | 0.24096 | 0.24096 | 0.0 | 3.70 -Neigh | 1.8769 | 1.8769 | 1.8769 | 0.0 | 28.80 -Comm | 0.16548 | 0.16548 | 0.16548 | 0.0 | 2.54 -Output | 0.0032616 | 0.0032616 | 0.0032616 | 0.0 | 0.05 -Modify | 3.5349 | 3.5349 | 3.5349 | 0.0 | 54.23 -Other | | 0.1774 | | | 2.72 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1351 ave 1351 max 1351 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5254 ave 5254 max 5254 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5254 -Ave neighs/atom = 0.938214 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 766 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule -800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Memory usage per processor = 7.32042 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575 - 5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041 - 5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551 - 5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518 - 5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493 - 5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038 - 5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751 - 5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035 - 5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927 - 5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509 - 6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075 -Loop time of 1.37139 on 1 procs for 1000 steps with 5600 atoms - -Performance: 315008.398 tau/day, 729.186 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.1443 | 0.1443 | 0.1443 | 0.0 | 10.52 -Bond | 0.049211 | 0.049211 | 0.049211 | 0.0 | 3.59 -Neigh | 0.40564 | 0.40564 | 0.40564 | 0.0 | 29.58 -Comm | 0.033721 | 0.033721 | 0.033721 | 0.0 | 2.46 -Output | 0.00065017 | 0.00065017 | 0.00065017 | 0.0 | 0.05 -Modify | 0.70225 | 0.70225 | 0.70225 | 0.0 | 51.21 -Other | | 0.03562 | | | 2.60 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1347 ave 1347 max 1347 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5399 ave 5399 max 5399 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5399 -Ave neighs/atom = 0.964107 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 153 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 -800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Memory usage per processor = 7.32042 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547 - 6100 1.4199699 5.8764035 6.9917138 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644 - 6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912 - 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089 - 6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007 - 6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399 - 6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071 - 6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104 - 6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295 - 6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161 - 7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587 -Loop time of 1.38662 on 1 procs for 1000 steps with 5600 atoms - -Performance: 311550.061 tau/day, 721.181 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.14525 | 0.14525 | 0.14525 | 0.0 | 10.48 -Bond | 0.048966 | 0.048966 | 0.048966 | 0.0 | 3.53 -Neigh | 0.40266 | 0.40266 | 0.40266 | 0.0 | 29.04 -Comm | 0.033521 | 0.033521 | 0.033521 | 0.0 | 2.42 -Output | 0.00064969 | 0.00064969 | 0.00064969 | 0.0 | 0.05 -Modify | 0.71998 | 0.71998 | 0.71998 | 0.0 | 51.92 -Other | | 0.03559 | | | 2.57 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1284 ave 1284 max 1284 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5677 ave 5677 max 5677 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5677 -Ave neighs/atom = 1.01375 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 151 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Memory usage per processor = 7.32042 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105 - 7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125 - 7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191 - 7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083 - 7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005 - 7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388 - 7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969 - 7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222 - 7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539 - 7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293 - 8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532 -Loop time of 3.05773 on 1 procs for 1000 steps with 5600 atoms - -Performance: 141281.224 tau/day, 327.040 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.37231 | 0.37231 | 0.37231 | 0.0 | 12.18 -Bond | 0.07144 | 0.07144 | 0.07144 | 0.0 | 2.34 -Neigh | 1.3968 | 1.3968 | 1.3968 | 0.0 | 45.68 -Comm | 0.071773 | 0.071773 | 0.071773 | 0.0 | 2.35 -Output | 0.00065684 | 0.00065684 | 0.00065684 | 0.0 | 0.02 -Modify | 1.0951 | 1.0951 | 1.0951 | 0.0 | 35.82 -Other | | 0.04962 | | | 1.62 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2963 ave 2963 max 2963 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 25797 ave 25797 max 25797 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 25797 -Ave neighs/atom = 4.60661 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 334 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Memory usage per processor = 7.32428 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422 - 8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751 - 8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372 - 8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297 - 8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178 - 8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915 - 8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181 - 8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894 - 8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909 - 8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701 - 9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594 -Loop time of 2.94424 on 1 procs for 1000 steps with 5600 atoms - -Performance: 146727.069 tau/day, 339.646 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.57781 | 0.57781 | 0.57781 | 0.0 | 19.63 -Bond | 0.072705 | 0.072705 | 0.072705 | 0.0 | 2.47 -Neigh | 1.0768 | 1.0768 | 1.0768 | 0.0 | 36.57 -Comm | 0.052799 | 0.052799 | 0.052799 | 0.0 | 1.79 -Output | 0.00064921 | 0.00064921 | 0.00064921 | 0.0 | 0.02 -Modify | 1.1247 | 1.1247 | 1.1247 | 0.0 | 38.20 -Other | | 0.03878 | | | 1.32 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3244 ave 3244 max 3244 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 30929 ave 30929 max 30929 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 30929 -Ave neighs/atom = 5.52304 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 165 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Memory usage per processor = 7.32428 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468 - 9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506 - 9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019 - 9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646 - 9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819 - 9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816 - 9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606 - 9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953 - 9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761 - 9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473 - 10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177 -Loop time of 3.13351 on 1 procs for 1000 steps with 5600 atoms - -Performance: 137864.384 tau/day, 319.131 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.68 | 0.68 | 0.68 | 0.0 | 21.70 -Bond | 0.073233 | 0.073233 | 0.073233 | 0.0 | 2.34 -Neigh | 1.1775 | 1.1775 | 1.1775 | 0.0 | 37.58 -Comm | 0.057102 | 0.057102 | 0.057102 | 0.0 | 1.82 -Output | 0.00068927 | 0.00068927 | 0.00068927 | 0.0 | 0.02 -Modify | 1.1058 | 1.1058 | 1.1058 | 0.0 | 35.29 -Other | | 0.03924 | | | 1.25 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3635 ave 3635 max 3635 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 38235 ave 38235 max 38235 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 38235 -Ave neighs/atom = 6.82768 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 165 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Memory usage per processor = 7.32811 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455 - 10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324 - 10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629 - 10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924 - 10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076 - 10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106 - 10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706 - 10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299 - 10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395 - 10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071 - 11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746 -Loop time of 3.22377 on 1 procs for 1000 steps with 5600 atoms - -Performance: 134004.591 tau/day, 310.196 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.74959 | 0.74959 | 0.74959 | 0.0 | 23.25 -Bond | 0.073572 | 0.073572 | 0.073572 | 0.0 | 2.28 -Neigh | 1.1793 | 1.1793 | 1.1793 | 0.0 | 36.58 -Comm | 0.057446 | 0.057446 | 0.057446 | 0.0 | 1.78 -Output | 0.00065088 | 0.00065088 | 0.00065088 | 0.0 | 0.02 -Modify | 1.1241 | 1.1241 | 1.1241 | 0.0 | 34.87 -Other | | 0.03903 | | | 1.21 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3799 ave 3799 max 3799 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 39646 ave 39646 max 39646 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 39646 -Ave neighs/atom = 7.07964 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 158 -Dangerous builds = 0 - -Total wall time: 0:00:21 diff --git a/examples/rigid/log.5Oct16.rigid.tnr.g++.4 b/examples/rigid/log.5Oct16.rigid.tnr.g++.4 deleted file mode 100644 index 2a27702446e57a6adc0b139c69592a1b3594b6ed..0000000000000000000000000000000000000000 --- a/examples/rigid/log.5Oct16.rigid.tnr.g++.4 +++ /dev/null @@ -1,452 +0,0 @@ -LAMMPS (5 Oct 2016) -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule -800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 45 45 45 -Memory usage per processor = 6.96454 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 - 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 - 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 - 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 - 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 - 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 - 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 - 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 - 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 - 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 - 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 - 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 - 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 - 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 - 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432 - 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 - 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 - 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 - 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 - 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901 - 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 - 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 - 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 - 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026 - 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538 - 2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116 - 2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359 - 2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055 - 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189 - 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657 - 3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458 - 3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265 - 3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057 - 3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981 - 3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447 - 3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317 - 3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268 - 3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977 - 3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851 - 4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779 - 4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267 - 4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436 - 4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353 - 4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015 - 4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655 - 4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475 - 4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828 - 4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007 - 4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05 - 5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114 -Loop time of 3.14543 on 4 procs for 5000 steps with 5600 atoms - -Performance: 686709.553 tau/day, 1589.605 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.081628 | 0.12747 | 0.17984 | 12.8 | 4.05 -Bond | 0.037502 | 0.057149 | 0.076595 | 7.6 | 1.82 -Neigh | 0.65705 | 0.6588 | 0.66084 | 0.2 | 20.94 -Comm | 0.1653 | 0.23616 | 0.29975 | 12.9 | 7.51 -Output | 0.0021076 | 0.0028133 | 0.003227 | 0.9 | 0.09 -Modify | 1.8231 | 1.8972 | 1.9713 | 5.2 | 60.32 -Other | | 0.1658 | | | 5.27 - -Nlocal: 1400 ave 1868 max 905 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 648.25 ave 688 max 598 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Neighs: 1202.5 ave 1821 max 698 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 4810 -Ave neighs/atom = 0.858929 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 759 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule -800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Memory usage per processor = 6.98553 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407 - 5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113 - 5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599 - 5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984 - 5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427 - 5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784 - 5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228 - 5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215 - 5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708 - 5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003 - 6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208 -Loop time of 0.74555 on 4 procs for 1000 steps with 5600 atoms - -Performance: 579437.739 tau/day, 1341.291 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.020915 | 0.033416 | 0.047822 | 6.7 | 4.48 -Bond | 0.0076883 | 0.011506 | 0.015239 | 3.3 | 1.54 -Neigh | 0.14225 | 0.14262 | 0.14297 | 0.1 | 19.13 -Comm | 0.030192 | 0.0485 | 0.064376 | 7.2 | 6.51 -Output | 0.00039148 | 0.0005275 | 0.00062299 | 0.4 | 0.07 -Modify | 0.46557 | 0.47773 | 0.49051 | 1.7 | 64.08 -Other | | 0.03125 | | | 4.19 - -Nlocal: 1400 ave 1868 max 935 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 633.75 ave 695 max 541 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Neighs: 1263 ave 1799 max 710 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 5052 -Ave neighs/atom = 0.902143 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 153 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 -800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Memory usage per processor = 6.98553 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535 - 6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086 - 6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035 - 6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066 - 6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761 - 6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984 - 6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201 - 6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245 - 6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922 - 6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422 - 7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504 -Loop time of 0.761012 on 4 procs for 1000 steps with 5600 atoms - -Performance: 567665.504 tau/day, 1314.041 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.022122 | 0.034862 | 0.048912 | 6.6 | 4.58 -Bond | 0.0078702 | 0.011574 | 0.015191 | 3.2 | 1.52 -Neigh | 0.1398 | 0.14013 | 0.14044 | 0.1 | 18.41 -Comm | 0.029736 | 0.047586 | 0.064077 | 7.3 | 6.25 -Output | 0.00039291 | 0.00053465 | 0.00063396 | 0.4 | 0.07 -Modify | 0.48838 | 0.49907 | 0.50959 | 1.4 | 65.58 -Other | | 0.02726 | | | 3.58 - -Nlocal: 1400 ave 1832 max 970 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 652.5 ave 749 max 561 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 1407.5 ave 2071 max 748 min -Histogram: 1 1 0 0 0 0 0 0 1 1 - -Total # of neighbors = 5630 -Ave neighs/atom = 1.00536 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 149 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Memory usage per processor = 6.98553 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013 - 7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322 - 7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656 - 7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507 - 7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619 - 7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732 - 7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486 - 7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932 - 7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623 - 7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184 - 8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909 -Loop time of 1.40621 on 4 procs for 1000 steps with 5600 atoms - -Performance: 307209.818 tau/day, 711.134 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.057011 | 0.094542 | 0.13471 | 11.0 | 6.72 -Bond | 0.012043 | 0.017356 | 0.022935 | 3.8 | 1.23 -Neigh | 0.50655 | 0.50716 | 0.50781 | 0.1 | 36.07 -Comm | 0.060325 | 0.10627 | 0.14985 | 12.0 | 7.56 -Output | 0.0003705 | 0.00040978 | 0.00051475 | 0.3 | 0.03 -Modify | 0.60798 | 0.63453 | 0.65863 | 2.9 | 45.12 -Other | | 0.04594 | | | 3.27 - -Nlocal: 1400 ave 1820 max 1010 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 1576 ave 1694 max 1470 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 6543 ave 9989 max 3497 min -Histogram: 1 1 0 0 0 0 0 1 0 1 - -Total # of neighbors = 26172 -Ave neighs/atom = 4.67357 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 337 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Memory usage per processor = 7.00192 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992 - 8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258 - 8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554 - 8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743 - 8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374 - 8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616 - 8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813 - 8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261 - 8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108 - 8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314 - 9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783 -Loop time of 1.3981 on 4 procs for 1000 steps with 5600 atoms - -Performance: 308990.110 tau/day, 715.255 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.090644 | 0.15054 | 0.22186 | 13.5 | 10.77 -Bond | 0.013196 | 0.017756 | 0.022439 | 2.9 | 1.27 -Neigh | 0.40253 | 0.40269 | 0.40288 | 0.0 | 28.80 -Comm | 0.057128 | 0.13282 | 0.1979 | 15.4 | 9.50 -Output | 0.00036597 | 0.00040632 | 0.0004673 | 0.2 | 0.03 -Modify | 0.62613 | 0.65125 | 0.67228 | 2.1 | 46.58 -Other | | 0.04265 | | | 3.05 - -Nlocal: 1400 ave 1770 max 1095 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Nghost: 1578.5 ave 1693 max 1493 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 7868 ave 12041 max 4579 min -Histogram: 1 1 0 0 0 0 1 0 0 1 - -Total # of neighbors = 31472 -Ave neighs/atom = 5.62 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 167 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Memory usage per processor = 7.00192 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195 - 9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818 - 9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101 - 9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889 - 9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919 - 9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297 - 9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945 - 9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026 - 9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122 - 9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308 - 10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946 -Loop time of 1.38185 on 4 procs for 1000 steps with 5600 atoms - -Performance: 312625.215 tau/day, 723.669 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11291 | 0.17289 | 0.23942 | 12.0 | 12.51 -Bond | 0.013814 | 0.017709 | 0.022031 | 2.5 | 1.28 -Neigh | 0.40444 | 0.4048 | 0.40511 | 0.0 | 29.29 -Comm | 0.055045 | 0.12527 | 0.18875 | 14.9 | 9.07 -Output | 0.0003531 | 0.00038058 | 0.00045681 | 0.2 | 0.03 -Modify | 0.60769 | 0.62523 | 0.64283 | 1.7 | 45.25 -Other | | 0.03557 | | | 2.57 - -Nlocal: 1400 ave 1669 max 1139 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 1761.5 ave 1898 max 1632 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 9311.75 ave 12525 max 5959 min -Histogram: 1 0 1 0 0 0 0 1 0 1 - -Total # of neighbors = 37247 -Ave neighs/atom = 6.65125 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 165 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Memory usage per processor = 7.00192 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347 - 10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687 - 10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554 - 10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609 - 10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799 - 10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631 - 10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754 - 10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533 - 10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992 - 10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683 - 11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165 -Loop time of 1.36647 on 4 procs for 1000 steps with 5600 atoms - -Performance: 316143.197 tau/day, 731.813 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.13847 | 0.19365 | 0.24916 | 9.9 | 14.17 -Bond | 0.014236 | 0.017841 | 0.02132 | 2.2 | 1.31 -Neigh | 0.37634 | 0.37662 | 0.37685 | 0.0 | 27.56 -Comm | 0.057297 | 0.11588 | 0.17429 | 13.5 | 8.48 -Output | 0.00035167 | 0.00037664 | 0.00044203 | 0.2 | 0.03 -Modify | 0.61282 | 0.62929 | 0.64128 | 1.4 | 46.05 -Other | | 0.03282 | | | 2.40 - -Nlocal: 1400 ave 1607 max 1199 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 1819.25 ave 1940 max 1712 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 9882 ave 12628 max 7201 min -Histogram: 1 0 1 0 0 0 0 1 0 1 - -Total # of neighbors = 39528 -Ave neighs/atom = 7.05857 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 156 -Dangerous builds = 0 - -Total wall time: 0:00:10 diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c5e0f6abab7b7eb657e529096265fa9d3a9bfcff --- /dev/null +++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 @@ -0,0 +1,127 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Demonstrate SNAP Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.160 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.16 +Lattice spacing in x,y,z = 3.16 3.16 3.16 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 128 atoms + Time spent = 0.000223637 secs + +mass 1 183.84 + +# choose potential + +include Mo_Chen_PRM2017.snap + +# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) +# Generated by Materials Virtual Lab +# Definition of SNAP potential. +pair_style snap +pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo +Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 +SNAP Element = Mo, Radius 0.5, Weight 1 +Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 +SNAP keyword rcutfac 4.615858 +SNAP keyword twojmax 6 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.61586 + ghost atom cutoff = 5.61586 + binsize = 2.80793, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -22.405975 0 -22.3675 2575.7657 + 10 294.77555 -22.405305 0 -22.3675 2756.6894 + 20 279.53011 -22.40335 0 -22.3675 3285.8272 + 30 255.52174 -22.40027 0 -22.3675 4122.8933 + 40 224.7299 -22.396321 0 -22.367499 5204.3499 + 50 189.67529 -22.391825 0 -22.367499 6449.1308 + 60 153.18862 -22.387145 0 -22.367499 7765.911 + 70 118.14998 -22.382652 0 -22.367499 9061.1616 + 80 87.224916 -22.378685 0 -22.367499 10247.68 + 90 62.623892 -22.37553 0 -22.367498 11250.067 + 100 45.9103 -22.373386 0 -22.367498 12011.726 +Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms + +Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.3906 | 3.3906 | 3.3906 | 0.0 | 99.97 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00039721 | 0.00039721 | 0.00039721 | 0.0 | 0.01 +Output | 0.00023007 | 0.00023007 | 0.00023007 | 0.0 | 0.01 +Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.01 +Other | | 0.0002868 | | | 0.01 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 727 ave 727 max 727 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7424 ave 7424 max 7424 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..c25f1f5530856ab7dc5492526aa168c9dafd6fad --- /dev/null +++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 @@ -0,0 +1,127 @@ +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Demonstrate SNAP Ta potential + +# Initialize simulation + +variable nsteps index 100 +variable nrep equal 4 +variable a equal 3.160 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 4 +variable ny equal ${nrep} +variable ny equal 4 +variable nz equal ${nrep} +variable nz equal 4 + +boundary p p p + +lattice bcc $a +lattice bcc 3.16 +Lattice spacing in x,y,z = 3.16 3.16 3.16 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 4 0 ${ny} 0 ${nz} +region box block 0 4 0 4 0 ${nz} +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 128 atoms + Time spent = 0.000277281 secs + +mass 1 183.84 + +# choose potential + +include Mo_Chen_PRM2017.snap + +# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) +# Generated by Materials Virtual Lab +# Definition of SNAP potential. +pair_style snap +pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo +Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18 +SNAP Element = Mo, Radius 0.5, Weight 1 +Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18 +SNAP keyword rcutfac 4.615858 +SNAP keyword twojmax 6 + + +# Setup output + +thermo 10 +thermo_modify norm yes + +# Set up NVE run + +timestep 0.5e-3 +neighbor 1.0 bin +neigh_modify once no every 1 delay 0 check yes + +# Run MD + +velocity all create 300.0 4928459 +fix 1 all nve +run ${nsteps} +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.61586 + ghost atom cutoff = 5.61586 + binsize = 2.80793, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -22.405975 0 -22.3675 2575.7657 + 10 294.63153 -22.405286 0 -22.3675 2753.4662 + 20 278.98535 -22.40328 0 -22.3675 3272.416 + 30 254.38916 -22.400125 0 -22.3675 4091.8933 + 40 222.91191 -22.396088 0 -22.367499 5148.5505 + 50 187.16984 -22.391504 0 -22.367499 6362.2454 + 60 150.08253 -22.386747 0 -22.367499 7643.2732 + 70 114.60307 -22.382197 0 -22.367499 8900.2448 + 80 83.449257 -22.378201 0 -22.367499 10047.619 + 90 58.862643 -22.375048 0 -22.367498 11012.233 + 100 42.41931 -22.372939 0 -22.367498 11740.641 +Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms + +Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63 +Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03 +Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01 +Other | | 0.00481 | | | 0.25 + +Nlocal: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 431 ave 431 max 431 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1856 ave 1856 max 1856 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7424 +Ave neighs/atom = 58 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 b/examples/snap/log.20Apr18.snap.Ta06A.g++.1 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.1 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.1 index 647ffac8b4326efa8ce7f6fca6b4ee9e577d32f5..d2296852a051bc6d12c58924a802357574a47d6e 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 +++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (5 Oct 2016) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000328064 secs mass 1 180.88 # choose potential -include Ta06A_pot.snap +include Ta06A.snap # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # Definition of SNAP potential Ta_Cand06A @@ -48,10 +51,9 @@ variable zblz equal 73 # Specify hybrid with SNAP, ZBL -pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 73 ${zblz} pair_coeff 1 1 zbl 73 73 @@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1 Reading potential file Ta06A.snapparam with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 SNAP keyword twojmax 6 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 # Setup output @@ -85,13 +88,23 @@ fix 1 all nve run ${nsteps} run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.8 ghost atom cutoff = 5.8 - binsize = 2.9 -> bins = 5 5 5 -Memory usage per processor = 2.92823 Mbytes + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.85157 0 -11.813095 2717.1661 10 295.96579 -11.851053 0 -11.813095 2696.1559 @@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press 80 124.04276 -11.829003 0 -11.813094 1537.703 90 97.37622 -11.825582 0 -11.813094 1734.9662 100 75.007873 -11.822714 0 -11.813094 1930.8005 -Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms +Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms -Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.4295 | 3.4295 | 3.4295 | 0.0 | 99.97 +Pair | 2.5313 | 2.5313 | 2.5313 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00043988 | 0.00043988 | 0.00043988 | 0.0 | 0.01 -Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00 -Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01 -Other | | 0.0002978 | | | 0.01 +Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02 +Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01 +Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 0.01 +Other | | 0.0003583 | | | 0.01 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -133,4 +146,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 b/examples/snap/log.20Apr18.snap.Ta06A.g++.4 similarity index 71% rename from examples/snap/log.5Oct16.snap.Ta06A.g++.4 rename to examples/snap/log.20Apr18.snap.Ta06A.g++.4 index 19d64c557c33538c702da0ddfb4fa1b30c336f8e..4d26481d5de2ccb00bbc364d70af786f458ec2e2 100644 --- a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 +++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (5 Oct 2016) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000288486 secs mass 1 180.88 # choose potential -include Ta06A_pot.snap +include Ta06A.snap # DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) # Definition of SNAP potential Ta_Cand06A @@ -48,10 +51,9 @@ variable zblz equal 73 # Specify hybrid with SNAP, ZBL -pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 ${zblcutouter} -pair_style hybrid/overlay snap zbl 4 4.8 - +pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 ${zblcutouter} snap +pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 73 ${zblz} pair_coeff 1 1 zbl 73 73 @@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1 Reading potential file Ta06A.snapparam with DATE: 2014-09-05 SNAP keyword rcutfac 4.67637 SNAP keyword twojmax 6 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 # Setup output @@ -85,13 +88,23 @@ fix 1 all nve run ${nsteps} run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.8 ghost atom cutoff = 5.8 - binsize = 2.9 -> bins = 5 5 5 -Memory usage per processor = 2.91109 Mbytes + binsize = 2.9, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair zbl, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair snap, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.85157 0 -11.813095 2717.1661 10 295.8664 -11.85104 0 -11.813095 2702.935 @@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press 80 121.80051 -11.828715 0 -11.813094 1627.6911 90 95.262635 -11.825311 0 -11.813094 1812.9327 100 73.194645 -11.822481 0 -11.813094 1995.2199 -Loop time of 0.89193 on 4 procs for 100 steps with 128 atoms +Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms -Performance: 4.843 ns/day, 4.955 hours/ns, 112.116 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.84444 | 0.86772 | 0.88108 | 1.6 | 97.29 +Pair | 1.2867 | 1.309 | 1.35 | 2.1 | 96.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.009577 | 0.023049 | 0.046417 | 9.8 | 2.58 -Output | 0.00024009 | 0.00026137 | 0.00027895 | 0.1 | 0.03 -Modify | 8.2493e-05 | 9.352e-05 | 0.00010061 | 0.1 | 0.01 -Other | | 0.0008071 | | | 0.09 +Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72 +Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04 +Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01 +Other | | 0.001728 | | | 0.13 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -133,4 +146,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:00 +Total wall time: 0:00:01 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.1 b/examples/snap/log.20Apr18.snap.W.2940.g++.1 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.1 rename to examples/snap/log.20Apr18.snap.W.2940.g++.1 index 8c74380b8b7246dad9bf1079f17ad1ef8e56f7b8..19b2bfb40d88b1fd6dd62ab892dba1f463a48b03 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.1 +++ b/examples/snap/log.20Apr18.snap.W.2940.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000190258 secs mass 1 183.84 # choose potential -include W_2940_2017_2.pot.snap -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap @@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 #Nomenclature on the snap files are Element_DakotaID_Year_Month @@ -99,7 +103,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 5.14696 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.028325 0 -10.98985 3010.497 10 293.40666 -11.027479 0 -10.989849 3246.0559 @@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 58.605244 -10.997364 0 -10.989848 11289.914 90 39.754503 -10.994946 0 -10.989848 11824.945 100 32.524085 -10.994019 0 -10.989848 11932.118 -Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms +Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms -Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.826 | 11.826 | 11.826 | 0.0 | 99.99 +Pair | 9.6961 | 9.6961 | 9.6961 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00044084 | 0.00044084 | 0.00044084 | 0.0 | 0.00 -Output | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 0.00 -Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00 -Other | | 0.0002718 | | | 0.00 +Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00 +Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00 +Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 0.00 +Other | | 0.0003347 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -141,4 +145,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:09 diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.4 b/examples/snap/log.20Apr18.snap.W.2940.g++.4 similarity index 79% rename from examples/snap/log.21Feb17.snap.W.2940.g++.4 rename to examples/snap/log.20Apr18.snap.W.2940.g++.4 index 97ed5cc8d12728a0e1d9fb2bc79729188ad7c569..dfa63fc6ea208d4552b8533a1a32fd73bc88d4fe 100644 --- a/examples/snap/log.21Feb17.snap.W.2940.g++.4 +++ b/examples/snap/log.20Apr18.snap.W.2940.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000309944 secs mass 1 183.84 # choose potential -include W_2940_2017_2.pot.snap -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017 +include W_2940_2017_2.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap @@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 #Nomenclature on the snap files are Element_DakotaID_Year_Month @@ -99,7 +103,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 5.12833 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -11.028325 0 -10.98985 3010.497 10 293.22504 -11.027456 0 -10.989849 3258.275 @@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 56.127265 -10.997046 0 -10.989848 11551.687 90 38.025013 -10.994724 0 -10.989847 12069.936 100 31.768127 -10.993922 0 -10.989847 12145.648 -Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms +Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms -Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.9594 | 2.9866 | 3.0319 | 1.6 | 98.39 +Pair | 5.0497 | 5.0762 | 5.092 | 0.8 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0024238 | 0.047825 | 0.075032 | 12.5 | 1.58 -Output | 0.00021601 | 0.00024045 | 0.00027442 | 0.0 | 0.01 -Modify | 9.6798e-05 | 0.00011188 | 0.00011802 | 0.0 | 0.00 -Other | | 0.000698 | | | 0.02 +Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49 +Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02 +Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00 +Other | | 0.002315 | | | 0.04 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -141,4 +145,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:05 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 similarity index 83% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 index 846eef269ce580ca63d730be0fb1ced38da1bf58..3f40936308b21d4e3d0ed1e8e83145c5cfd9d0f7 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 +++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000431538 secs mass 1 183.84 mass 2 4.0026 @@ -42,15 +45,15 @@ group helium type 2 5 atoms in group helium # choose potential -include W.SNAP_HePair.pot -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +include W_2940_2017_2_He_JW2013.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000 @@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -134,7 +138,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 7.6729 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -10.438105 0 -10.39963 -5445.2808 10 290.48923 -10.436885 0 -10.399629 -5646.4813 @@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press 80 85.903126 -10.410645 0 -10.399628 857.74986 90 65.223651 -10.407993 0 -10.399628 1494.2746 100 59.833542 -10.407302 0 -10.399628 1938.9164 -Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms +Loop time of 8.902 on 1 procs for 100 steps with 128 atoms -Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.072 | 11.072 | 11.072 | 0.0 | 99.99 -Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00 -Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00 -Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00 -Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00 -Other | | 0.0003119 | | | 0.00 +Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98 +Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00 +Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01 +Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00 +Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.00 +Other | | 0.0003953 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156 Neighbor list builds = 1 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:09 diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 similarity index 84% rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 index 9bcbd288aa664cf29025090e8c0937e2580d905a..4ec85a63d014085449367848dbfd2c6f787a41e4 100644 --- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 +++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 @@ -1,4 +1,6 @@ -LAMMPS (13 Feb 2017) +LAMMPS (20 Apr 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential # Initialize simulation @@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms + Time spent = 0.000274658 secs mass 1 183.84 mass 2 4.0026 @@ -42,15 +45,15 @@ group helium type 2 5 atoms in group helium # choose potential -include W.SNAP_HePair.pot -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 +include W_2940_2017_2_He_JW2013.snap +# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000 @@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 -SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 +SNAP keyword bzeroflag 0 +SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (../pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -134,7 +138,7 @@ Neighbor list info ... pair build: full/bin/atomonly stencil: full/bin/3d bin: standard -Memory usage per processor = 7.65426 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -10.438105 0 -10.39963 -5445.2808 10 292.13979 -10.437097 0 -10.39963 -5516.3963 @@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press 80 79.985938 -10.409886 0 -10.399628 2392.1106 90 62.568933 -10.407652 0 -10.399628 3141.7027 100 56.697933 -10.406899 0 -10.399628 3583.9538 -Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms +Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms -Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.7363 | 2.8122 | 2.8636 | 2.9 | 97.79 +Pair | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.011014 | 0.062439 | 0.13842 | 19.3 | 2.17 -Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01 -Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00 -Other | | 0.0006654 | | | 0.02 +Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00 +Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02 +Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00 +Other | | 0.002119 | | | 0.04 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:04 diff --git a/lib/atc/ATC_Method.cpp b/lib/atc/ATC_Method.cpp index b1f3fa2545e74c68f882c434361c52b2091c8a95..5d61a7bed8ede5dfe033a952baf9d288e69a0054 100644 --- a/lib/atc/ATC_Method.cpp +++ b/lib/atc/ATC_Method.cpp @@ -2015,8 +2015,8 @@ pecified LammpsInterface::instance()->int_allmax(&send_size,&max_size); if (comm_rank == 0) { - int intbuf[max_size]; - double buf[max_size]; + int *intbuf = new int[max_size]; + double *buf = new double[max_size]; for (int iproc = 1; iproc < nprocs; iproc++) { LammpsInterface::instance()->int_recv(intbuf,max_size,iproc); LammpsInterface::instance()->recv(buf,max_size,iproc); @@ -2024,15 +2024,19 @@ pecified out << intbuf[i] << " " << buf[i] << "\n"; } } + delete[] intbuf; + delete[] buf; } else { - int intbuf[send_size]; - double buf[send_size]; + int *intbuf = new int[send_size]; + double *buf = new double[send_size]; for (int i = 0; i < send_size; i++) { intbuf[i] = id2tag[i]; buf[i] = atomicVolumeMatrix(i,i); } LammpsInterface::instance()->int_send(intbuf,send_size); LammpsInterface::instance()->send(buf,send_size); + delete[] intbuf; + delete[] buf; } } diff --git a/lib/atc/Array.h b/lib/atc/Array.h index 9df6cbbda245d1bc4730d124a1a6980bbad2dae4..21e66a95512b4b73b2e66e482312d8dd09110d19 100644 --- a/lib/atc/Array.h +++ b/lib/atc/Array.h @@ -4,7 +4,7 @@ #include #include #include -#include +#include // for macros #include "MatrixDef.h" diff --git a/lib/atc/Array2D.h b/lib/atc/Array2D.h index 8d3af47e12c14bea9e852928fea9b9cdee180009..25f895f72ccbaa82323ca1617d66f2fe8d519aba 100644 --- a/lib/atc/Array2D.h +++ b/lib/atc/Array2D.h @@ -2,10 +2,9 @@ #define ARRAY2D_H #include +#include #include #include -#include -#include #include "Array.h" diff --git a/lib/atc/ElectronPhononExchange.cpp b/lib/atc/ElectronPhononExchange.cpp index 2ed25fc557dd8494a9556a4fe86fa199fbc34d41..0ccc8ec67e1c70df9ff298eb0ee5b13b83afc006 100644 --- a/lib/atc/ElectronPhononExchange.cpp +++ b/lib/atc/ElectronPhononExchange.cpp @@ -5,7 +5,7 @@ #include #include -#include +#include using ATC_Utility::command_line; using ATC_Utility::str2dbl; diff --git a/lib/atc/FE_Element.cpp b/lib/atc/FE_Element.cpp index cfc59aa601d8b8019d5efdff63ffa3a6abc24a81..9eec08c483e971a4574c41ea653856a776841b41 100644 --- a/lib/atc/FE_Element.cpp +++ b/lib/atc/FE_Element.cpp @@ -8,7 +8,7 @@ #include "Utility.h" // Other headers -#include "math.h" +#include using ATC_Utility::dbl_geq; using ATC_Utility::det3; diff --git a/lib/atc/FE_Engine.cpp b/lib/atc/FE_Engine.cpp index d8d6e3e440b364c30a25f568d0ff076d729b3e06..efcde66d782fa9ce27bd596ad3418645c6b30b2f 100644 --- a/lib/atc/FE_Engine.cpp +++ b/lib/atc/FE_Engine.cpp @@ -7,8 +7,8 @@ #include "KernelFunction.h" #include "Utility.h" #include "MPI_Wrappers.h" -#include -#include +#include +#include #include #include @@ -352,8 +352,9 @@ namespace ATC{ // each segment of the piecewise funcion is length-normalized separately else if (strcmp(arg[argIdx],"position-number-density")==0) { argIdx++; - double y[nx],w[nx]; - int n[nx]; + double *y = new double[nx]; + double *w = new double[nx]; + int *n = new int[nx]; int nn = 0; while (argIdx < narg) { if (! is_numeric(arg[argIdx])) break; @@ -369,7 +370,7 @@ namespace ATC{ double w0 = w[i-1]; double dw = w[i]-w0; double lx = 0; - double l[dn]; + double *l = new double[dn]; for (int j = 0; j < dn; ++j) { double x = (j+0.5)/dn; double dl = w0+x*dw; @@ -380,7 +381,11 @@ namespace ATC{ for (int j = 0; j < dn; ++j) { dx(k++) = scale*l[j]; } + delete[] l; } + delete[] y; + delete[] w; + delete[] n; } // construct relative values from a density function // evaluate for a domain (0,1) diff --git a/lib/atc/FE_Interpolate.cpp b/lib/atc/FE_Interpolate.cpp index 3f41e3002994db342561e2a5b8f2a6f5112ee9ec..19753a80079a6fe7e4e69d1cc624ef55c2ab56cb 100644 --- a/lib/atc/FE_Interpolate.cpp +++ b/lib/atc/FE_Interpolate.cpp @@ -5,7 +5,7 @@ #include "FE_Quadrature.h" // Other headers -#include "math.h" +#include using std::map; using std::vector; diff --git a/lib/atc/FE_Mesh.cpp b/lib/atc/FE_Mesh.cpp index 6225a1b192af060bdbccecd5d59ddd014414b1e8..b090bf2881bdbb9855c7098ccc7b5f2a6d4a4f7a 100644 --- a/lib/atc/FE_Mesh.cpp +++ b/lib/atc/FE_Mesh.cpp @@ -6,7 +6,7 @@ #include "OutputManager.h" #include "Utility.h" #include -#include +#include #include #include #include diff --git a/lib/atc/FE_Mesh.h b/lib/atc/FE_Mesh.h index b37cb1e8bad05ef6639e8aa83cb4b83327b844b7..be40d7cb28e21265646d5320a2ecce105eddb98c 100644 --- a/lib/atc/FE_Mesh.h +++ b/lib/atc/FE_Mesh.h @@ -12,7 +12,7 @@ #include #include #include -#include +#include #include #include #include "mpi.h" diff --git a/lib/atc/Function.cpp b/lib/atc/Function.cpp index 0bd759695c0839db48d423dbe858a78b6de9c090..12396937bd75a149285d92ae3435964dcc399738 100644 --- a/lib/atc/Function.cpp +++ b/lib/atc/Function.cpp @@ -1,3 +1,6 @@ +#ifndef _WIN32 +#include +#endif #include "Function.h" #include "ATC_Error.h" #include "LammpsInterface.h" @@ -58,9 +61,13 @@ namespace ATC { { string type = args[0]; int narg = nargs -1; - double dargs[narg]; +#ifdef _WIN32 + double *dargs = (double *) _alloca(sizeof(double) * narg); +#else + double *dargs = (double *) alloca(sizeof(double) * narg); +#endif for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]); - + return function(type, narg, dargs); } @@ -192,7 +199,11 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL; { string type = args[0]; int narg = nargs -1; - double dargs[narg]; +#ifdef _WIN32 + double *dargs = (double *) _alloca(sizeof(double) * narg); +#else + double *dargs = (double *) alloca(sizeof(double) * narg); +#endif for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]); return function(type, narg, dargs); diff --git a/lib/atc/Function.h b/lib/atc/Function.h index 7368589e96ef65a958ce445040c3b92eaccd95e8..4572009f92a39729fb4b5342aaeb691b8099a76d 100644 --- a/lib/atc/Function.h +++ b/lib/atc/Function.h @@ -1,7 +1,7 @@ #ifndef XT_FUNCTION_H #define XT_FUNCTION_H -#include +#include #include #include #include diff --git a/lib/atc/GMRES.h b/lib/atc/GMRES.h index 0cffe9837f952b59f0f29f260107b90e6739267c..a64fc70c009bfa5cd51766ca67c1dbe32bc5be75 100644 --- a/lib/atc/GMRES.h +++ b/lib/atc/GMRES.h @@ -19,7 +19,7 @@ // //***************************************************************** -#include +#include template diff --git a/lib/atc/InterscaleOperators.h b/lib/atc/InterscaleOperators.h index 4681801e732dfacf1e2510cff8e09d70b08d9bd5..0ddca1dc67a08d4adb299a3648ddfad8a5f5b931 100644 --- a/lib/atc/InterscaleOperators.h +++ b/lib/atc/InterscaleOperators.h @@ -279,7 +279,7 @@ namespace ATC { typename std::map::iterator it = list.find(tag); if (it==list.end()) return NULL; return it->second; - }; + } /** helper function to add a data entry to a list */ template @@ -290,7 +290,7 @@ namespace ATC { throw ATC_Error("Tried to add another Quantity with tag "+tag+" in InterscaleManager::add_quantity"); typename std::template pair myPair(tag,quantity); list.insert(myPair); - }; + } /** helper function to add a data entry to a list when it requires neighbor communication*/ template @@ -302,7 +302,7 @@ namespace ATC { if (quantity->atom_type() == PROC_GHOST) { commList.push_back(quantity); } - }; + } /** helper function to fina a data entry in a list */ template @@ -311,7 +311,7 @@ namespace ATC { typename std::map::iterator it = list.find(tag); if (it!=list.end()) return it->second; return NULL; - }; + } /** helper function to force the reset of all data in a list */ template @@ -319,7 +319,7 @@ namespace ATC { { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) (it->second)->force_reset(); - }; + } /** helper function to set the memory type to temporary of a list */ template @@ -327,7 +327,7 @@ namespace ATC { { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) (it->second)->set_memory_type(TEMPORARY); - }; + } /** helper function to perform intialization for dfs of a list */ template @@ -336,7 +336,7 @@ namespace ATC { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) { (it->second)->dfsFound_ = false; } - }; + } /** helper function to start the dfs visit for list */ template @@ -349,7 +349,7 @@ namespace ATC { if ((it->second)->memory_type()==TEMPORARY) list.erase(it++); else ++it; } - }; + } // PAQ helper functions /** helper function to adjust local atom count for all data in a list before exchange, only valid with quantities that do that are aware of atom counts */ @@ -359,7 +359,7 @@ namespace ATC { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) { (it->second)->reset_nlocal(); } - }; + } /** helper function to indicate lammps data is stale for all data in a list before exchange, only valid with PAQs */ template @@ -367,7 +367,7 @@ namespace ATC { { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) (it->second)->lammps_force_reset(); - }; + } /** helper function to size all data in a list, only valid with comm lists */ template @@ -375,7 +375,7 @@ namespace ATC { { for (typename std::vector::iterator it = list.begin(); it != list.end(); ++it) (*it)->quantity(); - }; + } /** helper function to pack all data in a list before exchange, only valid with quantities that do work before parallel communication */ template @@ -384,7 +384,7 @@ namespace ATC { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) { (it->second)->prepare_exchange(); } - }; + } /** helper function to extract all data in a list after exchange, only valid with quantities that do work after parallel communication */ template @@ -393,7 +393,7 @@ namespace ATC { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) { (it->second)->post_exchange(); } - }; + } /** helper function to determine memory usage of all data in a list, only valid with PAQs */ template @@ -401,7 +401,7 @@ namespace ATC { { for (typename std::map::const_iterator it = list.begin(); it != list.end(); ++it) usage += (it->second)->memory_usage(); - }; + } /** helper function to pack arrays of all data before exchange in a list, only valid with PAQs */ template @@ -410,7 +410,7 @@ namespace ATC { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) { index += (it->second)->pack_exchange(i,&buffer[index]); } - }; + } /** helper function to unpack arrays of all data after exchange in a list, only valid with PAQs */ template @@ -418,7 +418,7 @@ namespace ATC { { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) index += (it->second)->unpack_exchange(i,&buffer[index]); - }; + } /** helper function to pack arrays of all data in a list, only valid with comm lists */ template @@ -427,7 +427,7 @@ namespace ATC { { for (typename std::vector::iterator it = list.begin(); it != list.end(); ++it) size += (*it)->pack_comm(index,&buf[size],pbc_flag,pbc); - }; + } /** helper function to unpack arrays of all data in a list, only valid with comm lists */ template @@ -435,7 +435,7 @@ namespace ATC { { for (typename std::vector::iterator it = list.begin(); it != list.end(); ++it) size += (*it)->unpack_comm(index,&buf[size]); - }; + } /** helper function to grow arrays of all data in a list, only valid with PAQs */ template @@ -443,7 +443,7 @@ namespace ATC { { for (typename std::map::iterator it = list.begin(); it != list.end(); ++it) (it->second)->grow_lammps_array(nmax,prefix_+it->first); - }; + } /** helper function to copy arrays of all data in a list, only valid with PAQs */ template diff --git a/lib/atc/KD_Tree.cpp b/lib/atc/KD_Tree.cpp index 362bd70d34bd35f8d94d18d7c52e36978dab0f03..1432663e8064b60b8862e707d99aa010fb0245c1 100644 --- a/lib/atc/KD_Tree.cpp +++ b/lib/atc/KD_Tree.cpp @@ -1,5 +1,5 @@ #include "KD_Tree.h" -#include +#include using std::vector; diff --git a/lib/atc/KD_Tree.h b/lib/atc/KD_Tree.h index 6c788c407112948bbcbbed4f3c8d2f612728fa69..3877cd40993bd910744b19b94b898842431af1b2 100644 --- a/lib/atc/KD_Tree.h +++ b/lib/atc/KD_Tree.h @@ -4,7 +4,7 @@ #include "Array2D.h" #include "MatrixDef.h" #include "MatrixLibrary.h" -#include +#include #include #include diff --git a/lib/atc/KernelFunction.cpp b/lib/atc/KernelFunction.cpp index 91f99a61494f185145af66f0d709dc209af7e6e0..80e41a15509bd1c4efd77f42e5d55e30e0a6f910 100644 --- a/lib/atc/KernelFunction.cpp +++ b/lib/atc/KernelFunction.cpp @@ -1,5 +1,5 @@ #include "KernelFunction.h" -#include "math.h" +#include #include #include "ATC_Error.h" #include "Quadrature.h" diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp index d584d159eaade8822f93af0e92d05004e1032d14..2238d930f4d4fb3f5eb25fac636168743e35d0f3 100644 --- a/lib/atc/LammpsInterface.cpp +++ b/lib/atc/LammpsInterface.cpp @@ -131,15 +131,15 @@ void LammpsInterface::sparse_allsum(SparseMatrix &toShare) const if (error != MPI_SUCCESS) throw ATC_Error("error in sparse_allsum_numrows "+to_string(error)); // adjust row sendcounts because recRowsCRS is off by one - int rowCounts[nProcs]; - int sizeCounts[nProcs]; + int *rowCounts = new int[nProcs]; + int *sizeCounts = new int[nProcs]; // set up total size of receive buffers for Allgatherv calls int totalRowsCRS = 0; int totalSize = 0; // set up array of displacements for Allgatherv calls - int rowOffsets[nProcs]; + int *rowOffsets = new int[nProcs]; rowOffsets[0] = 0; - int sizeOffsets[nProcs]; + int *sizeOffsets = new int[nProcs]; sizeOffsets[0] = 0; for (int i = 0; i < nProcs; i++) { // find the total number of entries to share in the mpi calls below @@ -156,8 +156,8 @@ void LammpsInterface::sparse_allsum(SparseMatrix &toShare) const // get actual rows INDEX *rec_ia = new INDEX[totalRowsCRS]; if (toShare.size() == 0) { - double dummy[0]; - error = MPI_Allgatherv(dummy, 0, MPI_INT, + double dummy; + error = MPI_Allgatherv(&dummy, 0, MPI_INT, rec_ia, rowCounts, rowOffsets, MPI_INT, lammps_->world); } else @@ -211,6 +211,10 @@ void LammpsInterface::sparse_allsum(SparseMatrix &toShare) const toShare += tempMat; } } + delete[] rowCounts; + delete[] sizeCounts; + delete[] rowOffsets; + delete[] sizeOffsets; delete[] recInfo; delete[] rec_ia; diff --git a/lib/atc/LammpsInterface.h b/lib/atc/LammpsInterface.h index ff2b4ba9b2696dfb270ba6e50191b73cea5ba1e7..2032571da5df99e642da3b761eb1464c176ed098 100644 --- a/lib/atc/LammpsInterface.h +++ b/lib/atc/LammpsInterface.h @@ -2,7 +2,7 @@ #define LAMMPS_INTERFACE_H #include -#include +#include #include #include #include @@ -315,7 +315,7 @@ class LammpsInterface { } else { int commSize = comm_size(); - double recv[commSize]; + double *recv = new double[commSize]; MPI_Wrappers::gather(lammps_->world,data,recv); if (rank_zero()) { full_msg << " ATC:" << tag; @@ -324,6 +324,7 @@ class LammpsInterface { } full_msg << "\n"; } + delete[] recv; } if (rank_zero()) { std::string mesg = full_msg.str(); @@ -577,13 +578,13 @@ class LammpsInterface { void destroy_2d_int_array(int **i) const; int ** grow_2d_int_array(int **array, int n1, int n2, const char *name) const; template - T * grow_array(T *&array, int n, const char *name) const {return lammps_->memory->grow(array,n,name);}; + T * grow_array(T *&array, int n, const char *name) const {return lammps_->memory->grow(array,n,name);} template - void destroy_array(T * array) {lammps_->memory->destroy(array);}; + void destroy_array(T * array) {lammps_->memory->destroy(array);} template - T ** grow_array(T **&array, int n1, int n2, const char *name) const {return lammps_->memory->grow(array,n1,n2,name);}; + T ** grow_array(T **&array, int n1, int n2, const char *name) const {return lammps_->memory->grow(array,n1,n2,name);} template - void destroy_array(T ** array) const {lammps_->memory->destroy(array);}; + void destroy_array(T ** array) const {lammps_->memory->destroy(array);} /*@}*/ /** \name Methods that interface with Update class */ diff --git a/lib/atc/MPI_Wrappers.cpp b/lib/atc/MPI_Wrappers.cpp index 9468644c53da762a871e64f7e569ab88605bc243..b8a8ab77b734d03442b30b0f3d8fadec53a3e886 100644 --- a/lib/atc/MPI_Wrappers.cpp +++ b/lib/atc/MPI_Wrappers.cpp @@ -94,7 +94,8 @@ namespace MPI_Wrappers { { int myRank; MPI_Comm_rank(MPI_COMM_WORLD, &myRank); - DOUBLE_RANK in[count],out[count]; + DOUBLE_RANK *in = new DOUBLE_RANK[count]; + DOUBLE_RANK *out = new DOUBLE_RANK[count]; for (int i = 0; i < count; i++) { in[i].val = send_buf[i]; in[i].rank = myRank; @@ -105,6 +106,8 @@ namespace MPI_Wrappers { for (int i = 0; i < count; i++) { rec_buf[i] = out[i].val; } + delete[] in; + delete[] out; return out[0].rank; } @@ -154,14 +157,16 @@ namespace MPI_Wrappers { { int error; int numprocs = size(comm); - int sizes[numprocs]; - int displacements[numprocs]; + int *sizes = new int[numprocs]; + int *displacements = new int[numprocs]; for (int i = 0; i < numprocs; ++i) { sizes[i] = 1; displacements[i] = i; } error = MPI_Scatterv(send_buf, sizes, displacements, MPI_INT, rec_buf, count, MPI_INT, 0, comm); if (error != MPI_SUCCESS) throw ATC_Error("error in int_scatter "+to_string(error)); + delete[] sizes; + delete[] displacements; } void allgatherv(MPI_Comm comm, double *send_buf, int send_count, diff --git a/lib/atc/Makefile.mpi b/lib/atc/Makefile.mpi index ec941efdcb6c0b0171440306653fa9522b8b65cf..c1ce0500ea5f717cec4d44f538127d330440312b 100644 --- a/lib/atc/Makefile.mpi +++ b/lib/atc/Makefile.mpi @@ -52,4 +52,4 @@ fastdep.exe: ../../src/DEPEND/fastdep.c clean: -rm -f *.o *~ .depend $(LIB) fastdep.exe -sinclude $(DEPENDS) +sinclude .depend diff --git a/lib/atc/OutputManager.cpp b/lib/atc/OutputManager.cpp index 414c5173e7b7cfb1bde38a5a263480eccec264d5..4340c8b8b0a3ca3c308be3838385a2b36a7b3c9a 100644 --- a/lib/atc/OutputManager.cpp +++ b/lib/atc/OutputManager.cpp @@ -1,6 +1,6 @@ #include #include -#include +#include #include #include "OutputManager.h" #include "ATC_Error.h" diff --git a/lib/atc/PrescribedDataManager.h b/lib/atc/PrescribedDataManager.h index 05f553ab2db9955c631c65ef122ae5768d213c92..738c34d593d5e9100422cd80622cc19dc2e7cc89 100644 --- a/lib/atc/PrescribedDataManager.h +++ b/lib/atc/PrescribedDataManager.h @@ -154,7 +154,7 @@ namespace ATC { std::set fluxes; //list of nodes to insert. //1 for nodes to insert, 0 for nodes not to insert. - int toInsert[nNodes_]; + int *toInsert = new int[nNodes_]; for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0; const std::map < std::pair , Array < XT_Function * > > & sources = faceSources_.find(thisField)->second; @@ -178,6 +178,7 @@ namespace ATC { for (int node = 0; node < nNodes_; ++node) { if (toInsert[node]) fluxes.insert(node); } + delete[] toInsert; return fluxes; } @@ -189,7 +190,7 @@ namespace ATC { { //list of nodes to insert. //1 for nodes to insert, 0 for nodes not to insert. - int toInsert[nNodes_]; + int *toInsert = new int[nNodes_]; for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0; const std::map < std::pair , Array < XT_Function * > > & sources = faceSources_.find(thisField)->second; @@ -213,6 +214,7 @@ namespace ATC { for (int node = 0; node < nNodes_; ++node) { if (toInsert[node]) fluxes.insert(node); } + delete[] toInsert; } /** */ @@ -223,7 +225,7 @@ namespace ATC { std::set fluxes; //list of nodes to insert. //1 for nodes to insert, 0 for nodes not to insert. - int toInsert[nNodes_]; + int *toInsert = new int[nNodes_]; for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0; const Array2D < XT_Function *> & sources = elementSources_.find(thisField)->second; @@ -244,6 +246,7 @@ namespace ATC { for (int node = 0; node < nNodes_; ++node) { if (toInsert[node]) fluxes.insert(node); } + delete[] toInsert; return fluxes; } @@ -255,7 +258,7 @@ namespace ATC { { //list of nodes to insert. //1 for nodes to insert, 0 for nodes not to insert. - int toInsert[nNodes_]; + int *toInsert = new int[nNodes_]; for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0; const Array2D < XT_Function *> & sources = elementSources_.find(thisField)->second; @@ -276,6 +279,7 @@ namespace ATC { for (int node = 0; node < nNodes_; ++node) { if (toInsert[node]) fluxes.insert(node); } + delete[] toInsert; } /** */ diff --git a/lib/atc/ShapeFunction.h b/lib/atc/ShapeFunction.h index 724e66924feadf790deaf17bbda8b64e84edb44a..62b2138cd7fd7b994d7aaa5d7c071ec21c27966e 100644 --- a/lib/atc/ShapeFunction.h +++ b/lib/atc/ShapeFunction.h @@ -5,10 +5,10 @@ #include "DependencyManager.h" #include "PaqAtcUtility.h" -#include -#include -#include -#include +#include +#include +#include +#include namespace ATC { diff --git a/lib/atc/SparseMatrix-inl.h b/lib/atc/SparseMatrix-inl.h index 8d6aec78dca94f04503caf662761ff203d4e75e7..f70dd0361d3cf52e519fef06abc07f0518c86b21 100644 --- a/lib/atc/SparseMatrix-inl.h +++ b/lib/atc/SparseMatrix-inl.h @@ -67,9 +67,9 @@ void SparseMatrix::_create(INDEX size, INDEX nrows) // assign memory to hold matrix try { - _val = (_size*nrows) ? new T [_size] : NULL; - _ia = (_size*nrows) ? new INDEX [_nRowsCRS+1] : NULL; - _ja = (_size*nrows) ? new INDEX [_size] : NULL; + _val = (_size && nrows) ? new T [_size] : NULL; + _ia = (_size && nrows) ? new INDEX [_nRowsCRS+1] : NULL; + _ja = (_size && nrows) ? new INDEX [_size] : NULL; } catch (std::exception &e) { diff --git a/lib/atc/Utility.h b/lib/atc/Utility.h index f9e99ff194fb8245618c791858cd308208876a1d..d975d4804ae87ac5ee9043ae206bedbf1e815782 100644 --- a/lib/atc/Utility.h +++ b/lib/atc/Utility.h @@ -13,7 +13,7 @@ #include #include #include -#include "math.h" +#include #include "ATC_Error.h" diff --git a/lib/awpmd/ivutils/include/cerf.h b/lib/awpmd/ivutils/include/cerf.h index 207fe8f4590b7e762c8c327340b69e6ee7d1d672..b094c4144f6d7dd49d023cc20669087871507625 100644 --- a/lib/awpmd/ivutils/include/cerf.h +++ b/lib/awpmd/ivutils/include/cerf.h @@ -42,11 +42,6 @@ Software Foundation, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. // -//#include -//#include - -//#include "f77-fcn.h" - // // Abramowitz and Stegun: (eqn: 7.1.14) gives this continued // fraction for erfc(z) @@ -242,4 +237,4 @@ const Complex cerf( const Complex z ) // 2.2 1.7 0.135021+0.153161i | 0.135021 +0.153161 1.65541359 -1.276707 // 2.2 2.7 0.127900+0.096330i | 0.127900 +0.096330 0.98619434 +0.000564 -# endif \ No newline at end of file +# endif diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h index 0211a96034448869676e0a7739df88fcea3e2b6d..400b3fb7d2e970e1773ade440ff25ce1b295139f 100644 --- a/lib/awpmd/ivutils/include/logexc.h +++ b/lib/awpmd/ivutils/include/logexc.h @@ -1,9 +1,9 @@ # ifndef LOGEXC_H # define LOGEXC_H -#include -#include -#include +#include +#include +#include #include #include diff --git a/lib/awpmd/ivutils/include/vector_3.h b/lib/awpmd/ivutils/include/vector_3.h index 75ef801a2ea7a1194c1169b68ebb8d2ca4cb54b9..3e3d9e6e0b249a941e90ad34039a3de5fb03a998 100644 --- a/lib/awpmd/ivutils/include/vector_3.h +++ b/lib/awpmd/ivutils/include/vector_3.h @@ -84,7 +84,7 @@ # include # include # include -# include +# include // some compilers don't define PI! # ifndef M_PI diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps index 9a7de0647db57eeb3d62ee866e71f6e363b6c802..a0d8515bc104f985584d18726c79914c67227cdf 100644 --- a/lib/colvars/Makefile.deps +++ b/lib/colvars/Makefile.deps @@ -1,9 +1,9 @@ $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ colvarparse.h colvaratoms.h colvardeps.h $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \ colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -29,7 +29,7 @@ $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_alb.h $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvarbias.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \ colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -42,8 +42,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ - colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \ - colvartypes.h colvar.h colvarparse.h colvardeps.h \ + colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ + colvarvalue.h colvar.h colvarparse.h colvardeps.h \ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ lepton/include/lepton/windowsIncludes.h \ @@ -55,7 +55,7 @@ $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_histogram.h colvarbias.h colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \ colvarparse.h colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -68,8 +68,8 @@ $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarbias_meta.h colvarbias.h colvargrid.h $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \ - colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \ - colvartypes.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \ + colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \ + colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \ colvardeps.h lepton/include/Lepton.h \ lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ @@ -171,7 +171,7 @@ $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \ colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvardeps.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \ colvarparse.h $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \ @@ -204,7 +204,7 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \ $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \ - colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \ + colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \ colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \ lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \ lepton/include/lepton/ExpressionTreeNode.h \ diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index 5a4e8b617a9007fff02e87233b8f8dfebb1e7a25..c5b6d906c1ec063fac7ee5e48b39a41c4e841e96 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -7,6 +7,10 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include +#include +#include + #include "colvarmodule.h" #include "colvarvalue.h" #include "colvarparse.h" @@ -14,15 +18,6 @@ #include "colvarcomp.h" #include "colvarscript.h" -// used in build_atom_list() -#include - - -/// Compare two cvcs using their names -/// Used to sort CVC array in scripted coordinates -bool compare(colvar::cvc *i, colvar::cvc *j) { - return i->name < j->name; -} colvar::colvar() @@ -34,6 +29,15 @@ colvar::colvar() } +namespace { + /// Compare two cvcs using their names + /// Used to sort CVC array in scripted coordinates + bool compare(colvar::cvc *i, colvar::cvc *j) + { + return i->name < j->name; + } +} + int colvar::init(std::string const &conf) { cvm::log("Initializing a new collective variable.\n"); @@ -143,6 +147,9 @@ int colvar::init(std::string const &conf) x.type(cvc_value); x_reported.type(cvc_value); } + + set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar)); + // If using scripted biases, any colvar may receive bias forces // and will need its gradient if (cvm::scripted_forces()) { @@ -198,6 +205,7 @@ int colvar::init(std::string const &conf) if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature bool b_periodic = true; period = cvcs[0]->period; + wrap_center = cvcs[0]->wrap_center; for (i = 1; i < cvcs.size(); i++) { if (!cvcs[i]->b_periodic || cvcs[i]->period != period) { b_periodic = false; @@ -211,6 +219,14 @@ int colvar::init(std::string const &conf) set_enabled(f_cv_periodic, b_periodic); } + // Allow scripted/custom functions to be defined as periodic + if ( (is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && is_enabled(f_cv_scalar) ) { + if (get_keyval(conf, "period", period, 0.)) { + set_enabled(f_cv_periodic, true); + get_keyval(conf, "wrapAround", wrap_center, 0.); + } + } + // check that cvcs are compatible for (i = 0; i < cvcs.size(); i++) { @@ -443,8 +459,6 @@ int colvar::init_grid_parameters(std::string const &conf) upper_boundary.type(value()); upper_wall.type(value()); - set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar)); - if (is_enabled(f_cv_scalar)) { if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) { @@ -1503,7 +1517,7 @@ cvm::real colvar::update_forces_energy() vr += (0.5 * dt) * f_ext / ext_mass; xr += dt * vr; xr.apply_constraints(); - if (this->is_enabled(f_cv_periodic)) this->wrap(xr); + this->wrap(xr); } // Now adding the force on the actual colvar (for those biases that @@ -1714,9 +1728,18 @@ colvarvalue colvar::dist2_rgrad(colvarvalue const &x1, void colvar::wrap(colvarvalue &x) const { - if (is_enabled(f_cv_homogeneous)) { - (cvcs[0])->wrap(x); + if ( !is_enabled(f_cv_periodic) ) { + return; + } + + if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) { + // Scripted functions do their own wrapping, as cvcs might not be periodic + cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5); + x.real_value -= shift * period; + } else { + cvcs[0]->wrap(x); } + return; } @@ -2244,7 +2267,7 @@ void colvar::calc_runave() runave.type(value().type()); runave.reset(); - // first-step operations + // first-step operationsf if (cvm::debug()) cvm::log("Colvar \""+this->name+ diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 32c329460d06cfa5ceba43e245aa08a0d0810100..271231fb2aa2c6c6404c2f19f752cb80edfc66bf 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -216,6 +216,7 @@ public: /// Period, if this variable is periodic cvm::real period; + cvm::real wrap_center; /// \brief Expand the boundaries of multiples of width, to keep the diff --git a/lib/colvars/colvar_UIestimator.h b/lib/colvars/colvar_UIestimator.h index 36ed938119d41232dfdbdc42589cd35f8f67a735..759b8d54a034800bd9bebce1cb34753ca6bcef89 100644 --- a/lib/colvars/colvar_UIestimator.h +++ b/lib/colvars/colvar_UIestimator.h @@ -731,6 +731,6 @@ namespace UIestimator { } } }; -}; +} #endif diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp index 1be6f42e594f86adf16a5b4702a631a6bef9c1e7..c8dcfc076619f881a3a217d4e794d52a9838c44e 100644 --- a/lib/colvars/colvaratoms.cpp +++ b/lib/colvars/colvaratoms.cpp @@ -7,6 +7,10 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. +#include +#include +#include + #include "colvarmodule.h" #include "colvarproxy.h" #include "colvarparse.h" @@ -436,7 +440,7 @@ int cvm::atom_group::parse(std::string const &group_conf) } bool b_print_atom_ids = false; - get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent); + get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false); // Calculate all required properties (such as total mass) setup(); @@ -715,13 +719,10 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf) "if provided, must be non-zero.\n", INPUT_ERROR); return COLVARS_ERROR; } - } else { - // if not, rely on existing atom indices for the group - group_for_fit->create_sorted_ids(); - ref_pos.resize(group_for_fit->size()); } - cvm::load_coords(ref_pos_file.c_str(), ref_pos, group_for_fit->sorted_ids, + ref_pos.resize(group_for_fit->size()); + cvm::load_coords(ref_pos_file.c_str(), &ref_pos, group_for_fit, ref_pos_col, ref_pos_col_value); } @@ -789,33 +790,39 @@ void cvm::atom_group::do_feature_side_effects(int id) } -int cvm::atom_group::create_sorted_ids(void) +int cvm::atom_group::create_sorted_ids() { // Only do the work if the vector is not yet populated - if (sorted_ids.size()) + if (sorted_atoms_ids.size()) return COLVARS_OK; - std::list temp_id_list; - for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) { - temp_id_list.push_back(ai->id); - } - temp_id_list.sort(); - temp_id_list.unique(); - if (temp_id_list.size() != this->size()) { - cvm::error("Error: duplicate atom IDs in atom group? (found " + - cvm::to_str(temp_id_list.size()) + - " unique atom IDs instead of" + - cvm::to_str(this->size()) + ").\n"); - return COLVARS_ERROR; + // Sort the internal IDs + std::list sorted_atoms_ids_list; + for (size_t i = 0; i < this->size(); i++) { + sorted_atoms_ids_list.push_back(atoms_ids[i]); } - sorted_ids = std::vector (temp_id_list.size()); - unsigned int id_i = 0; - std::list::iterator li; - for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) { - sorted_ids[id_i] = *li; - id_i++; + sorted_atoms_ids_list.sort(); + sorted_atoms_ids_list.unique(); + if (sorted_atoms_ids_list.size() != this->size()) { + return cvm::error("Error: duplicate atom IDs in atom group? (found " + + cvm::to_str(sorted_atoms_ids_list.size()) + + " unique atom IDs instead of " + + cvm::to_str(this->size()) + ").\n", BUG_ERROR); } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + + // Compute map between sorted and unsorted elements + sorted_atoms_ids.resize(this->size()); + sorted_atoms_ids_map.resize(this->size()); + std::list::iterator lsii = sorted_atoms_ids_list.begin(); + size_t ii = 0; + for ( ; ii < this->size(); lsii++, ii++) { + sorted_atoms_ids[ii] = *lsii; + size_t const pos = std::find(atoms_ids.begin(), atoms_ids.end(), *lsii) - + atoms_ids.begin(); + sorted_atoms_ids_map[ii] = pos; + } + + return COLVARS_OK; } diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h index 0dda6ab792d8ae20afcf6a9aeaa615675f332d1b..93ae594aae893e303fff493487c6b49e7cf09ae8 100644 --- a/lib/colvars/colvaratoms.h +++ b/lib/colvars/colvaratoms.h @@ -227,9 +227,16 @@ protected: /// \brief Array of atom objects std::vector atoms; - /// \brief Array of atom identifiers for the MD program (0-based) + /// \brief Internal atom IDs for host code std::vector atoms_ids; + /// Sorted list of internal atom IDs (populated on-demand by + /// create_sorted_ids); used to read coordinate files + std::vector sorted_atoms_ids; + + /// Map entries of sorted_atoms_ids onto the original positions in the group + std::vector sorted_atoms_ids_map; + /// \brief Dummy atom position cvm::atom_pos dummy_atom_pos; @@ -273,19 +280,34 @@ public: return atoms.size(); } - std::string const print_atom_ids() const; - /// \brief If this option is on, this group merely acts as a wrapper /// for a fixed position; any calls to atoms within or to /// functions that return disaggregated data will fail bool b_dummy; - /// Sorted list of zero-based (internal) atom ids - /// (populated on-demand by create_sorted_ids) - std::vector sorted_ids; + /// Internal atom IDs (populated during initialization) + inline std::vector const &ids() const + { + return atoms_ids; + } + + std::string const print_atom_ids() const; + + /// Allocates and populates sorted_ids and sorted_ids_map + int create_sorted_ids(); - /// Allocates and populates the sorted list of atom ids - int create_sorted_ids(void); + /// Sorted internal atom IDs (populated on-demand by create_sorted_ids); + /// used to read coordinate files + inline std::vector const &sorted_ids() const + { + return sorted_atoms_ids; + } + + /// Map entries of sorted_atoms_ids onto the original positions in the group + inline std::vector const &sorted_ids_map() const + { + return sorted_atoms_ids_map; + } /// Detect whether two groups share atoms /// If yes, returns 1-based number of a common atom; else, returns 0 diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp index b3b5b3eb1654df12992b2fafb206d82851d3788b..771955a4fa354222b300b2e3cefcfb71c81c2c12 100644 --- a/lib/colvars/colvarbias_abf.cpp +++ b/lib/colvars/colvarbias_abf.cpp @@ -17,17 +17,17 @@ colvarbias_abf::colvarbias_abf(char const *key) : colvarbias(key), b_UI_estimator(false), b_CZAR_estimator(false), + pabf_freq(0), system_force(NULL), gradients(NULL), - pmf(NULL), samples(NULL), + pmf(NULL), z_gradients(NULL), z_samples(NULL), czar_gradients(NULL), czar_pmf(NULL), last_gradients(NULL), - last_samples(NULL), - pabf_freq(0) + last_samples(NULL) { } @@ -315,8 +315,6 @@ colvarbias_abf::~colvarbias_abf() int colvarbias_abf::update() { - int iter; - if (cvm::debug()) cvm::log("Updating ABF bias " + this->name); size_t i; @@ -368,7 +366,12 @@ int colvarbias_abf::update() if ( b_integrate ) { if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) { cvm::real err; - iter = pmf->integrate(integrate_steps, integrate_tol, err); + int iter = pmf->integrate(integrate_steps, integrate_tol, err); + if ( iter == integrate_steps ) { + cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(integrate_tol) + + " in " + cvm::to_str(integrate_steps) + + " steps. Residual error: " + cvm::to_str(err)); + } pmf->set_zero_minimum(); // TODO: do this only when necessary } } @@ -485,7 +488,6 @@ int colvarbias_abf::update() int colvarbias_abf::replica_share() { - int p; if ( !cvm::replica_enabled() ) { cvm::error("Error: shared ABF: No replicas.\n"); @@ -507,6 +509,7 @@ int colvarbias_abf::replica_share() { char* msg_data = new char[msg_total]; if (cvm::replica_index() == 0) { + int p; // Replica 0 collects the delta gradient and count from the others. for (p = 1; p < cvm::replica_num(); p++) { // Receive the deltas. diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp index 589de1d32af44a82d8b6beb78e8ee3d5f5ec8fc3..39b84b26d195dc59eae8bbced3ef40ef14f4cbb9 100644 --- a/lib/colvars/colvarcomp.cpp +++ b/lib/colvars/colvarcomp.cpp @@ -21,6 +21,9 @@ colvar::cvc::cvc() b_try_scalable(true) { init_cvc_requires(); + sup_coeff = 1.0; + period = 0.0; + wrap_center = 0.0; } @@ -30,43 +33,52 @@ colvar::cvc::cvc(std::string const &conf) b_periodic(false), b_try_scalable(true) { + init_cvc_requires(); + sup_coeff = 1.0; + period = 0.0; + wrap_center = 0.0; + init(conf); +} + + +int colvar::cvc::init(std::string const &conf) +{ + int error_code = COLVARS_OK; if (cvm::debug()) cvm::log("Initializing cvc base object.\n"); - init_cvc_requires(); - - if (get_keyval(conf, "name", this->name, std::string(""), parse_silent)) { + get_keyval(conf, "name", this->name, this->name); + if (name.size() > 0) { // Temporary description until child object is initialized description = "cvc " + name; } else { description = "uninitialized cvc"; } - get_keyval(conf, "componentCoeff", sup_coeff, 1.0); - get_keyval(conf, "componentExp", sup_np, 1); + get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff); + get_keyval(conf, "componentExp", sup_np, sup_np); - get_keyval(conf, "period", period, 0.0); - get_keyval(conf, "wrapAround", wrap_center, 0.0); + get_keyval(conf, "period", period, period); + get_keyval(conf, "wrapAround", wrap_center, wrap_center); - get_keyval_feature((colvarparse *)this, conf, "debugGradients", + get_keyval_feature(dynamic_cast(this), conf, "debugGradients", f_cvc_debug_gradient, false, parse_silent); - { - bool b_no_PBC = false; - get_keyval(conf, "forceNoPBC", b_no_PBC, false); - if (b_no_PBC) { - disable(f_cvc_pbc_minimum_image); - } else { - enable(f_cvc_pbc_minimum_image); - } - // this does not use get_keyval_feature() only for backward compatibility + bool b_no_PBC = !is_enabled(f_cvc_pbc_minimum_image); // Enabled by default + get_keyval(conf, "forceNoPBC", b_no_PBC, b_no_PBC); + if (b_no_PBC) { + disable(f_cvc_pbc_minimum_image); + } else { + enable(f_cvc_pbc_minimum_image); } // Attempt scalable calculations when in parallel? (By default yes, if available) - get_keyval(conf, "scalable", b_try_scalable, true); + get_keyval(conf, "scalable", b_try_scalable, b_try_scalable); if (cvm::debug()) cvm::log("Done initializing cvc base object.\n"); + + return error_code; } diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h index 52078a3a3059cb91315ac9f52e62b2f06e1e55f3..b5c3b16098c94f3fa94140b1259f016ef6581187 100644 --- a/lib/colvars/colvarcomp.h +++ b/lib/colvars/colvarcomp.h @@ -98,12 +98,14 @@ public: /// \brief Constructor /// - /// At least one constructor which reads a string should be defined - /// for every class inheriting from cvc \param conf Contents - /// of the configuration file pertaining to this \link cvc - /// \endlink + /// Calls the init() function of the class cvc(std::string const &conf); + /// An init function should be defined for every class inheriting from cvc + /// \param conf Contents of the configuration file pertaining to this \link + /// cvc \endlink + virtual int init(std::string const &conf); + /// \brief Within the constructor, make a group parse its own /// options from the provided configuration string /// Returns reference to new group @@ -231,7 +233,7 @@ public: virtual colvarvalue dist2_rgrad(colvarvalue const &x1, colvarvalue const &x2) const; - /// \brief Wrapp value (for periodic/symmetric cvcs) + /// \brief Wrap value (for periodic/symmetric cvcs) virtual void wrap(colvarvalue &x) const; /// \brief Pointers to all atom groups, to let colvars collect info diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp index 9911f4c87edef9c17605403f21a0ffc1a45826e9..57b2a9a625fa01c49a8301b34b7e5f688096f8b4 100644 --- a/lib/colvars/colvarcomp_distances.cpp +++ b/lib/colvars/colvarcomp_distances.cpp @@ -148,7 +148,7 @@ void colvar::distance_vec::apply_force(colvarvalue const &force) cvm::real colvar::distance_vec::dist2(colvarvalue const &x1, colvarvalue const &x2) const { - return cvm::position_dist2(x1.rvector_value, x2.rvector_value); + return (cvm::position_distance(x1.rvector_value, x2.rvector_value)).norm2(); } @@ -192,7 +192,7 @@ colvar::distance_z::distance_z(std::string const &conf) // this group is optional ref2 = parse_group(conf, "ref2", true); - if (ref2 && ref2->size()) { + if ( ref2 ) { cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\""); fixed_axis = false; if (key_lookup(conf, "axis")) @@ -306,7 +306,7 @@ void colvar::distance_z::apply_force(colvarvalue const &force) if (!ref1->noforce) ref1->apply_colvar_force(force.real_value); - if (ref2 && ref2->size() && !ref2->noforce) + if (ref2 && !ref2->noforce) ref2->apply_colvar_force(force.real_value); if (!main->noforce) @@ -464,7 +464,7 @@ void colvar::distance_xy::apply_force(colvarvalue const &force) if (!ref1->noforce) ref1->apply_colvar_force(force.real_value); - if (ref2 && ref2->size() && !ref2->noforce) + if (ref2 && !ref2->noforce) ref2->apply_colvar_force(force.real_value); if (!main->noforce) @@ -979,14 +979,12 @@ colvar::rmsd::rmsd(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, rely on existing atom indices for the group - atoms->create_sorted_ids(); - ref_pos.resize(atoms->size()); } - cvm::load_coords(ref_pos_file.c_str(), ref_pos, atoms->sorted_ids, - ref_pos_col, ref_pos_col_value); + ref_pos.resize(atoms->size()); + + cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms, + ref_pos_col, ref_pos_col_value); } } @@ -1172,13 +1170,11 @@ colvar::eigenvector::eigenvector(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } ref_pos.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &ref_pos, atoms, + file_col, file_col_value); } } @@ -1249,13 +1245,11 @@ colvar::eigenvector::eigenvector(std::string const &conf) cvm::error("Error: vectorColValue, if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } eigenvec.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), eigenvec, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &eigenvec, atoms, + file_col, file_col_value); } } diff --git a/lib/colvars/colvarcomp_rotations.cpp b/lib/colvars/colvarcomp_rotations.cpp index 2650a9fe18efaaff66e6711d73be99a715d17ec1..498ef7c2f548f0cc6593725c52fb24d341c72822 100644 --- a/lib/colvars/colvarcomp_rotations.cpp +++ b/lib/colvars/colvarcomp_rotations.cpp @@ -50,12 +50,11 @@ colvar::orientation::orientation(std::string const &conf) "if provided, must be non-zero.\n"); return; } - } else { - // if not, use atom indices - atoms->create_sorted_ids(); } + ref_pos.resize(atoms->size()); - cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value); + cvm::load_coords(file_name.c_str(), &ref_pos, atoms, + file_col, file_col_value); } } diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index a058ad55c2a4911324c9cd07b4ea7bb1e1afb147..80bd6670d3f13317bdf10da43a48cee5b482ec61 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -549,7 +549,7 @@ void colvardeps::init_cv_requires() { f_req_exclude(f_cv_custom_function, f_cv_scripted); init_feature(f_cv_periodic, "periodic", f_type_static); - f_req_self(f_cv_periodic, f_cv_homogeneous); + f_req_self(f_cv_periodic, f_cv_scalar); init_feature(f_cv_scalar, "scalar", f_type_static); init_feature(f_cv_linear, "linear", f_type_static); init_feature(f_cv_homogeneous, "homogeneous", f_type_static); diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp index 1ac4aae133c3a225aa8d4a8bb2dbdd1c3ac381cb..407b336afd7b09e49a05c1550096bf318f4f06f3 100644 --- a/lib/colvars/colvargrid.cpp +++ b/lib/colvars/colvargrid.cpp @@ -329,7 +329,6 @@ void integrate_potential::update_div_local(const std::vector &ix0) const int linear_index = address(ix0); int i, j, k; std::vector ix = ix0; - const cvm::real * g; if (nd == 2) { // gradients at grid points surrounding the current scalar grid point @@ -783,7 +782,7 @@ void integrate_potential::atimes(const std::vector &A, std::vector &b, std::vector &x) { - for (size_t i=0; i &b, std::ve iter=0; atimes(x,r); - for (j=0;j &b, std::ve bkden = 1.0; while (iter < itmax) { ++iter; - for (bknum=0.0,j=0;j -#include +#include #include "colvarmodule.h" #include "colvarparse.h" @@ -30,10 +30,10 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) depth_s = 0; cv_traj_os = NULL; - // pointer to the proxy object if (proxy == NULL) { - proxy = proxy_in; - parse = new colvarparse(); + proxy = proxy_in; // Pointer to the proxy object + parse = new colvarparse(); // Parsing object for global options + version_int = proxy->get_version_from_string(COLVARS_VERSION); } else { // TODO relax this error to handle multiple molecules in VMD // once the module is not static anymore @@ -58,22 +58,24 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) // "it_restart" will be set by the input state file, if any; // "it" should be updated by the proxy colvarmodule::it = colvarmodule::it_restart = 0; - colvarmodule::it_restart_from_state_file = true; - colvarmodule::use_scripted_forces = false; + use_scripted_forces = false; + scripting_after_biases = false; - colvarmodule::b_analysis = false; + b_analysis = false; colvarmodule::debug_gradients_step_size = 1.0e-07; colvarmodule::rotation::monitor_crossings = false; colvarmodule::rotation::crossing_threshold = 1.0e-02; - colvarmodule::cv_traj_freq = 100; - colvarmodule::restart_out_freq = proxy->restart_frequency(); + cv_traj_freq = 100; + restart_out_freq = proxy->restart_frequency(); // by default overwrite the existing trajectory file - colvarmodule::cv_traj_append = false; + cv_traj_append = false; + + cv_traj_write_labels = true; } @@ -189,26 +191,27 @@ int colvarmodule::parse_config(std::string &conf) { extra_conf.clear(); - // parse global options + // Parse global options if (catch_input_errors(parse_global_params(conf))) { return get_error(); } - // parse the options for collective variables + // Parse the options for collective variables if (catch_input_errors(parse_colvars(conf))) { return get_error(); } - // parse the options for biases + // Parse the options for biases if (catch_input_errors(parse_biases(conf))) { return get_error(); } - // done parsing known keywords, check that all keywords found were valid ones + // Done parsing known keywords, check that all keywords found were valid ones if (catch_input_errors(parse->check_keywords(conf, "colvarmodule"))) { return get_error(); } + // Parse auto-generated configuration (e.g. for back-compatibility) if (extra_conf.size()) { catch_input_errors(parse_global_params(extra_conf)); catch_input_errors(parse_colvars(extra_conf)); @@ -222,13 +225,11 @@ int colvarmodule::parse_config(std::string &conf) cvm::log("Collective variables module (re)initialized.\n"); cvm::log(cvm::line_marker); - // update any necessary proxy data + // Update any necessary proxy data proxy->setup(); - if (cv_traj_os != NULL) { - // configuration might have changed, better redo the labels - write_traj_label(*cv_traj_os); - } + // configuration might have changed, better redo the labels + cv_traj_write_labels = true; return get_error(); } @@ -279,15 +280,18 @@ int colvarmodule::parse_global_params(std::string const &conf) parse->get_keyval(conf, "colvarsTrajAppend", cv_traj_append, cv_traj_append, colvarparse::parse_silent); - parse->get_keyval(conf, "scriptedColvarForces", use_scripted_forces, false); + parse->get_keyval(conf, "scriptedColvarForces", + use_scripted_forces, use_scripted_forces); - parse->get_keyval(conf, "scriptingAfterBiases", scripting_after_biases, true); + parse->get_keyval(conf, "scriptingAfterBiases", + scripting_after_biases, scripting_after_biases); if (use_scripted_forces && !proxy->force_script_defined) { - cvm::error("User script for scripted colvar forces not found.", INPUT_ERROR); + return cvm::error("User script for scripted colvar forces not found.", + INPUT_ERROR); } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + return cvm::get_error(); } @@ -432,13 +436,13 @@ int colvarmodule::parse_biases(std::string const &conf) } -int colvarmodule::num_variables() const +size_t colvarmodule::num_variables() const { return colvars.size(); } -int colvarmodule::num_variables_feature(int feature_id) const +size_t colvarmodule::num_variables_feature(int feature_id) const { size_t n = 0; for (std::vector::const_iterator cvi = colvars.begin(); @@ -452,13 +456,13 @@ int colvarmodule::num_variables_feature(int feature_id) const } -int colvarmodule::num_biases() const +size_t colvarmodule::num_biases() const { return biases.size(); } -int colvarmodule::num_biases_feature(int feature_id) const +size_t colvarmodule::num_biases_feature(int feature_id) const { size_t n = 0; for (std::vector::const_iterator bi = biases.begin(); @@ -472,7 +476,7 @@ int colvarmodule::num_biases_feature(int feature_id) const } -int colvarmodule::num_biases_type(std::string const &type) const +size_t colvarmodule::num_biases_type(std::string const &type) const { size_t n = 0; for (std::vector::const_iterator bi = biases.begin(); @@ -971,13 +975,20 @@ int colvarmodule::write_restart_file(std::string const &out_name) int colvarmodule::write_traj_files() { if (cv_traj_os == NULL) { - open_traj_file(cv_traj_name); + if (open_traj_file(cv_traj_name) != COLVARS_OK) { + return cvm::get_error(); + } else { + cv_traj_write_labels = true; + } } // write labels in the traj file every 1000 lines and at first timestep - if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) { + if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || + cvm::step_relative() == 0 || + cv_traj_write_labels) { write_traj_label(*cv_traj_os); } + cv_traj_write_labels = false; if ((cvm::step_absolute() % cv_traj_freq) == 0) { write_traj(*cv_traj_os); @@ -1064,7 +1075,7 @@ int colvarmodule::reset() { parse->init(); - cvm::log("Resetting the Collective Variables Module.\n"); + cvm::log("Resetting the Collective Variables module.\n"); // Iterate backwards because we are deleting the elements as we go for (std::vector::reverse_iterator bi = biases.rbegin(); @@ -1073,6 +1084,7 @@ int colvarmodule::reset() delete *bi; // the bias destructor updates the biases array } biases.clear(); + biases_active_.clear(); // Iterate backwards because we are deleting the elements as we go for (std::vector::reverse_iterator cvi = colvars.rbegin(); @@ -1088,7 +1100,7 @@ int colvarmodule::reset() proxy->reset(); if (cv_traj_os != NULL) { - // Do not close file here, as we might not be done with it yet. + // Do not close traj file here, as we might not be done with it yet. proxy->flush_output_stream(cv_traj_os); } @@ -1188,12 +1200,10 @@ std::istream & colvarmodule::read_restart(std::istream &is) // read global restart information std::string restart_conf; if (is >> colvarparse::read_block("configuration", restart_conf)) { - if (it_restart_from_state_file) { - parse->get_keyval(restart_conf, "step", - it_restart, (size_t) 0, - colvarparse::parse_silent); + parse->get_keyval(restart_conf, "step", + it_restart, (size_t) 0, + colvarparse::parse_silent); it = it_restart; - } std::string restart_version; parse->get_keyval(restart_conf, "version", restart_version, std::string(""), @@ -1688,40 +1698,59 @@ int cvm::read_index_file(char const *filename) return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } + int cvm::load_atoms(char const *file_name, cvm::atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value) + double pdb_field_value) { return proxy->load_atoms(file_name, atoms, pdb_field, pdb_field_value); } + int cvm::load_coords(char const *file_name, - std::vector &pos, - const std::vector &indices, + std::vector *pos, + cvm::atom_group *atoms, std::string const &pdb_field, - double const pdb_field_value) + double pdb_field_value) { - // Differentiate between PDB and XYZ files - // for XYZ files, use CVM internal parser - // otherwise call proxy function for PDB + int error_code = COLVARS_OK; + + std::string const ext(strlen(file_name) > 4 ? + (file_name + (strlen(file_name) - 4)) : + file_name); + + atoms->create_sorted_ids(); + + std::vector sorted_pos(atoms->size(), cvm::rvector(0.0)); - std::string const ext(strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name); + // Differentiate between PDB and XYZ files if (colvarparse::to_lower_cppstr(ext) == std::string(".xyz")) { - if ( pdb_field.size() > 0 ) { - cvm::error("Error: PDB column may not be specified for XYZ coordinate file.\n", INPUT_ERROR); - return COLVARS_ERROR; + if (pdb_field.size() > 0) { + return cvm::error("Error: PDB column may not be specified " + "for XYZ coordinate files.\n", INPUT_ERROR); } - return cvm::load_coords_xyz(file_name, pos, indices); + // For XYZ files, use internal parser + error_code |= cvm::load_coords_xyz(file_name, &sorted_pos, atoms); } else { - return proxy->load_coords(file_name, pos, indices, pdb_field, pdb_field_value); + // Otherwise, call proxy function for PDB + error_code |= proxy->load_coords(file_name, + sorted_pos, atoms->sorted_ids(), + pdb_field, pdb_field_value); } + + std::vector const &map = atoms->sorted_ids_map(); + for (size_t i = 0; i < atoms->size(); i++) { + (*pos)[map[i]] = sorted_pos[i]; + } + + return error_code; } int cvm::load_coords_xyz(char const *filename, - std::vector &pos, - const std::vector &indices) + std::vector *pos, + cvm::atom_group *atoms) { std::ifstream xyz_is(filename); unsigned int natoms; @@ -1736,12 +1765,12 @@ int cvm::load_coords_xyz(char const *filename, cvm::getline(xyz_is, line); cvm::getline(xyz_is, line); xyz_is.width(255); - std::vector::iterator pos_i = pos.begin(); + std::vector::iterator pos_i = pos->begin(); - if (pos.size() != natoms) { // Use specified indices + if (pos->size() != natoms) { // Use specified indices int next = 0; // indices are zero-based - std::vector::const_iterator index = indices.begin(); - for ( ; pos_i != pos.end() ; pos_i++, index++) { + std::vector::const_iterator index = atoms->sorted_ids().begin(); + for ( ; pos_i != pos->end() ; pos_i++, index++) { while ( next < *index ) { cvm::getline(xyz_is, line); @@ -1751,7 +1780,7 @@ int cvm::load_coords_xyz(char const *filename, xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2]; } } else { // Use all positions - for ( ; pos_i != pos.end() ; pos_i++) { + for ( ; pos_i != pos->end() ; pos_i++) { xyz_is >> symbol; xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2]; } @@ -1792,17 +1821,13 @@ void cvm::request_total_force() proxy->request_total_force(true); } -cvm::rvector cvm::position_distance(atom_pos const &pos1, - atom_pos const &pos2) + +cvm::rvector cvm::position_distance(cvm::atom_pos const &pos1, + cvm::atom_pos const &pos2) { return proxy->position_distance(pos1, pos2); } -cvm::real cvm::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) -{ - return proxy->position_dist2(pos1, pos2); -} cvm::real cvm::rand_gaussian(void) { diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 64a98b77a02d59eae598a3f223214fc103018263..f3d99a2b234baf4a72300b4c59c3c9595d318b12 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -73,8 +73,17 @@ private: /// Impossible to initialize the main object without arguments colvarmodule(); + /// Integer representing the version string (allows comparisons) + int version_int; + public: + /// Get the version number (higher = more recent) + int version_number() const + { + return version_int; + } + friend class colvarproxy; // TODO colvarscript should be unaware of colvarmodule's internals friend class colvarscript; @@ -158,10 +167,6 @@ public: return it; } - /// If true, get it_restart from the state file; if set to false, - /// the MD program is providing it - bool it_restart_from_state_file; - /// \brief Finite difference step size (if there is no dynamics, or /// if gradients need to be tested independently from the size of /// dt) @@ -306,19 +311,19 @@ private: public: /// Return how many variables are defined - int num_variables() const; + size_t num_variables() const; /// Return how many variables have this feature enabled - int num_variables_feature(int feature_id) const; + size_t num_variables_feature(int feature_id) const; /// Return how many biases are defined - int num_biases() const; + size_t num_biases() const; /// Return how many biases have this feature enabled - int num_biases_feature(int feature_id) const; + size_t num_biases_feature(int feature_id) const; /// Return how many biases of this type are defined - int num_biases_type(std::string const &type) const; + size_t num_biases_type(std::string const &type) const; /// Return the names of time-dependent biases with forces enabled (ABF, /// metadynamics, etc) @@ -479,9 +484,6 @@ public: /// Print a message to the main log and set global error code static int error(std::string const &message, int code = COLVARS_ERROR); - /// Print a message to the main log and exit normally - static void exit(std::string const &message); - // Replica exchange commands. static bool replica_enabled(); static int replica_index(); @@ -495,15 +497,6 @@ public: static rvector position_distance(atom_pos const &pos1, atom_pos const &pos2); - /// \brief Get the square distance between two positions (with - /// periodic boundary conditions handled transparently) - /// - /// Note: in the case of periodic boundary conditions, this provides - /// an analytical square distance (while taking the square of - /// position_distance() would produce leads to a cusp) - static real position_dist2(atom_pos const &pos1, - atom_pos const &pos2); - /// \brief Names of groups from a Gromacs .ndx file to be read at startup std::list index_group_names; @@ -513,29 +506,36 @@ public: /// \brief Read a Gromacs .ndx file int read_index_file(char const *filename); - - /// \brief Create atoms from a file \param filename name of the file - /// (usually a PDB) \param atoms array of the atoms to be allocated - /// \param pdb_field (optiona) if "filename" is a PDB file, use this - /// field to determine which are the atoms to be set + /// \brief Select atom IDs from a file (usually PDB) \param filename name of + /// the file \param atoms array into which atoms read from "filename" will be + /// appended \param pdb_field (optional) if the file is a PDB and this + /// string is non-empty, select atoms for which this field is non-zero + /// \param pdb_field_value (optional) if non-zero, select only atoms whose + /// pdb_field equals this static int load_atoms(char const *filename, atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); - - /// \brief Load the coordinates for a group of atoms from a file - /// (PDB or XYZ) + double pdb_field_value = 0.0); + + /// \brief Load coordinates for a group of atoms from a file (PDB or XYZ); + /// if "pos" is already allocated, the number of its elements must match the + /// number of entries in "filename" \param filename name of the file \param + /// pos array of coordinates \param atoms group containing the atoms (used + /// to obtain internal IDs) \param pdb_field (optional) if the file is a PDB + /// and this string is non-empty, select atoms for which this field is + /// non-zero \param pdb_field_value (optional) if non-zero, select only + /// atoms whose pdb_field equals this static int load_coords(char const *filename, - std::vector &pos, - const std::vector &indices, + std::vector *pos, + atom_group *atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); /// \brief Load the coordinates for a group of atoms from an /// XYZ file static int load_coords_xyz(char const *filename, - std::vector &pos, - const std::vector &indices); + std::vector *pos, + atom_group *atoms); /// Frequency for collective variables trajectory output static size_t cv_traj_freq; @@ -568,6 +568,9 @@ protected: /// Appending to the existing trajectory file? bool cv_traj_append; + /// Write labels at the next iteration + bool cv_traj_write_labels; + private: /// Counter for the current depth in the object hierarchy (useg e.g. in output) diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp index 8767d5f459090854cf19ad011f579e752c6d2230..86338dfd1b81768de686dfba86bfea964240eca0 100644 --- a/lib/colvars/colvarproxy.cpp +++ b/lib/colvars/colvarproxy.cpp @@ -8,7 +8,7 @@ // Colvars repository at GitHub. #include -#include +#include #if defined(_OPENMP) #include @@ -26,7 +26,10 @@ -colvarproxy_system::colvarproxy_system() {} +colvarproxy_system::colvarproxy_system() +{ + reset_pbc_lattice(); +} colvarproxy_system::~colvarproxy_system() {} @@ -55,10 +58,73 @@ bool colvarproxy_system::total_forces_same_step() const } -cvm::real colvarproxy_system::position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) +inline int round_to_integer(cvm::real x) { - return (position_distance(pos1, pos2)).norm2(); + return std::floor(x+0.5); +} + + +void colvarproxy_system::update_pbc_lattice() +{ + // Periodicity is assumed in all directions + + if (boundaries_type == boundaries_unsupported || + boundaries_type == boundaries_non_periodic) { + cvm::error("Error: setting PBC lattice with unsupported boundaries.\n", + BUG_ERROR); + return; + } + + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_y, unit_cell_z); + reciprocal_cell_x = v/(v*unit_cell_x); + } + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_z, unit_cell_x); + reciprocal_cell_y = v/(v*unit_cell_y); + } + { + cvm::rvector const v = cvm::rvector::outer(unit_cell_x, unit_cell_y); + reciprocal_cell_z = v/(v*unit_cell_z); + } +} + + +void colvarproxy_system::reset_pbc_lattice() +{ + unit_cell_x.reset(); + unit_cell_y.reset(); + unit_cell_z.reset(); + reciprocal_cell_x.reset(); + reciprocal_cell_y.reset(); + reciprocal_cell_z.reset(); +} + + +cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1, + cvm::atom_pos const &pos2) + const +{ + if (boundaries_type == boundaries_unsupported) { + cvm::error("Error: unsupported boundary conditions.\n", INPUT_ERROR); + } + + cvm::rvector diff = (pos2 - pos1); + + if (boundaries_type == boundaries_non_periodic) return diff; + + cvm::real const x_shift = round_to_integer(reciprocal_cell_x*diff); + cvm::real const y_shift = round_to_integer(reciprocal_cell_y*diff); + cvm::real const z_shift = round_to_integer(reciprocal_cell_z*diff); + + diff.x -= x_shift*unit_cell_x.x + y_shift*unit_cell_y.x + + z_shift*unit_cell_z.x; + diff.y -= x_shift*unit_cell_x.y + y_shift*unit_cell_y.y + + z_shift*unit_cell_z.y; + diff.z -= x_shift*unit_cell_x.z + y_shift*unit_cell_y.z + + z_shift*unit_cell_z.z; + + return diff; } @@ -132,7 +198,7 @@ void colvarproxy_atoms::clear_atom(int index) int colvarproxy_atoms::load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, - double const) + double) { return cvm::error("Error: loading atom identifiers from a file " "is currently not implemented.\n", @@ -142,9 +208,9 @@ int colvarproxy_atoms::load_atoms(char const *filename, int colvarproxy_atoms::load_coords(char const *filename, std::vector &pos, - const std::vector &indices, + std::vector const &sorted_ids, std::string const &pdb_field, - double const) + double) { return cvm::error("Error: loading atomic coordinates from a file " "is currently not implemented.\n", @@ -661,6 +727,7 @@ int colvarproxy_io::close_output_stream(std::string const &output_name) for ( ; osi != output_files.end(); osi++, osni++) { if (*osni == output_name) { ((std::ofstream *) (*osi))->close(); + delete *osi; output_files.erase(osi); output_stream_names.erase(osni); return COLVARS_OK; @@ -729,3 +796,13 @@ size_t colvarproxy::restart_frequency() return 0; } + +int colvarproxy::get_version_from_string(char const *version_string) +{ + std::string const v(version_string); + std::istringstream is(v.substr(0, 4) + v.substr(5, 2) + v.substr(8, 2)); + int newint; + is >> newint; + return newint; +} + diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h index bf290482704af3204518c0ffae7daf5ad5d88c0b..845f93c9bcde6b2654b86fcc9b52baee998ec8a4 100644 --- a/lib/colvars/colvarproxy.h +++ b/lib/colvars/colvarproxy.h @@ -14,6 +14,7 @@ #include #include "colvarmodule.h" +#include "colvartypes.h" #include "colvarvalue.h" @@ -29,7 +30,7 @@ /// To interface to a new MD engine, the simplest solution is to derive a new /// class from \link colvarproxy \endlink. Currently implemented are: \link /// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link -/// colvarproxy_vmd, \endlink. +/// colvarproxy_vmd \endlink. // forward declarations @@ -68,14 +69,16 @@ public: /// \brief Get the PBC-aware distance vector between two positions virtual cvm::rvector position_distance(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2) = 0; + cvm::atom_pos const &pos2) const; - /// \brief Get the PBC-aware square distance between two positions; - /// may need to be reimplemented independently from position_distance() for optimization purposes - virtual cvm::real position_dist2(cvm::atom_pos const &pos1, - cvm::atom_pos const &pos2); + /// Recompute PBC reciprocal lattice (assumes XYZ periodicity) + void update_pbc_lattice(); - /// Tell the proxy whether total forces are needed (may not always be available) + /// Set the lattice vectors to zero + void reset_pbc_lattice(); + + /// \brief Tell the proxy whether total forces are needed (they may not + /// always be available) virtual void request_total_force(bool yesno); /// Are total forces being used? @@ -83,6 +86,29 @@ public: /// Are total forces from the current step available? virtual bool total_forces_same_step() const; + +protected: + + /// \brief Type of boundary conditions + /// + /// Orthogonal and triclinic cells are made available to objects. + /// For any other conditions (mixed periodicity, triclinic cells in LAMMPS) + /// minimum-image distances are computed by the host engine regardless. + enum Boundaries_type { + boundaries_non_periodic, + boundaries_pbc_ortho, + boundaries_pbc_triclinic, + boundaries_unsupported + }; + + /// Type of boundary conditions + Boundaries_type boundaries_type; + + /// Bravais lattice vectors + cvm::rvector unit_cell_x, unit_cell_y, unit_cell_z; + + /// Reciprocal lattice vectors + cvm::rvector reciprocal_cell_x, reciprocal_cell_y, reciprocal_cell_z; }; @@ -121,24 +147,30 @@ public: /// (costly) set the corresponding atoms_ncopies to zero virtual void clear_atom(int index); - /// \brief Read atom identifiers from a file \param filename name of - /// the file (usually a PDB) \param atoms array to which atoms read - /// from "filename" will be appended \param pdb_field (optiona) if - /// "filename" is a PDB file, use this field to determine which are - /// the atoms to be set + /// \brief Select atom IDs from a file (usually PDB) \param filename name of + /// the file \param atoms array to which atoms read from "filename" will be + /// appended \param pdb_field (optional) if the file is a PDB and this + /// string is non-empty, select atoms for which this field is non-zero + /// \param pdb_field_value (optional) if non-zero, select only atoms whose + /// pdb_field equals this virtual int load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, - double const pdb_field_value = 0.0); - - /// \brief Load the coordinates for a group of atoms from a file - /// (usually a PDB); if "pos" is already allocated, the number of its - /// elements must match the number of atoms in "filename" + double pdb_field_value = 0.0); + + /// \brief Load a set of coordinates from a file (usually PDB); if "pos" is + /// already allocated, the number of its elements must match the number of + /// entries in "filename" \param filename name of the file \param pos array + /// of coordinates \param sorted_ids array of sorted internal IDs, used to + /// loop through the file only once \param pdb_field (optional) if the file + /// is a PDB and this string is non-empty, select atoms for which this field + /// is non-zero \param pdb_field_value (optional) if non-zero, select only + /// atoms whose pdb_field equals this virtual int load_coords(char const *filename, std::vector &pos, - const std::vector &indices, + std::vector const &sorted_ids, std::string const &pdb_field, - double const pdb_field_value = 0.0); + double pdb_field_value = 0.0); /// Clear atomic data int reset(); @@ -636,6 +668,15 @@ public: return b_simulation_running; } + /// Convert a version string "YYYY-MM-DD" into an integer + int get_version_from_string(char const *version_string); + + /// Get the version number (higher = more recent) + int version_number() const + { + return version_int; + } + protected: /// Whether a simulation is running (warn against irrecovarable errors) @@ -644,6 +685,9 @@ protected: /// Whether the entire module should be deallocated by the host engine bool b_delete_requested; + /// Integer representing the version string (allows comparisons) + int version_int; + }; diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index dc4b8bd07e420d83289b99f458ed2bf935ab210e..68f5cd13ab14eae1d71a47eba46d8729167966cd 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2018-01-17" +#define COLVARS_VERSION "2018-04-29" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp index 0977496b9e1c252e52c5670f44321796cfafd889..a55e4c65d921261c3f428cdef0f7211c8c5ad6a1 100644 --- a/lib/colvars/colvarscript.cpp +++ b/lib/colvars/colvarscript.cpp @@ -8,8 +8,7 @@ // Colvars repository at GitHub. #include -#include -#include +#include #define COLVARSCRIPT_CPP #include "colvarscript.h" diff --git a/lib/colvars/colvartypes.cpp b/lib/colvars/colvartypes.cpp index b604606d4628911138f2553215db9d7b3c306630..2b45d77e078478e755b76194d2f39851e0c3881c 100644 --- a/lib/colvars/colvartypes.cpp +++ b/lib/colvars/colvartypes.cpp @@ -7,8 +7,8 @@ // If you wish to distribute your changes, please submit them to the // Colvars repository at GitHub. -#include -#include +#include +#include #include "colvarmodule.h" #include "colvartypes.h" diff --git a/lib/colvars/colvartypes.h b/lib/colvars/colvartypes.h index 97257d18ad66d1da99b0b74586190e735687850b..4ef9557dcbf400c2e7adfc846207874632b134ac 100644 --- a/lib/colvars/colvartypes.h +++ b/lib/colvars/colvartypes.h @@ -130,7 +130,7 @@ public: } } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { size_t i; for (i = 0; i < this->size(); i++) { @@ -138,7 +138,7 @@ public: } } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { size_t i; for (i = 0; i < this->size(); i++) { @@ -146,7 +146,8 @@ public: } } - inline friend vector1d operator + (vector1d const &v1, vector1d const &v2) + inline friend vector1d operator + (vector1d const &v1, + vector1d const &v2) { check_sizes(v1.size(), v2.size()); vector1d result(v1.size()); @@ -157,7 +158,8 @@ public: return result; } - inline friend vector1d operator - (vector1d const &v1, vector1d const &v2) + inline friend vector1d operator - (vector1d const &v1, + vector1d const &v2) { check_sizes(v1.size(), v2.size()); vector1d result(v1.size()); @@ -168,7 +170,7 @@ public: return result; } - inline friend vector1d operator * (vector1d const &v, cvm::real const &a) + inline friend vector1d operator * (vector1d const &v, cvm::real a) { vector1d result(v.size()); size_t i; @@ -178,12 +180,12 @@ public: return result; } - inline friend vector1d operator * (cvm::real const &a, vector1d const &v) + inline friend vector1d operator * (cvm::real a, vector1d const &v) { return v * a; } - inline friend vector1d operator / (vector1d const &v, cvm::real const &a) + inline friend vector1d operator / (vector1d const &v, cvm::real a) { vector1d result(v.size()); size_t i; @@ -246,7 +248,8 @@ public: } /// Assign a vector to a slice of this vector - inline void sliceassign(size_t const i1, size_t const i2, vector1d const &v) + inline void sliceassign(size_t const i1, size_t const i2, + vector1d const &v) { if ((i2 < i1) || (i2 >= this->size())) { cvm::error("Error: trying to slice a vector using incorrect boundaries.\n"); @@ -259,12 +262,13 @@ public: /// Formatted output - inline size_t output_width(size_t const &real_width) const + inline size_t output_width(size_t real_width) const { return real_width*(this->size()) + 3*(this->size()-1) + 4; } - inline friend std::istream & operator >> (std::istream &is, cvm::vector1d &v) + inline friend std::istream & operator >> (std::istream &is, + cvm::vector1d &v) { if (v.size() == 0) return is; size_t const start_pos = is.tellg(); @@ -288,7 +292,8 @@ public: return is; } - inline friend std::ostream & operator << (std::ostream &os, cvm::vector1d const &v) + inline friend std::ostream & operator << (std::ostream &os, + cvm::vector1d const &v) { std::streamsize const w = os.width(); std::streamsize const p = os.precision(); @@ -377,6 +382,15 @@ protected: { return vector1d(length, data); } + inline int set(cvm::vector1d const &v) const + { + if (v.size() != length) { + return cvm::error("Error: setting a matrix row from a vector of " + "incompatible size.\n", BUG_ERROR); + } + for (size_t i = 0; i < length; i++) data[i] = v[i]; + return COLVARS_OK; + } }; std::vector data; @@ -515,9 +529,12 @@ public: { if ((m1.outer_length != m2.outer_length) || (m1.inner_length != m2.inner_length)) { - cvm::error("Error: trying to perform an operation between matrices of different sizes, "+ - cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+ - cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n"); + cvm::error("Error: trying to perform an operation between " + "matrices of different sizes, "+ + cvm::to_str(m1.outer_length)+"x"+ + cvm::to_str(m1.inner_length)+" and "+ + cvm::to_str(m2.outer_length)+"x"+ + cvm::to_str(m2.inner_length)+".\n"); } } @@ -539,7 +556,7 @@ public: } } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { size_t i; for (i = 0; i < data.size(); i++) { @@ -547,7 +564,7 @@ public: } } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { size_t i; for (i = 0; i < data.size(); i++) { @@ -555,7 +572,8 @@ public: } } - inline friend matrix2d operator + (matrix2d const &m1, matrix2d const &m2) + inline friend matrix2d operator + (matrix2d const &m1, + matrix2d const &m2) { check_sizes(m1, m2); matrix2d result(m1.outer_length, m1.inner_length); @@ -566,7 +584,8 @@ public: return result; } - inline friend matrix2d operator - (matrix2d const &m1, matrix2d const &m2) + inline friend matrix2d operator - (matrix2d const &m1, + matrix2d const &m2) { check_sizes(m1, m2); matrix2d result(m1.outer_length, m1.inner_length); @@ -577,7 +596,7 @@ public: return result; } - inline friend matrix2d operator * (matrix2d const &m, cvm::real const &a) + inline friend matrix2d operator * (matrix2d const &m, cvm::real a) { matrix2d result(m.outer_length, m.inner_length); size_t i; @@ -587,12 +606,12 @@ public: return result; } - inline friend matrix2d operator * (cvm::real const &a, matrix2d const &m) + inline friend matrix2d operator * (cvm::real a, matrix2d const &m) { return m * a; } - inline friend matrix2d operator / (matrix2d const &m, cvm::real const &a) + inline friend matrix2d operator / (matrix2d const &m, cvm::real a) { matrix2d result(m.outer_length, m.inner_length); size_t i; @@ -602,34 +621,17 @@ public: return result; } - /// Matrix multiplication -// inline friend matrix2d const & operator * (matrix2d const &m1, matrix2d const &m2) -// { -// matrix2d result(m1.outer_length, m2.inner_length); -// if (m1.inner_length != m2.outer_length) { -// cvm::error("Error: trying to multiply two matrices of incompatible sizes, "+ -// cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+ -// cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n"); -// } else { -// size_t i, j, k; -// for (i = 0; i < m1.outer_length; i++) { -// for (j = 0; j < m2.inner_length; j++) { -// for (k = 0; k < m1.inner_length; k++) { -// result[i][j] += m1[i][k] * m2[k][j]; -// } -// } -// } -// } -// return result; -// } - /// vector-matrix multiplication - inline friend vector1d operator * (vector1d const &v, matrix2d const &m) + inline friend vector1d operator * (vector1d const &v, + matrix2d const &m) { vector1d result(m.inner_length); if (m.outer_length != v.size()) { - cvm::error("Error: trying to multiply a vector and a matrix of incompatible sizes, "+ - cvm::to_str(v.size()) + " and " + cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) + ".\n"); + cvm::error("Error: trying to multiply a vector and a matrix " + "of incompatible sizes, "+ + cvm::to_str(v.size()) + " and " + + cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) + + ".\n"); } else { size_t i, k; for (i = 0; i < m.inner_length; i++) { @@ -641,25 +643,6 @@ public: return result; } -// /// matrix-vector multiplication (unused for now) -// inline friend vector1d const & operator * (matrix2d const &m, vector1d const &v) -// { -// vector1d result(m.outer_length); -// if (m.inner_length != v.size()) { -// cvm::error("Error: trying to multiply a matrix and a vector of incompatible sizes, "+ -// cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) -// + " and " + cvm::to_str(v.length) + ".\n"); -// } else { -// size_t i, k; -// for (i = 0; i < m.outer_length; i++) { -// for (k = 0; k < m.inner_length; k++) { -// result[i] += m[i][k] * v[k]; -// } -// } -// } -// return result; -// } - /// Formatted output friend std::ostream & operator << (std::ostream &os, matrix2d const &m) @@ -725,49 +708,52 @@ public: cvm::real x, y, z; inline rvector() - : x(0.0), y(0.0), z(0.0) - {} + { + reset(); + } - inline rvector(cvm::real const &x_i, - cvm::real const &y_i, - cvm::real const &z_i) - : x(x_i), y(y_i), z(z_i) - {} + /// \brief Set all components to zero + inline void reset() + { + set(0.0); + } + + inline rvector(cvm::real x_i, cvm::real y_i, cvm::real z_i) + { + set(x_i, y_i, z_i); + } inline rvector(cvm::vector1d const &v) - : x(v[0]), y(v[1]), z(v[2]) - {} + { + set(v[0], v[1], v[2]); + } inline rvector(cvm::real t) - : x(t), y(t), z(t) - {} + { + set(t); + } - /// \brief Set all components to a scalar value - inline void set(cvm::real const &value) { + /// \brief Set all components to a scalar + inline void set(cvm::real value) + { x = y = z = value; } /// \brief Assign all components - inline void set(cvm::real const &x_i, - cvm::real const &y_i, - cvm::real const &z_i) { + inline void set(cvm::real x_i, cvm::real y_i, cvm::real z_i) + { x = x_i; y = y_i; z = z_i; } - /// \brief Set all components to zero - inline void reset() { - x = y = z = 0.0; - } - /// \brief Access cartesian components by index - inline cvm::real & operator [] (int const &i) { + inline cvm::real & operator [] (int i) { return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x; } /// \brief Access cartesian components by index - inline cvm::real const & operator [] (int const &i) const { + inline cvm::real operator [] (int i) const { return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x; } @@ -780,14 +766,6 @@ public: return result; } - inline cvm::rvector & operator = (cvm::real const &v) - { - x = v; - y = v; - z = v; - return *this; - } - inline void operator += (cvm::rvector const &v) { x += v.x; @@ -802,7 +780,7 @@ public: z -= v.z; } - inline void operator *= (cvm::real const &v) + inline void operator *= (cvm::real v) { x *= v; y *= v; @@ -832,13 +810,14 @@ public: return (n > 0. ? cvm::rvector(x, y, z)/n : cvm::rvector(1., 0., 0.)); } - static inline size_t output_width(size_t const &real_width) + static inline size_t output_width(size_t real_width) { return 3*real_width + 10; } - static inline cvm::rvector outer(cvm::rvector const &v1, cvm::rvector const &v2) + static inline cvm::rvector outer(cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector( v1.y*v2.z - v2.y*v1.z, -v1.x*v2.z + v2.x*v1.z, @@ -850,41 +829,35 @@ public: return cvm::rvector(-v.x, -v.y, -v.z); } - friend inline int operator == (cvm::rvector const &v1, cvm::rvector const &v2) - { - return (v1.x == v2.x) && (v1.y == v2.y) && (v1.z == v2.z); - } - - friend inline int operator != (cvm::rvector const &v1, cvm::rvector const &v2) - { - return (v1.x != v2.x) || (v1.y != v2.y) || (v1.z != v2.z); - } - - friend inline cvm::rvector operator + (cvm::rvector const &v1, cvm::rvector const &v2) + friend inline cvm::rvector operator + (cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector(v1.x + v2.x, v1.y + v2.y, v1.z + v2.z); } - friend inline cvm::rvector operator - (cvm::rvector const &v1, cvm::rvector const &v2) + friend inline cvm::rvector operator - (cvm::rvector const &v1, + cvm::rvector const &v2) { return cvm::rvector(v1.x - v2.x, v1.y - v2.y, v1.z - v2.z); } - friend inline cvm::real operator * (cvm::rvector const &v1, cvm::rvector const &v2) + /// Inner (dot) product + friend inline cvm::real operator * (cvm::rvector const &v1, + cvm::rvector const &v2) { return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z; } - friend inline cvm::rvector operator * (cvm::real const &a, cvm::rvector const &v) + friend inline cvm::rvector operator * (cvm::real a, cvm::rvector const &v) { return cvm::rvector(a*v.x, a*v.y, a*v.z); } - friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real const &a) + friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real a) { return cvm::rvector(a*v.x, a*v.y, a*v.z); } - friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real const &a) + friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real a) { return cvm::rvector(v.x/a, v.y/a, v.z/a); } @@ -946,15 +919,9 @@ public: {} /// Constructor component by component - inline rmatrix(cvm::real const &xxi, - cvm::real const &xyi, - cvm::real const &xzi, - cvm::real const &yxi, - cvm::real const &yyi, - cvm::real const &yzi, - cvm::real const &zxi, - cvm::real const &zyi, - cvm::real const &zzi) + inline rmatrix(cvm::real xxi, cvm::real xyi, cvm::real xzi, + cvm::real yxi, cvm::real yyi, cvm::real yzi, + cvm::real zxi, cvm::real zyi, cvm::real zzi) : cvm::matrix2d(3, 3) { this->xx() = xxi; @@ -983,31 +950,13 @@ public: inline cvm::rmatrix transpose() const { - return cvm::rmatrix(this->xx(), - this->yx(), - this->zx(), - this->xy(), - this->yy(), - this->zy(), - this->xz(), - this->yz(), - this->zz()); + return cvm::rmatrix(this->xx(), this->yx(), this->zx(), + this->xy(), this->yy(), this->zy(), + this->xz(), this->yz(), this->zz()); } friend cvm::rvector operator * (cvm::rmatrix const &m, cvm::rvector const &r); - // friend inline cvm::rmatrix const operator * (cvm::rmatrix const &m1, cvm::rmatrix const &m2) { - // return cvm::rmatrix (m1.xx()*m2.xx() + m1.xy()*m2.yx() + m1.xz()*m2.yz(), - // m1.xx()*m2.xy() + m1.xy()*m2.yy() + m1.xz()*m2.zy(), - // m1.xx()*m2.xz() + m1.xy()*m2.yz() + m1.xz()*m2.zz(), - // m1.yx()*m2.xx() + m1.yy()*m2.yx() + m1.yz()*m2.yz(), - // m1.yx()*m2.xy() + m1.yy()*m2.yy() + m1.yz()*m2.yy(), - // m1.yx()*m2.xz() + m1.yy()*m2.yz() + m1.yz()*m2.yz(), - // m1.zx()*m2.xx() + m1.zy()*m2.yx() + m1.zz()*m2.yz(), - // m1.zx()*m2.xy() + m1.zy()*m2.yy() + m1.zz()*m2.yy(), - // m1.zx()*m2.xz() + m1.zy()*m2.yz() + m1.zz()*m2.yz()); - // } - }; @@ -1031,7 +980,7 @@ public: cvm::real q0, q1, q2, q3; /// Constructor from a 3-d vector - inline quaternion(cvm::real const &x, cvm::real const &y, cvm::real const &z) + inline quaternion(cvm::real x, cvm::real y, cvm::real z) : q0(0.0), q1(x), q2(y), q3(z) {} @@ -1041,10 +990,10 @@ public: {} /// Constructor component by component - inline quaternion(cvm::real const &q0i, - cvm::real const &q1i, - cvm::real const &q2i, - cvm::real const &q3i) + inline quaternion(cvm::real q0i, + cvm::real q1i, + cvm::real q2i, + cvm::real q3i) : q0(q0i), q1(q1i), q2(q2i), q3(q3i) {} @@ -1055,9 +1004,9 @@ public: /// "Constructor" after Euler angles (in radians) /// /// http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles - inline void set_from_euler_angles(cvm::real const &phi_in, - cvm::real const &theta_in, - cvm::real const &psi_in) + inline void set_from_euler_angles(cvm::real phi_in, + cvm::real theta_in, + cvm::real psi_in) { q0 = ( (std::cos(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::cos(psi_in/2.0)) + (std::sin(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::sin(psi_in/2.0)) ); @@ -1079,7 +1028,7 @@ public: } /// \brief Set all components to a scalar - inline void set(cvm::real const &value = 0.0) + inline void set(cvm::real value) { q0 = q1 = q2 = q3 = value; } @@ -1087,7 +1036,7 @@ public: /// \brief Set all components to zero (null quaternion) inline void reset() { - q0 = q1 = q2 = q3 = 0.0; + set(0.0); } /// \brief Set the q0 component to 1 and the others to 0 (quaternion @@ -1099,7 +1048,7 @@ public: } /// Tell the number of characters required to print a quaternion, given that of a real number - static inline size_t output_width(size_t const &real_width) + static inline size_t output_width(size_t real_width) { return 4*real_width + 13; } @@ -1113,7 +1062,7 @@ public: friend std::istream & operator >> (std::istream &is, cvm::quaternion &q); /// Access the quaternion as a 4-d array (return a reference) - inline cvm::real & operator [] (int const &i) { + inline cvm::real & operator [] (int i) { switch (i) { case 0: return this->q0; @@ -1130,7 +1079,7 @@ public: } /// Access the quaternion as a 4-d array (return a value) - inline cvm::real operator [] (int const &i) const { + inline cvm::real operator [] (int i) const { switch (i) { case 0: return this->q0; @@ -1175,12 +1124,12 @@ public: return cvm::quaternion(q0, -q1, -q2, -q3); } - inline void operator *= (cvm::real const &a) + inline void operator *= (cvm::real a) { q0 *= a; q1 *= a; q2 *= a; q3 *= a; } - inline void operator /= (cvm::real const &a) + inline void operator /= (cvm::real a) { q0 /= a; q1 /= a; q2 /= a; q3 /= a; } @@ -1215,19 +1164,22 @@ public: } - friend inline cvm::quaternion operator + (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator + (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0+q.q0, h.q1+q.q1, h.q2+q.q2, h.q3+q.q3); } - friend inline cvm::quaternion operator - (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator - (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0-q.q0, h.q1-q.q1, h.q2-q.q2, h.q3-q.q3); } /// \brief Provides the quaternion product. \b NOTE: for the inner /// product use: \code h.inner (q); \endcode - friend inline cvm::quaternion operator * (cvm::quaternion const &h, cvm::quaternion const &q) + friend inline cvm::quaternion operator * (cvm::quaternion const &h, + cvm::quaternion const &q) { return cvm::quaternion(h.q0*q.q0 - h.q1*q.q1 - h.q2*q.q2 - h.q3*q.q3, h.q0*q.q1 + h.q1*q.q0 + h.q2*q.q3 - h.q3*q.q2, @@ -1235,18 +1187,18 @@ public: h.q0*q.q3 + h.q3*q.q0 + h.q1*q.q2 - h.q2*q.q1); } - friend inline cvm::quaternion operator * (cvm::real const &c, + friend inline cvm::quaternion operator * (cvm::real c, cvm::quaternion const &q) { return cvm::quaternion(c*q.q0, c*q.q1, c*q.q2, c*q.q3); } friend inline cvm::quaternion operator * (cvm::quaternion const &q, - cvm::real const &c) + cvm::real c) { return cvm::quaternion(q.q0*c, q.q1*c, q.q2*c, q.q3*c); } friend inline cvm::quaternion operator / (cvm::quaternion const &q, - cvm::real const &c) + cvm::real c) { return cvm::quaternion(q.q0/c, q.q1/c, q.q2/c, q.q3/c); } @@ -1407,7 +1359,7 @@ public: std::vector< cvm::vector1d > dQ0_1, dQ0_2; /// Allocate space for the derivatives of the rotation - inline void request_group1_gradients(size_t const &n) + inline void request_group1_gradients(size_t n) { dS_1.resize(n, cvm::matrix2d(4, 4)); dL0_1.resize(n, cvm::rvector(0.0, 0.0, 0.0)); @@ -1415,7 +1367,7 @@ public: } /// Allocate space for the derivatives of the rotation - inline void request_group2_gradients(size_t const &n) + inline void request_group2_gradients(size_t n) { dS_2.resize(n, cvm::matrix2d(4, 4)); dL0_2.resize(n, cvm::rvector(0.0, 0.0, 0.0)); @@ -1448,7 +1400,7 @@ public: } /// Constructor after an axis of rotation and an angle (in radians) - inline rotation(cvm::real const &angle, cvm::rvector const &axis) + inline rotation(cvm::real angle, cvm::rvector const &axis) : b_debug_gradients(false) { cvm::rvector const axis_n = axis.unit(); @@ -1500,20 +1452,18 @@ public: if (q.q0 != 0.0) { - // cvm::real const x = iprod/q.q0; - - cvm::real const dspindx = (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0))); + cvm::real const dspindx = + (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0))); - return - cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)), - dspindx * ((1.0/q.q0) * axis.x), - dspindx * ((1.0/q.q0) * axis.y), - dspindx * ((1.0/q.q0) * axis.z)); + return cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)), + dspindx * ((1.0/q.q0) * axis.x), + dspindx * ((1.0/q.q0) * axis.y), + dspindx * ((1.0/q.q0) * axis.z)); } else { // (1/(1+x^2)) ~ (1/x)^2 - return - cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0); - // XX TODO: What if iprod == 0? XX + // The documentation of spinAngle discourages its use when q_vec and + // axis are not close + return cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0); } } diff --git a/lib/gpu/Makefile.linux_multi b/lib/gpu/Makefile.linux_multi new file mode 100644 index 0000000000000000000000000000000000000000..02b405ac35114402cbd5609b635748fd2df37e55 --- /dev/null +++ b/lib/gpu/Makefile.linux_multi @@ -0,0 +1,53 @@ +# /* ---------------------------------------------------------------------- +# Generic Linux Makefile for CUDA +# - Change CUDA_ARCH for your GPU +# ------------------------------------------------------------------------- */ + +# which file will be copied to Makefile.lammps + +EXTRAMAKE = Makefile.lammps.standard + +ifeq ($(CUDA_HOME),) +CUDA_HOME = /usr/local/cuda +endif + +NVCC = nvcc + +# Kepler CUDA +#CUDA_ARCH = -arch=sm_35 +# newer CUDA +#CUDA_ARCH = -arch=sm_13 +# older CUDA +#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE + +CUDA_ARCH = -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 + +# this setting should match LAMMPS Makefile +# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL + +LMP_INC = -DLAMMPS_SMALLBIG + +# precision for GPU calculations +# -D_SINGLE_SINGLE # Single precision for all calculations +# -D_DOUBLE_DOUBLE # Double precision for all calculations +# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double + +CUDA_PRECISION = -D_SINGLE_DOUBLE + +CUDA_INCLUDE = -I$(CUDA_HOME)/include +CUDA_LIB = -L$(CUDA_HOME)/lib64 +CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98" + +CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC +CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias + +BIN_DIR = ./ +OBJ_DIR = ./ +LIB_DIR = ./ +AR = ar +BSH = /bin/sh + +CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini + +include Nvidia.makefile_multi + diff --git a/lib/gpu/Makefile.linux_opencl b/lib/gpu/Makefile.linux_opencl index e6358907785d1db0fb4c70c6e672ef33700956e4..640562dca535665d246d1b08e7350724309d3587 100644 --- a/lib/gpu/Makefile.linux_opencl +++ b/lib/gpu/Makefile.linux_opencl @@ -6,10 +6,10 @@ EXTRAMAKE = Makefile.lammps.opencl -OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi +# OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi # OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler # OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress -# OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device +OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device # this setting should match LAMMPS Makefile # one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index 5f692cf66c8bbe9834ca36f81786fef1ad2e9ae5..0d7214260da804c79a26413b51458623f71c078a 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -77,7 +77,12 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ $(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \ $(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \ $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \ - $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o + $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \ + $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \ + $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \ + $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \ @@ -133,7 +138,12 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye_cubin.h \ $(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl_cubin.h \ $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \ - $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h + $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \ + $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \ + $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \ + $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h all: $(OBJ_DIR) $(GPU_LIB) $(EXECS) @@ -809,6 +819,66 @@ $(OBJ_DIR)/lal_lj_cubic.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic.cpp $(OBJ_DIR)/l $(OBJ_DIR)/lal_lj_cubic_ext.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic_ext.cpp lal_base_atomic.h $(CUDR) -o $@ -c lal_lj_cubic_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/dipole_long_lj.cubin: lal_dipole_long_lj.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_dipole_long_lj.cu + +$(OBJ_DIR)/dipole_long_lj_cubin.h: $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj.cubin + $(BIN2C) -c -n dipole_long_lj $(OBJ_DIR)/dipole_long_lj.cubin > $(OBJ_DIR)/dipole_long_lj_cubin.h + +$(OBJ_DIR)/lal_dipole_long_lj.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj.cpp $(OBJ_DIR)/dipole_long_lj_cubin.h $(OBJ_DIR)/lal_base_dipole.o + $(CUDR) -o $@ -c lal_dipole_long_lj.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_dipole_long_lj_ext.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj_ext.cpp lal_base_dipole.h + $(CUDR) -o $@ -c lal_dipole_long_lj_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lj_expand_coul_long.cubin: lal_lj_expand_coul_long.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_expand_coul_long.cu + +$(OBJ_DIR)/lj_expand_coul_long_cubin.h: $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long.cubin + $(BIN2C) -c -n lj_expand_coul_long $(OBJ_DIR)/lj_expand_coul_long.cubin > $(OBJ_DIR)/lj_expand_coul_long_cubin.h + +$(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long.cpp $(OBJ_DIR)/lj_expand_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o + $(CUDR) -o $@ -c lal_lj_expand_coul_long.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h + $(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul_long_cs.cu + +$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin + $(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o + $(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h + $(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu + +$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin + $(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o + $(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h + $(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu + +$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin + $(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o + $(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h + $(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) + $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H) $(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda diff --git a/lib/gpu/Nvidia.makefile_multi b/lib/gpu/Nvidia.makefile_multi new file mode 100644 index 0000000000000000000000000000000000000000..94cfd4af6b8cd376a2c4497011f8ab71a7b63b5f --- /dev/null +++ b/lib/gpu/Nvidia.makefile_multi @@ -0,0 +1,896 @@ +CUDA = $(NVCC) $(CUDA_INCLUDE) $(CUDA_OPTS) -Icudpp_mini $(CUDA_ARCH) \ + $(CUDA_PRECISION) +CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PRECISION) $(CUDA_INCLUDE) \ + $(CUDPP_OPT) +CUDA_LINK = $(CUDA_LIB) -lcudart +BIN2C = $(CUDA_HOME)/bin/bin2c + +GPU_LIB = $(LIB_DIR)/libgpu.a + +# Headers for Geryon +UCL_H = $(wildcard ./geryon/ucl*.h) +NVC_H = $(wildcard ./geryon/nvc*.h) $(UCL_H) +NVD_H = $(wildcard ./geryon/nvd*.h) $(UCL_H) lal_preprocessor.h +# Headers for Pair Stuff +PAIR_H = lal_atom.h lal_answer.h lal_neighbor_shared.h \ + lal_neighbor.h lal_precision.h lal_device.h \ + lal_balance.h lal_pppm.h + +ALL_H = $(NVD_H) $(PAIR_H) + +EXECS = $(BIN_DIR)/nvc_get_devices +ifdef CUDPP_OPT +CUDPP = $(OBJ_DIR)/cudpp.o $(OBJ_DIR)/cudpp_plan.o \ + $(OBJ_DIR)/cudpp_maximal_launch.o $(OBJ_DIR)/cudpp_plan_manager.o \ + $(OBJ_DIR)/radixsort_app.cu_o $(OBJ_DIR)/scan_app.cu_o +endif +OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ + $(OBJ_DIR)/lal_neighbor.o $(OBJ_DIR)/lal_neighbor_shared.o \ + $(OBJ_DIR)/lal_device.o $(OBJ_DIR)/lal_base_atomic.o \ + $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_base_ellipsoid.o \ + $(OBJ_DIR)/lal_base_dipole.o $(OBJ_DIR)/lal_base_three.o \ + $(OBJ_DIR)/lal_base_dpd.o \ + $(OBJ_DIR)/lal_pppm.o $(OBJ_DIR)/lal_pppm_ext.o \ + $(OBJ_DIR)/lal_gayberne.o $(OBJ_DIR)/lal_gayberne_ext.o \ + $(OBJ_DIR)/lal_re_squared.o $(OBJ_DIR)/lal_re_squared_ext.o \ + $(OBJ_DIR)/lal_lj.o $(OBJ_DIR)/lal_lj_ext.o \ + $(OBJ_DIR)/lal_lj96.o $(OBJ_DIR)/lal_lj96_ext.o \ + $(OBJ_DIR)/lal_lj_expand.o $(OBJ_DIR)/lal_lj_expand_ext.o \ + $(OBJ_DIR)/lal_lj_coul.o $(OBJ_DIR)/lal_lj_coul_ext.o \ + $(OBJ_DIR)/lal_lj_coul_long.o $(OBJ_DIR)/lal_lj_coul_long_ext.o \ + $(OBJ_DIR)/lal_lj_dsf.o $(OBJ_DIR)/lal_lj_dsf_ext.o \ + $(OBJ_DIR)/lal_lj_class2_long.o $(OBJ_DIR)/lal_lj_class2_long_ext.o \ + $(OBJ_DIR)/lal_coul_long.o $(OBJ_DIR)/lal_coul_long_ext.o \ + $(OBJ_DIR)/lal_morse.o $(OBJ_DIR)/lal_morse_ext.o \ + $(OBJ_DIR)/lal_charmm_long.o $(OBJ_DIR)/lal_charmm_long_ext.o \ + $(OBJ_DIR)/lal_lj_sdk.o $(OBJ_DIR)/lal_lj_sdk_ext.o \ + $(OBJ_DIR)/lal_lj_sdk_long.o $(OBJ_DIR)/lal_lj_sdk_long_ext.o \ + $(OBJ_DIR)/lal_eam.o $(OBJ_DIR)/lal_eam_ext.o \ + $(OBJ_DIR)/lal_eam_fs_ext.o $(OBJ_DIR)/lal_eam_alloy_ext.o \ + $(OBJ_DIR)/lal_buck.o $(OBJ_DIR)/lal_buck_ext.o \ + $(OBJ_DIR)/lal_buck_coul.o $(OBJ_DIR)/lal_buck_coul_ext.o \ + $(OBJ_DIR)/lal_buck_coul_long.o $(OBJ_DIR)/lal_buck_coul_long_ext.o \ + $(OBJ_DIR)/lal_table.o $(OBJ_DIR)/lal_table_ext.o \ + $(OBJ_DIR)/lal_yukawa.o $(OBJ_DIR)/lal_yukawa_ext.o \ + $(OBJ_DIR)/lal_born.o $(OBJ_DIR)/lal_born_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf.o $(OBJ_DIR)/lal_born_coul_wolf_ext.o \ + $(OBJ_DIR)/lal_born_coul_long.o $(OBJ_DIR)/lal_born_coul_long_ext.o \ + $(OBJ_DIR)/lal_dipole_lj.o $(OBJ_DIR)/lal_dipole_lj_ext.o \ + $(OBJ_DIR)/lal_dipole_lj_sf.o $(OBJ_DIR)/lal_dipole_lj_sf_ext.o \ + $(OBJ_DIR)/lal_colloid.o $(OBJ_DIR)/lal_colloid_ext.o \ + $(OBJ_DIR)/lal_gauss.o $(OBJ_DIR)/lal_gauss_ext.o \ + $(OBJ_DIR)/lal_yukawa_colloid.o $(OBJ_DIR)/lal_yukawa_colloid_ext.o \ + $(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \ + $(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \ + $(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \ + $(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \ + $(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \ + $(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \ + $(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \ + $(OBJ_DIR)/lal_lj_coul_msm.o $(OBJ_DIR)/lal_lj_coul_msm_ext.o \ + $(OBJ_DIR)/lal_lj_gromacs.o $(OBJ_DIR)/lal_lj_gromacs_ext.o \ + $(OBJ_DIR)/lal_dpd.o $(OBJ_DIR)/lal_dpd_ext.o \ + $(OBJ_DIR)/lal_tersoff.o $(OBJ_DIR)/lal_tersoff_ext.o \ + $(OBJ_DIR)/lal_tersoff_zbl.o $(OBJ_DIR)/lal_tersoff_zbl_ext.o \ + $(OBJ_DIR)/lal_tersoff_mod.o $(OBJ_DIR)/lal_tersoff_mod_ext.o \ + $(OBJ_DIR)/lal_coul.o $(OBJ_DIR)/lal_coul_ext.o \ + $(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \ + $(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \ + $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \ + $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \ + $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \ + $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \ + $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o + +CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ + $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \ + $(OBJ_DIR)/neighbor_cpu.cubin $(OBJ_DIR)/neighbor_cpu_cubin.h \ + $(OBJ_DIR)/neighbor_gpu.cubin $(OBJ_DIR)/neighbor_gpu_cubin.h \ + $(OBJ_DIR)/pppm_f.cubin $(OBJ_DIR)/pppm_f_cubin.h \ + $(OBJ_DIR)/pppm_d.cubin $(OBJ_DIR)/pppm_d_cubin.h \ + $(OBJ_DIR)/ellipsoid_nbor.cubin $(OBJ_DIR)/ellipsoid_nbor_cubin.h \ + $(OBJ_DIR)/gayberne.cubin $(OBJ_DIR)/gayberne_lj.cubin \ + $(OBJ_DIR)/gayberne_cubin.h $(OBJ_DIR)/gayberne_lj_cubin.h \ + $(OBJ_DIR)/re_squared.cubin $(OBJ_DIR)/re_squared_lj.cubin \ + $(OBJ_DIR)/re_squared_cubin.h $(OBJ_DIR)/re_squared_lj_cubin.h \ + $(OBJ_DIR)/lj.cubin $(OBJ_DIR)/lj_cubin.h \ + $(OBJ_DIR)/lj96.cubin $(OBJ_DIR)/lj96_cubin.h \ + $(OBJ_DIR)/lj_expand.cubin $(OBJ_DIR)/lj_expand_cubin.h \ + $(OBJ_DIR)/lj_coul.cubin $(OBJ_DIR)/lj_coul_cubin.h \ + $(OBJ_DIR)/lj_coul_long.cubin $(OBJ_DIR)/lj_coul_long_cubin.h \ + $(OBJ_DIR)/lj_dsf.cubin $(OBJ_DIR)/lj_dsf_cubin.h \ + $(OBJ_DIR)/lj_class2_long.cubin $(OBJ_DIR)/lj_class2_long_cubin.h \ + $(OBJ_DIR)/coul_long.cubin $(OBJ_DIR)/coul_long_cubin.h \ + $(OBJ_DIR)/morse.cubin $(OBJ_DIR)/morse_cubin.h \ + $(OBJ_DIR)/charmm_long.cubin $(OBJ_DIR)/charmm_long_cubin.h \ + $(OBJ_DIR)/lj_sdk.cubin $(OBJ_DIR)/lj_sdk_cubin.h \ + $(OBJ_DIR)/lj_sdk_long.cubin $(OBJ_DIR)/lj_sdk_long_cubin.h \ + $(OBJ_DIR)/eam.cubin $(OBJ_DIR)/eam_cubin.h \ + $(OBJ_DIR)/buck.cubin $(OBJ_DIR)/buck_cubin.h \ + $(OBJ_DIR)/buck_coul_long.cubin $(OBJ_DIR)/buck_coul_long_cubin.h \ + $(OBJ_DIR)/buck_coul.cubin $(OBJ_DIR)/buck_coul_cubin.h \ + $(OBJ_DIR)/table.cubin $(OBJ_DIR)/table_cubin.h \ + $(OBJ_DIR)/yukawa.cubin $(OBJ_DIR)/yukawa_cubin.h \ + $(OBJ_DIR)/born.cubin $(OBJ_DIR)/born_cubin.h \ + $(OBJ_DIR)/born_coul_wolf.cubin $(OBJ_DIR)/born_coul_wolf_cubin.h \ + $(OBJ_DIR)/born_coul_long.cubin $(OBJ_DIR)/born_coul_long_cubin.h \ + $(OBJ_DIR)/dipole_lj.cubin $(OBJ_DIR)/dipole_lj_cubin.h \ + $(OBJ_DIR)/dipole_lj_sf.cubin $(OBJ_DIR)/dipole_lj_sf_cubin.h \ + $(OBJ_DIR)/colloid.cubin $(OBJ_DIR)/colloid_cubin.h \ + $(OBJ_DIR)/gauss.cubin $(OBJ_DIR)/gauss_cubin.h \ + $(OBJ_DIR)/yukawa_colloid.cubin $(OBJ_DIR)/yukawa_colloid_cubin.h \ + $(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye_cubin.h \ + $(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf_cubin.h \ + $(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw_cubin.h \ + $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta_cubin.h \ + $(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck_cubin.h \ + $(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie_cubin.h \ + $(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft_cubin.h \ + $(OBJ_DIR)/lj_coul_msm.cubin $(OBJ_DIR)/lj_coul_msm_cubin.h \ + $(OBJ_DIR)/lj_gromacs.cubin $(OBJ_DIR)/lj_gromacs_cubin.h \ + $(OBJ_DIR)/dpd.cubin $(OBJ_DIR)/dpd_cubin.h \ + $(OBJ_DIR)/tersoff.cubin $(OBJ_DIR)/tersoff_cubin.h \ + $(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl_cubin.h \ + $(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod_cubin.h \ + $(OBJ_DIR)/coul.cubin $(OBJ_DIR)/coul_cubin.h \ + $(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye_cubin.h \ + $(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl_cubin.h \ + $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \ + $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \ + $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \ + $(OBJ_DIR)/lj_expand_coul_long.cubin 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lal_ufm_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_dpd.o: $(ALL_H) lal_dpd.h lal_dpd.cpp $(OBJ_DIR)/dpd_cubin.h $(OBJ_DIR)/lal_base_dpd.o + $(CUDR) -o $@ -c lal_dpd.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_dpd_ext.o: $(ALL_H) lal_dpd.h lal_dpd_ext.cpp lal_base_dpd.h + $(CUDR) -o $@ -c lal_dpd_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/tersoff.cubin: lal_tersoff.cu lal_precision.h lal_tersoff_extra.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_tersoff.cu + +$(OBJ_DIR)/tersoff_cubin.h: $(OBJ_DIR)/tersoff.cubin $(OBJ_DIR)/tersoff.cubin + $(BIN2C) -c -n tersoff $(OBJ_DIR)/tersoff.cubin > $(OBJ_DIR)/tersoff_cubin.h + +$(OBJ_DIR)/lal_tersoff.o: $(ALL_H) lal_tersoff.h lal_tersoff.cpp $(OBJ_DIR)/tersoff_cubin.h $(OBJ_DIR)/lal_base_three.o + $(CUDR) -o $@ -c lal_tersoff.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_tersoff_ext.o: $(ALL_H) lal_tersoff.h lal_tersoff_ext.cpp lal_base_three.h + $(CUDR) -o $@ -c lal_tersoff_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/tersoff_zbl.cubin: lal_tersoff_zbl.cu lal_precision.h lal_tersoff_zbl_extra.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_tersoff_zbl.cu + +$(OBJ_DIR)/tersoff_zbl_cubin.h: $(OBJ_DIR)/tersoff_zbl.cubin $(OBJ_DIR)/tersoff_zbl.cubin + $(BIN2C) -c -n tersoff_zbl $(OBJ_DIR)/tersoff_zbl.cubin > $(OBJ_DIR)/tersoff_zbl_cubin.h + +$(OBJ_DIR)/lal_tersoff_zbl.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl.cpp $(OBJ_DIR)/tersoff_zbl_cubin.h $(OBJ_DIR)/lal_base_three.o + $(CUDR) -o $@ -c lal_tersoff_zbl.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_tersoff_zbl_ext.o: $(ALL_H) lal_tersoff_zbl.h lal_tersoff_zbl_ext.cpp lal_base_three.h + $(CUDR) -o $@ -c lal_tersoff_zbl_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/tersoff_mod.cubin: lal_tersoff_mod.cu lal_precision.h lal_tersoff_mod_extra.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_tersoff_mod.cu + +$(OBJ_DIR)/tersoff_mod_cubin.h: $(OBJ_DIR)/tersoff_mod.cubin $(OBJ_DIR)/tersoff_mod.cubin + $(BIN2C) -c -n tersoff_mod $(OBJ_DIR)/tersoff_mod.cubin > $(OBJ_DIR)/tersoff_mod_cubin.h + +$(OBJ_DIR)/lal_tersoff_mod.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod.cpp $(OBJ_DIR)/tersoff_mod_cubin.h $(OBJ_DIR)/lal_base_three.o + $(CUDR) -o $@ -c lal_tersoff_mod.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_tersoff_mod_ext.o: $(ALL_H) lal_tersoff_mod.h lal_tersoff_mod_ext.cpp lal_base_three.h + $(CUDR) -o $@ -c lal_tersoff_mod_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/coul.cubin: lal_coul.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul.cu + +$(OBJ_DIR)/coul_cubin.h: $(OBJ_DIR)/coul.cubin $(OBJ_DIR)/coul.cubin + $(BIN2C) -c -n coul $(OBJ_DIR)/coul.cubin > $(OBJ_DIR)/coul_cubin.h + +$(OBJ_DIR)/lal_coul.o: $(ALL_H) lal_coul.h lal_coul.cpp $(OBJ_DIR)/coul_cubin.h $(OBJ_DIR)/lal_base_charge.o + $(CUDR) -o $@ -c lal_coul.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_ext.o: $(ALL_H) lal_coul.h lal_coul_ext.cpp lal_base_charge.h + $(CUDR) -o $@ -c lal_coul_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/coul_debye.cubin: lal_coul_debye.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_debye.cu + +$(OBJ_DIR)/coul_debye_cubin.h: $(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye.cubin + $(BIN2C) -c -n coul_debye $(OBJ_DIR)/coul_debye.cubin > $(OBJ_DIR)/coul_debye_cubin.h + +$(OBJ_DIR)/lal_coul_debye.o: $(ALL_H) lal_coul_debye.h lal_coul_debye.cpp $(OBJ_DIR)/coul_debye_cubin.h $(OBJ_DIR)/lal_base_charge.o + $(CUDR) -o $@ -c lal_coul_debye.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_debye_ext.o: $(ALL_H) lal_coul_debye.h lal_coul_debye_ext.cpp lal_base_charge.h + $(CUDR) -o $@ -c lal_coul_debye_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/zbl.cubin: lal_zbl.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_zbl.cu + +$(OBJ_DIR)/zbl_cubin.h: $(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl.cubin + $(BIN2C) -c -n zbl $(OBJ_DIR)/zbl.cubin > $(OBJ_DIR)/zbl_cubin.h + +$(OBJ_DIR)/lal_zbl.o: $(ALL_H) lal_zbl.h lal_zbl.cpp $(OBJ_DIR)/zbl_cubin.h $(OBJ_DIR)/lal_base_atomic.o + $(CUDR) -o $@ -c lal_zbl.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_zbl_ext.o: $(ALL_H) lal_zbl.h lal_zbl_ext.cpp lal_base_atomic.h + $(CUDR) -o $@ -c lal_zbl_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lj_cubic.cubin: lal_lj_cubic.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_cubic.cu + +$(OBJ_DIR)/lj_cubic_cubin.h: $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic.cubin + $(BIN2C) -c -n lj_cubic $(OBJ_DIR)/lj_cubic.cubin > $(OBJ_DIR)/lj_cubic_cubin.h + +$(OBJ_DIR)/lal_lj_cubic.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic.cpp $(OBJ_DIR)/lj_cubic_cubin.h $(OBJ_DIR)/lal_base_atomic.o + $(CUDR) -o $@ -c lal_lj_cubic.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_lj_cubic_ext.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic_ext.cpp lal_base_atomic.h + $(CUDR) -o $@ -c lal_lj_cubic_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/dipole_long_lj.cubin: lal_dipole_long_lj.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_dipole_long_lj.cu + +$(OBJ_DIR)/dipole_long_lj_cubin.h: $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj.cubin + $(BIN2C) -c -n dipole_long_lj $(OBJ_DIR)/dipole_long_lj.cubin > $(OBJ_DIR)/dipole_long_lj_cubin.h + +$(OBJ_DIR)/lal_dipole_long_lj.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj.cpp $(OBJ_DIR)/dipole_long_lj_cubin.h $(OBJ_DIR)/lal_base_dipole.o + $(CUDR) -o $@ -c lal_dipole_long_lj.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_dipole_long_lj_ext.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj_ext.cpp lal_base_dipole.h + $(CUDR) -o $@ -c lal_dipole_long_lj_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lj_expand_coul_long.cubin: lal_lj_expand_coul_long.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_lj_expand_coul_long.cu + +$(OBJ_DIR)/lj_expand_coul_long_cubin.h: $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long.cubin + $(BIN2C) -c -n lj_expand_coul_long $(OBJ_DIR)/lj_expand_coul_long.cubin > $(OBJ_DIR)/lj_expand_coul_long_cubin.h + +$(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long.cpp $(OBJ_DIR)/lj_expand_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o + $(CUDR) -o $@ -c lal_lj_expand_coul_long.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h + $(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_long_cs.cu + +$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin + $(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o + $(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h + $(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu + +$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin + $(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o + $(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h + $(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu + +$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin + $(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o + $(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h + $(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) + +$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H) + $(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda + +$(GPU_LIB): $(OBJS) $(CUDPP) + $(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP) + @cp $(EXTRAMAKE) Makefile.lammps + +clean: + -rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CBNS) *.linkinfo + +veryclean: clean + -rm -rf *~ *.linkinfo + +cleanlib: + -rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CBNS) *.linkinfo diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile index bb071514474655a9fb36a73fab05635fa9ffdd99..86991a1e98f09ef30217e0c003239b9fcff8f11c 100644 --- a/lib/gpu/Opencl.makefile +++ b/lib/gpu/Opencl.makefile @@ -66,7 +66,12 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \ $(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \ $(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \ $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \ - $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o + $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \ + $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \ + $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \ + $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \ $(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/pppm_cl.h \ @@ -95,7 +100,9 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \ $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/coul_cl.h \ $(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/zbl_cl.h \ $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h \ - $(OBJ_DIR)/ufm_cl.h + $(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/dipole_long_lj_cl.h \ + $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/coul_long_cs_cl.h \ + $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h OCL_EXECS = $(BIN_DIR)/ocl_get_devices @@ -588,7 +595,52 @@ $(OBJ_DIR)/lal_ufm.o: $(ALL_H) lal_ufm.h lal_ufm.cpp $(OBJ_DIR)/ufm_cl.h $(OBJ_ $(OBJ_DIR)/lal_ufm_ext.o: $(ALL_H) lal_ufm.h lal_ufm_ext.cpp lal_base_atomic.h $(OCL) -o $@ -c lal_ufm_ext.cpp -I$(OBJ_DIR) -$(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp +$(OBJ_DIR)/dipole_long_lj_cl.h: lal_dipole_long_lj.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh dipole_long_lj $(PRE1_H) lal_dipole_long_lj.cu $(OBJ_DIR)/dipole_long_lj_cl.h; + +$(OBJ_DIR)/lal_dipole_long_lj.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj.cpp $(OBJ_DIR)/dipole_long_lj_cl.h $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o + $(OCL) -o $@ -c lal_dipole_long_lj.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_dipole_long_lj_ext.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj_ext.cpp lal_base_dipole.h + $(OCL) -o $@ -c lal_dipole_long_lj_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lj_expand_coul_long_cl.h: lal_lj_expand_coul_long.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh lj_expand_coul_long $(PRE1_H) lal_lj_expand_coul_long.cu $(OBJ_DIR)/lj_expand_coul_long_cl.h; + +$(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long.cpp $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/lal_base_charge.o + $(OCL) -o $@ -c lal_lj_expand_coul_long.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h + $(OCL) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/coul_long_cs_cl.h: lal_coul_long_cs.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh coul_long_cs $(PRE1_H) lal_coul_long_cs.cu $(OBJ_DIR)/coul_long_cs_cl.h; + +$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cl.h $(OBJ_DIR)/coul_long_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o + $(OCL) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h + $(OCL) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_long_cs_cl.h: lal_born_coul_long_cs.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh born_coul_long_cs $(PRE1_H) lal_born_coul_long_cs.cu $(OBJ_DIR)/born_coul_long_cs_cl.h; + +$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o + $(OCL) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h + $(OCL) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_wolf_cs_cl.h: lal_born_coul_wolf_cs.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh born_coul_wolf_cs $(PRE1_H) lal_born_coul_wolf_cs.cu $(OBJ_DIR)/born_coul_wolf_cs_cl.h; + +$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o + $(OCL) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h + $(OCL) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) + +$(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp $(OCL_H) $(OCL) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_OPENCL $(OCL_LINK) $(OCL_LIB): $(OBJS) $(PTXS) diff --git a/lib/gpu/cudpp_mini/cudpp.h b/lib/gpu/cudpp_mini/cudpp.h index 088b560abc87bccd73604646a64df252b87a04fb..2f38d780a545a1881fd7b858cef1bd42d8727ea3 100644 --- a/lib/gpu/cudpp_mini/cudpp.h +++ b/lib/gpu/cudpp_mini/cudpp.h @@ -300,7 +300,7 @@ #ifndef __CUDPP_H__ #define __CUDPP_H__ -#include // for size_t +#include // for size_t #ifdef __cplusplus extern "C" { diff --git a/lib/gpu/cudpp_mini/cudpp_plan.cpp b/lib/gpu/cudpp_mini/cudpp_plan.cpp index b64b7b37ff5161832607b54d50aa2719ab35237b..e92a857dd1e195c4c656975a17dcef97e10405c6 100644 --- a/lib/gpu/cudpp_mini/cudpp_plan.cpp +++ b/lib/gpu/cudpp_mini/cudpp_plan.cpp @@ -16,7 +16,7 @@ //#include "cudpp_spmvmult.h" #include "cudpp_radixsort.h" -#include +#include CUDPPPlanManager* CUDPPPlanManager::m_instance = NULL; diff --git a/lib/gpu/cudpp_mini/cudpp_util.h b/lib/gpu/cudpp_mini/cudpp_util.h index 5cff05e8182a9f5fb352e2303948f98128846be9..e1c21f3fe6d60074f6794ab82f7411caaa195765 100644 --- a/lib/gpu/cudpp_mini/cudpp_util.h +++ b/lib/gpu/cudpp_mini/cudpp_util.h @@ -25,7 +25,7 @@ #include #include #include -#include +#include #if (CUDA_VERSION >= 3000) #define LAUNCH_BOUNDS(x) __launch_bounds__((x)) diff --git a/lib/gpu/geryon/nvd_device.h b/lib/gpu/geryon/nvd_device.h index 2d2a751f85b47dbef4e08bb0ec69858a8ecc4798..129bdbbdef7b6af52792ccec44fb0446744e7c0e 100644 --- a/lib/gpu/geryon/nvd_device.h +++ b/lib/gpu/geryon/nvd_device.h @@ -260,6 +260,9 @@ class UCL_Device { /// List all devices along with all properties inline void print_all(std::ostream &out); + /// Select the platform that has accelerators (for compatibility with OpenCL) + inline int set_platform_accelerator(int pid=-1) { return UCL_SUCCESS; } + private: int _device, _num_devices; std::vector _properties; diff --git a/lib/gpu/geryon/nvd_macros.h b/lib/gpu/geryon/nvd_macros.h index e0e29b4c6f5d827231fcffb0dc57ca507dd70eac..08ff84991a914eda8deb24e23e5a5b65b52cfa13 100644 --- a/lib/gpu/geryon/nvd_macros.h +++ b/lib/gpu/geryon/nvd_macros.h @@ -1,7 +1,7 @@ #ifndef NVD_MACROS_H #define NVD_MACROS_H -#include +#include #include #include diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h index 138b03c091c7ceac39e4ef4a2c2c54b702f967a7..14455e38a50740784fe2c28fc3ae5a6673c85796 100644 --- a/lib/gpu/geryon/ocl_device.h +++ b/lib/gpu/geryon/ocl_device.h @@ -165,8 +165,8 @@ class UCL_Device { /// Get the current OpenCL device name inline std::string name() { return name(_device); } /// Get the OpenCL device name - inline std::string name(const int i) - { return std::string(_properties[i].name); } + inline std::string name(const int i) { + return std::string(_properties[i].name); } /// Get a string telling the type of the current device inline std::string device_type_name() { return device_type_name(_device); } @@ -280,6 +280,9 @@ class UCL_Device { /// Return the OpenCL type for the device inline cl_device_id & cl_device() { return _cl_device; } + /// Select the platform that has accelerators + inline int set_platform_accelerator(int pid=-1); + private: int _num_platforms; // Number of platforms int _platform; // UCL_Device ID for current platform @@ -311,8 +314,8 @@ UCL_Device::UCL_Device() { return; } else _num_platforms=static_cast(nplatforms); - - set_platform(0); + // note that platform 0 may not necessarily be associated with accelerators + set_platform_accelerator(); } UCL_Device::~UCL_Device() { @@ -320,6 +323,8 @@ UCL_Device::~UCL_Device() { } void UCL_Device::clear() { + _properties.clear(); + _cl_devices.clear(); if (_device>-1) { for (size_t i=0; i<_cq.size(); i++) { CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq.back())); @@ -353,7 +358,7 @@ int UCL_Device::set_platform(int pid) { _num_devices=0; return UCL_ERROR; } - cl_device_id device_list[_num_devices]; + cl_device_id *device_list = new cl_device_id[_num_devices]; CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,n,device_list, &n)); @@ -362,7 +367,7 @@ int UCL_Device::set_platform(int pid) { _cl_devices.push_back(device_list[i]); add_properties(device_list[i]); } - + delete[] device_list; return UCL_SUCCESS; } @@ -516,87 +521,117 @@ int UCL_Device::device_type(const int i) { // Set the CUDA device to the specified device number int UCL_Device::set(int num) { - clear(); - - cl_device_id device_list[_num_devices]; + cl_device_id *device_list = new cl_device_id[_num_devices]; cl_uint n; CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,_num_devices, device_list,&n)); _device=num; _cl_device=device_list[_device]; + delete[] device_list; return create_context(); } -// List all devices along with all properties +// List all devices from all platforms along with all properties void UCL_Device::print_all(std::ostream &out) { - if (num_devices() == 0) - out << "There is no device supporting OpenCL\n"; - for (int i=0; i +#include #include #ifdef __APPLE__ diff --git a/lib/gpu/geryon/ocl_memory.h b/lib/gpu/geryon/ocl_memory.h index 28bb88941f7dbff83faffee954ed3c8500b1f7c7..9692f4dd7bd5b619565ba03d625ad5b6edb807d4 100644 --- a/lib/gpu/geryon/ocl_memory.h +++ b/lib/gpu/geryon/ocl_memory.h @@ -407,7 +407,7 @@ inline void _ocl_build(cl_program &program, cl_device_id &device, size_t ms; CL_SAFE_CALL(clGetProgramBuildInfo(program, device,CL_PROGRAM_BUILD_LOG, 0, NULL, &ms)); - char build_log[ms]; + char *build_log = new char[ms]; CL_SAFE_CALL(clGetProgramBuildInfo(program,device,CL_PROGRAM_BUILD_LOG,ms, build_log, NULL)); @@ -416,6 +416,7 @@ inline void _ocl_build(cl_program &program, cl_device_id &device, << " Error compiling OpenCL Program...\n" << "----------------------------------------------------------\n"; std::cerr << build_log << std::endl; + delete[] build_log; } inline void _ocl_kernel_from_source(cl_context &context, cl_device_id &device, diff --git a/lib/gpu/geryon/ocl_timer.h b/lib/gpu/geryon/ocl_timer.h index 66b79dcab101db3cbc31bbaa00263d5b563081f8..1f56aeb364ccc73c3b6ce22fa2644f0c9413f64b 100644 --- a/lib/gpu/geryon/ocl_timer.h +++ b/lib/gpu/geryon/ocl_timer.h @@ -49,8 +49,6 @@ class UCL_Timer { inline void clear() { if (_initialized) { CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq)); - clReleaseEvent(start_event); - clReleaseEvent(stop_event); _initialized=false; _total_time=0.0; } @@ -107,6 +105,8 @@ class UCL_Timer { CL_SAFE_CALL(clGetEventProfilingInfo(start_event, CL_PROFILING_COMMAND_END, sizeof(cl_ulong), &tstart, NULL)); + clReleaseEvent(start_event); + clReleaseEvent(stop_event); return (tend-tstart)*t_factor; } diff --git a/lib/gpu/lal_answer.h b/lib/gpu/lal_answer.h index 790d9c1f8d16ba95e14902bd6603fc0e23ca7285..557c69b4714bc8368ad13c6b4a031141efd16e7c 100644 --- a/lib/gpu/lal_answer.h +++ b/lib/gpu/lal_answer.h @@ -16,7 +16,7 @@ #ifndef LAL_ANSWER_H #define LAL_ANSWER_H -#include +#include #include "mpi.h" #if defined(USE_OPENCL) diff --git a/lib/gpu/lal_atom.h b/lib/gpu/lal_atom.h index 1b4e17d972aeeca62d3a6bdc2bb2fb5dca823075..57880d7ca976c029ab7006b9c2a5035da8018cfc 100644 --- a/lib/gpu/lal_atom.h +++ b/lib/gpu/lal_atom.h @@ -16,7 +16,7 @@ #ifndef PAIR_GPU_ATOM_H #define PAIR_GPU_ATOM_H -#include +#include #include "mpi.h" #if defined(USE_OPENCL) @@ -322,10 +322,12 @@ class Atom { // Copy charges to device asynchronously inline void add_q_data() { + time_q.start(); if (_q_avail==false) { q.update_device(_nall,true); _q_avail=true; } + time_q.stop(); } // Cast quaternions to write buffer @@ -347,10 +349,12 @@ class Atom { // Copy quaternions to device /** Copies nall()*4 elements **/ inline void add_quat_data() { + time_quat.start(); if (_quat_avail==false) { quat.update_device(_nall*4,true); _quat_avail=true; } + time_quat.stop(); } /// Cast velocities and tags to write buffer diff --git a/lib/gpu/lal_balance.h b/lib/gpu/lal_balance.h index e90e94bee1c974fcc3d8084bbd63f21157ab65ea..6aee5952ed00baa99637162b500dbe0ffd0ec083 100644 --- a/lib/gpu/lal_balance.h +++ b/lib/gpu/lal_balance.h @@ -17,7 +17,7 @@ #define LAL_BALANCE_H #include "lal_device.h" -#include +#include #define _HD_BALANCE_EVERY 25 #define _HD_BALANCE_WEIGHT 0.5 diff --git a/lib/gpu/lal_beck_ext.cpp b/lib/gpu/lal_beck_ext.cpp index 226c2d477b53ebf444ea22eb1093efb194b6545d..dcba4e4f40b1ca65f5045e41d17a816f599ad906 100644 --- a/lib/gpu/lal_beck_ext.cpp +++ b/lib/gpu/lal_beck_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_beck.h" diff --git a/lib/gpu/lal_born_coul_long.cpp b/lib/gpu/lal_born_coul_long.cpp index 68695c49380ea9a0810a98ca0273686c6d3eb61c..116d44d58fd340e13b75439dab4d380dd13de89b 100644 --- a/lib/gpu/lal_born_coul_long.cpp +++ b/lib/gpu/lal_born_coul_long.cpp @@ -57,7 +57,7 @@ int BornCoulLongT::init(const int ntypes, double **host_cutsq, double **host_rho const double g_ewald) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,born_coul_long,"k_born_long"); + _screen,born_coul_long,"k_born_coul_long"); if (success!=0) return success; diff --git a/lib/gpu/lal_born_coul_long.cu b/lib/gpu/lal_born_coul_long.cu index 4cb4ea448fbf74374ce8b7ca7bd95b7cfda6505a..71e5e0ae502e8847bc006788deaf82da9477868d 100644 --- a/lib/gpu/lal_born_coul_long.cu +++ b/lib/gpu/lal_born_coul_long.cu @@ -29,7 +29,7 @@ texture q_tex; #define q_tex q_ #endif -__kernel void k_born_long(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_long(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1, const __global numtyp4 *restrict coeff2, const int lj_types, @@ -110,7 +110,7 @@ __kernel void k_born_long(const __global numtyp4 *restrict x_, forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2-factor_coul); } else forcecoul = (numtyp)0.0; - if (rsq < cutsq_sigma[mtype].y) { + if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq numtyp r = ucl_sqrt(rsq); rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x); r6inv = r2inv*r2inv*r2inv; @@ -127,7 +127,7 @@ __kernel void k_born_long(const __global numtyp4 *restrict x_, if (eflag>0) { if (rsq < cut_coulsq) e_coul += prefactor*(_erfc-factor_coul); - if (rsq < coeff1[mtype].w) { + if (rsq < cutsq_sigma[mtype].y) { numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + coeff2[mtype].z*r2inv*r6inv; energy+=factor_lj*(e-coeff2[mtype].w); @@ -149,7 +149,7 @@ __kernel void k_born_long(const __global numtyp4 *restrict x_, } // if ii } -__kernel void k_born_long_fast(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_long_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1_in, const __global numtyp4 *restrict coeff2_in, const __global numtyp *restrict sp_lj_in, @@ -232,7 +232,7 @@ __kernel void k_born_long_fast(const __global numtyp4 *restrict x_, forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2-factor_coul); } else forcecoul = (numtyp)0.0; - if (rsq < cutsq_sigma[mtype].y) { + if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq numtyp r = ucl_sqrt(rsq); rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x); r6inv = r2inv*r2inv*r2inv; @@ -249,7 +249,7 @@ __kernel void k_born_long_fast(const __global numtyp4 *restrict x_, if (eflag>0) { if (rsq < cut_coulsq) e_coul += prefactor*(_erfc-factor_coul); - if (rsq < coeff1[mtype].w) { + if (rsq < cutsq_sigma[mtype].y) { numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + coeff2[mtype].z*r2inv*r6inv; energy+=factor_lj*(e-coeff2[mtype].w); diff --git a/lib/gpu/lal_born_coul_long.h b/lib/gpu/lal_born_coul_long.h index e0de27c71cc19091887d0c162af5861e37759df0..d236b7b57feca914beb028aae304c91eddda1ff3 100644 --- a/lib/gpu/lal_born_coul_long.h +++ b/lib/gpu/lal_born_coul_long.h @@ -78,7 +78,7 @@ class BornCoulLong : public BaseCharge { numtyp _cut_coulsq, _qqrd2e, _g_ewald; - private: + protected: bool _allocated; void loop(const bool _eflag, const bool _vflag); }; diff --git a/lib/gpu/lal_born_coul_long_cs.cpp b/lib/gpu/lal_born_coul_long_cs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..e7fb946f148949f3b4d50dc71e662458f32977fd --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs.cpp @@ -0,0 +1,95 @@ +/*************************************************************************** + born_coul_long_cs.cpp + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/long/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifdef USE_OPENCL +#include "born_coul_long_cs_cl.h" +#elif defined(USE_CUDART) +const char *born_coul_long_cs=0; +#else +#include "born_coul_long_cs_cubin.h" +#endif + +#include "lal_born_coul_long_cs.h" +#include +using namespace LAMMPS_AL; +#define BornCoulLongCST BornCoulLongCS + +extern Device device; + +template +int BornCoulLongCST::init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_cut_ljsq, const double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,born_coul_long_cs,"k_born_coul_long_cs"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + this->shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + this->shared_types=true; + } + this->_lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; icoeff1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff1,host_write,host_rhoinv, + host_born1,host_born2,host_born3); + + this->coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff2,host_write,host_a,host_c, + host_d,host_offset); + + this->cutsq_sigma.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->cutsq_sigma,host_write,host_cutsq, + host_cut_ljsq,host_sigma); + + this->sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_lj[i]; + host_write[i+4]=host_special_coul[i]; + } + ucl_copy(this->sp_lj,host_write,8,false); + + this->_cut_coulsq=host_cut_coulsq; + this->_qqrd2e=qqrd2e; + this->_g_ewald=g_ewald; + + this->_allocated=true; + this->_max_bytes=this->coeff1.row_bytes()+this->coeff2.row_bytes() + +this->cutsq_sigma.row_bytes()+this->sp_lj.row_bytes(); + return 0; +} + +template class BornCoulLongCS; diff --git a/lib/gpu/lal_born_coul_long_cs.cu b/lib/gpu/lal_born_coul_long_cs.cu new file mode 100644 index 0000000000000000000000000000000000000000..b3e79d9ec841afd0d31cf64b5af1c74f9469a811 --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs.cu @@ -0,0 +1,325 @@ +// ************************************************************************** +// born_coul_long_cs.cu +// ------------------- +// Trung Dac Nguyen (Northwestern) +// +// Device code for acceleration of the born/coul/long/cs pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : June 2018 +// email : ndactrung@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL + +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +#else +texture pos_tex; +texture q_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#endif + +// Note: EWALD_P is different from that in lal_preprocessor.h +// acctyp is needed for these parameters +#define CS_EWALD_P (acctyp)9.95473818e-1 +#define B0 (acctyp)-0.1335096380159268 +#define B1 (acctyp)-2.57839507e-1 +#define B2 (acctyp)-1.37203639e-1 +#define B3 (acctyp)-8.88822059e-3 +#define B4 (acctyp)-5.80844129e-3 +#define B5 (acctyp)1.14652755e-1 + +#define EPSILON (acctyp)(1.0e-20) +#define EPS_EWALD (acctyp)(1.0e-6) +#define EPS_EWALD_SQR (acctyp)(1.0e-12) + +__kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1, + const __global numtyp4 *restrict coeff2, + const int lj_types, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_lj[8]; + sp_lj[0]=sp_lj_in[0]; + sp_lj[1]=sp_lj_in[1]; + sp_lj[2]=sp_lj_in[2]; + sp_lj[3]=sp_lj_in[3]; + sp_lj[4]=sp_lj_in[4]; + sp_lj[5]=sp_lj_in[5]; + sp_lj[6]=sp_lj_in[6]; + sp_lj[7]=sp_lj_in[7]; + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + if (rsq < cut_coulsq) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_born_coul_long_cs_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1_in, + const __global numtyp4 *restrict coeff2_in, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 coeff1[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[8]; + if (tid<8) + sp_lj[tid]=sp_lj_in[tid]; + if (tid0) + coeff2[tid]=coeff2_in[tid]; + } + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii0) { + if (rsq < cut_coulsq) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_born_coul_long_cs.h b/lib/gpu/lal_born_coul_long_cs.h new file mode 100644 index 0000000000000000000000000000000000000000..df0fa0fcd41c790932fd9f4bedd2eb8e982c4865 --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs.h @@ -0,0 +1,53 @@ +/*************************************************************************** + born_coul_long_cs.h + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/long/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_BORN_COUL_LONG_CS_H +#define LAL_BORN_COUL_LONG_CS_H + +#include "lal_born_coul_long.h" + +namespace LAMMPS_AL { + +template +class BornCoulLongCS : public BornCoulLong { + public: + BornCoulLongCS() {} + ~BornCoulLongCS() {} + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, double **host_cut_ljsq, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); +}; + +} + +#endif diff --git a/lib/gpu/lal_born_coul_long_cs_ext.cpp b/lib/gpu/lal_born_coul_long_cs_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..badc8b0808488569685a7d11c5224beb720ce534 --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs_ext.cpp @@ -0,0 +1,132 @@ +/*************************************************************************** + born_coul_long_cs_ext.cpp + ------------------- + Trung Dac Nguyen (ORNL) + + Functions for LAMMPS access to born/coul/long/cs acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_born_coul_long_cs.h" + +using namespace std; +using namespace LAMMPS_AL; + +static BornCoulLongCS BCLCSMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int bornclcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **sigma, double **offset, double *special_lj, + const int inum, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, int &gpu_mode, + FILE *screen, double **host_cut_ljsq, double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + BCLCSMF.clear(); + gpu_mode=BCLCSMF.device->gpu_mode(); + double gpu_split=BCLCSMF.device->particle_split(); + int first_gpu=BCLCSMF.device->first_device(); + int last_gpu=BCLCSMF.device->last_device(); + int world_me=BCLCSMF.device->world_me(); + int gpu_rank=BCLCSMF.device->gpu_rank(); + int procs_per_gpu=BCLCSMF.device->procs_per_gpu(); + + BCLCSMF.device->init_message(screen,"born/coul/long/cs",first_gpu,last_gpu); + + bool message=false; + if (BCLCSMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=BCLCSMF.init(ntypes, cutsq, host_rhoinv, host_born1, host_born2, + host_born3, host_a, host_c, host_d, sigma, offset, + special_lj, inum, nall, 300, maxspecial, cell_size, + gpu_split, screen, host_cut_ljsq, host_cut_coulsq, + host_special_coul, qqrd2e, g_ewald); + + BCLCSMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + BCLCSMF.estimate_gpu_overhead(); + return init_ok; +} + +void bornclcs_gpu_clear() { + BCLCSMF.clear(); +} + +int** bornclcs_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd) { + return BCLCSMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, boxlo, prd); +} + +void bornclcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd) { + BCLCSMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success, + host_q,nlocal,boxlo,prd); +} + +double bornclcs_gpu_bytes() { + return BCLCSMF.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_born_coul_long_ext.cpp b/lib/gpu/lal_born_coul_long_ext.cpp index feb7472e7446999ff0ba2b43496cbfcc38a2e361..d0825529b1bb8ed9bec9a2d858dce8f874dca116 100644 --- a/lib/gpu/lal_born_coul_long_ext.cpp +++ b/lib/gpu/lal_born_coul_long_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_born_coul_long.h" diff --git a/lib/gpu/lal_born_coul_wolf.cpp b/lib/gpu/lal_born_coul_wolf.cpp index 7ebd7b744fd6501a2710c3ad7143112aa9cf520e..c44b8414635abcb6a872b46544e52c1fa5a738da 100644 --- a/lib/gpu/lal_born_coul_wolf.cpp +++ b/lib/gpu/lal_born_coul_wolf.cpp @@ -57,7 +57,7 @@ int BornCoulWolfT::init(const int ntypes, double **host_cutsq, double **host_rho const double alf, const double e_shift, const double f_shift) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,born_coul_wolf,"k_born_wolf"); + _screen,born_coul_wolf,"k_born_coul_wolf"); if (success!=0) return success; diff --git a/lib/gpu/lal_born_coul_wolf.cu b/lib/gpu/lal_born_coul_wolf.cu index 0dc7d08c638d93bd9d0a5f0c1e37cd26e963e593..2c2249feeb7a34bdc899195aad60284aef51551a 100644 --- a/lib/gpu/lal_born_coul_wolf.cu +++ b/lib/gpu/lal_born_coul_wolf.cu @@ -31,7 +31,7 @@ texture q_tex; #define MY_PIS (acctyp)1.77245385090551602729 -__kernel void k_born_wolf(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_wolf(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1, const __global numtyp4 *restrict coeff2, const int lj_types, @@ -165,7 +165,7 @@ __kernel void k_born_wolf(const __global numtyp4 *restrict x_, } // if ii } -__kernel void k_born_wolf_fast(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_wolf_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1_in, const __global numtyp4 *restrict coeff2_in, const __global numtyp *restrict sp_lj_in, diff --git a/lib/gpu/lal_born_coul_wolf.h b/lib/gpu/lal_born_coul_wolf.h index 4b2406b989be7d41d57c3b6cb66c035d491d937d..4b817ee0ced7df7d975c14de7cf20fa2410cdea3 100644 --- a/lib/gpu/lal_born_coul_wolf.h +++ b/lib/gpu/lal_born_coul_wolf.h @@ -13,8 +13,8 @@ email : nguyentd@ornl.gov ***************************************************************************/ -#ifndef LAL_BORN_COUL_LONG_H -#define LAL_BORN_COUL_LONG_H +#ifndef LAL_BORN_COUL_WOLF_H +#define LAL_BORN_COUL_WOLF_H #include "lal_base_charge.h" @@ -79,7 +79,7 @@ class BornCoulWolf : public BaseCharge { numtyp _cut_coulsq,_qqrd2e,_alf,_e_shift,_f_shift; - private: + protected: bool _allocated; void loop(const bool _eflag, const bool _vflag); }; diff --git a/lib/gpu/lal_born_coul_wolf_cs.cpp b/lib/gpu/lal_born_coul_wolf_cs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..bdb1c31e557b9f91f9308036cdf31ee46d87271f --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs.cpp @@ -0,0 +1,97 @@ +/*************************************************************************** + born_coul_wolf_cs.cpp + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/wolf/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifdef USE_OPENCL +#include "born_coul_wolf_cs_cl.h" +#elif defined(USE_CUDART) +const char *born_coul_wolf_cs=0; +#else +#include "born_coul_wolf_cs_cubin.h" +#endif + +#include "lal_born_coul_wolf_cs.h" +#include +using namespace LAMMPS_AL; +#define BornCoulWolfCST BornCoulWolfCS + +extern Device device; + +template +int BornCoulWolfCST::init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_cut_ljsq, const double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double alf, const double e_shift, const double f_shift) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,born_coul_wolf_cs,"k_born_coul_wolf_cs"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + this->shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + this->shared_types=true; + } + this->_lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; icoeff1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff1,host_write,host_rhoinv, + host_born1,host_born2,host_born3); + + this->coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff2,host_write,host_a,host_c, + host_d,host_offset); + + this->cutsq_sigma.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->cutsq_sigma,host_write,host_cutsq, + host_cut_ljsq,host_sigma); + + this->sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_lj[i]; + host_write[i+4]=host_special_coul[i]; + } + ucl_copy(this->sp_lj,host_write,8,false); + + this->_cut_coulsq=host_cut_coulsq; + this->_qqrd2e=qqrd2e; + this->_alf=alf; + this->_e_shift=e_shift; + this->_f_shift=f_shift; + + this->_allocated=true; + this->_max_bytes=this->coeff1.row_bytes()+this->coeff2.row_bytes() + +this->cutsq_sigma.row_bytes()+this->sp_lj.row_bytes(); + return 0; +} + +template class BornCoulWolfCS; diff --git a/lib/gpu/lal_born_coul_wolf_cs.cu b/lib/gpu/lal_born_coul_wolf_cs.cu new file mode 100644 index 0000000000000000000000000000000000000000..847387bfe8c1adbe2e1f3f2a3ed21964d08c5989 --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs.cu @@ -0,0 +1,306 @@ +// ************************************************************************** +// born_coul_wolf_cs.cu +// ------------------- +// Trung Dac Nguyen (Northwestern) +// +// Device code for acceleration of the born/coul/wolf/cs pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : +// email : ndactrung@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL + +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +#else +texture pos_tex; +texture q_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#endif + +#define EPSILON (acctyp)(1.0e-20) +#define MY_PIS (acctyp)1.77245385090551602729 + +__kernel void k_born_coul_wolf_cs(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1, + const __global numtyp4 *restrict coeff2, + const int lj_types, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp alf, const numtyp e_shift, + const numtyp f_shift, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_lj[8]; + sp_lj[0]=sp_lj_in[0]; + sp_lj[1]=sp_lj_in[1]; + sp_lj[2]=sp_lj_in[2]; + sp_lj[3]=sp_lj_in[3]; + sp_lj[4]=sp_lj_in[4]; + sp_lj[5]=sp_lj_in[5]; + sp_lj[6]=sp_lj_in[6]; + sp_lj[7]=sp_lj_in[7]; + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) * + qtmp*qtmp*qqrd2e/(acctyp)t_per_atom; + e_coul += (acctyp)2.0*e_self; + } + + for ( ; nbor0) { + if (rsq < cut_coulsq) { + acctyp e=v_sh; + if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_born_coul_wolf_cs_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1_in, + const __global numtyp4 *restrict coeff2_in, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp alf, const numtyp e_shift, + const numtyp f_shift, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 coeff1[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[8]; + if (tid<8) + sp_lj[tid]=sp_lj_in[tid]; + if (tid0) + coeff2[tid]=coeff2_in[tid]; + } + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii0) { + acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) * + qtmp*qtmp*qqrd2e/(acctyp)t_per_atom; + e_coul += (acctyp)2.0*e_self; + } + + for ( ; nbor0) { + if (rsq < cut_coulsq) { + acctyp e=v_sh; + if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_born_coul_wolf_cs.h b/lib/gpu/lal_born_coul_wolf_cs.h new file mode 100644 index 0000000000000000000000000000000000000000..1d9de0a457f04027118aebe5e9f4c1c6c6561ad3 --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs.h @@ -0,0 +1,54 @@ +/*************************************************************************** + born_coul_wolf_cs.h + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/wolf/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_BORN_COUL_WOLF_CS_H +#define LAL_BORN_COUL_WOLF_CS_H + +#include "lal_born_coul_wolf.h" + +namespace LAMMPS_AL { + +template +class BornCoulWolfCS : public BornCoulWolf { + public: + BornCoulWolfCS() {} + ~BornCoulWolfCS() {} + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, double **host_cut_ljsq, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double alf, const double e_shift, + const double f_shift); +}; + +} + +#endif diff --git a/lib/gpu/lal_born_coul_wolf_cs_ext.cpp b/lib/gpu/lal_born_coul_wolf_cs_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..e2211644af1f5b662a4750686ae5afa28216441c --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs_ext.cpp @@ -0,0 +1,134 @@ +/*************************************************************************** + born_coul_wolf_cs_ext.cpp + ------------------- + Trung Dac Nguyen (Northwestern) + + Functions for LAMMPS access to born/coul/wolf/cs acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_born_coul_wolf_cs.h" + +using namespace std; +using namespace LAMMPS_AL; + +static BornCoulWolfCS BornCWCST; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int borncwcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **sigma, double **offset, double *special_lj, const int inum, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double **host_cut_ljsq, double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double alf, const double e_shift, const double f_shift) { + BornCWCST.clear(); + gpu_mode=BornCWCST.device->gpu_mode(); + double gpu_split=BornCWCST.device->particle_split(); + int first_gpu=BornCWCST.device->first_device(); + int last_gpu=BornCWCST.device->last_device(); + int world_me=BornCWCST.device->world_me(); + int gpu_rank=BornCWCST.device->gpu_rank(); + int procs_per_gpu=BornCWCST.device->procs_per_gpu(); + + BornCWCST.device->init_message(screen,"born/coul/wolf/cs",first_gpu,last_gpu); + + bool message=false; + if (BornCWCST.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=BornCWCST.init(ntypes, cutsq, host_rhoinv, host_born1, host_born2, + host_born3, host_a, host_c, host_d, sigma, + offset, special_lj, inum, nall, 300, + maxspecial, cell_size, gpu_split, screen, host_cut_ljsq, + host_cut_coulsq, host_special_coul, qqrd2e, + alf, e_shift, f_shift); + + BornCWCST.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + BornCWCST.estimate_gpu_overhead(); + return init_ok; +} + +void borncwcs_gpu_clear() { + BornCWCST.clear(); +} + +int** borncwcs_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd) { + return BornCWCST.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, boxlo, prd); +} + +void borncwcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd) { + BornCWCST.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success, + host_q,nlocal,boxlo,prd); +} + +double borncwcs_gpu_bytes() { + return BornCWCST.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_born_coul_wolf_ext.cpp b/lib/gpu/lal_born_coul_wolf_ext.cpp index 254b1c905b5c0991065bcc721bd3b770395040ba..d664f302128df2e33bfe873ed511276bbf756cc7 100644 --- a/lib/gpu/lal_born_coul_wolf_ext.cpp +++ b/lib/gpu/lal_born_coul_wolf_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_born_coul_wolf.h" diff --git a/lib/gpu/lal_born_ext.cpp b/lib/gpu/lal_born_ext.cpp index b1ebf5804c471d883761c89c8effc8a1969df4eb..63991889d90ee35dbeb5fb35ac686a8fa1a8745b 100644 --- a/lib/gpu/lal_born_ext.cpp +++ b/lib/gpu/lal_born_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_born.h" diff --git a/lib/gpu/lal_buck_coul_ext.cpp b/lib/gpu/lal_buck_coul_ext.cpp index e5a5e1315bbf845a770a92e97b7842ef156451db..2a089e20403d17f395cb135270919acbd608cc00 100644 --- a/lib/gpu/lal_buck_coul_ext.cpp +++ b/lib/gpu/lal_buck_coul_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_buck_coul.h" diff --git a/lib/gpu/lal_buck_coul_long_ext.cpp b/lib/gpu/lal_buck_coul_long_ext.cpp index 28a89746b3cdedaf44df8fa6907c2b6560d19d6e..c7e1cd1e35862d769ab135908670a69609865ac7 100644 --- a/lib/gpu/lal_buck_coul_long_ext.cpp +++ b/lib/gpu/lal_buck_coul_long_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_buck_coul_long.h" diff --git a/lib/gpu/lal_buck_ext.cpp b/lib/gpu/lal_buck_ext.cpp index 336aab6d4c5e72cffc63dc8d1f94f9194cc8b423..cc8b77c0a9f0e288d57cbc0ac762310ebac84b4e 100644 --- a/lib/gpu/lal_buck_ext.cpp +++ b/lib/gpu/lal_buck_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_buck.h" diff --git a/lib/gpu/lal_charmm_long_ext.cpp b/lib/gpu/lal_charmm_long_ext.cpp index e24c650be4dafb02a792f763406c3bebbdbdd8dc..743b510825515561bb110b4a42e01b82b43147a8 100644 --- a/lib/gpu/lal_charmm_long_ext.cpp +++ b/lib/gpu/lal_charmm_long_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_charmm_long.h" diff --git a/lib/gpu/lal_colloid_ext.cpp b/lib/gpu/lal_colloid_ext.cpp index 8e1b18e72f11bdefdbbb63ec6d74895047547c1c..961ad75925e5e0a18f585fd2e8f1a1cc17d72930 100644 --- a/lib/gpu/lal_colloid_ext.cpp +++ b/lib/gpu/lal_colloid_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_colloid.h" diff --git a/lib/gpu/lal_coul_debye_ext.cpp b/lib/gpu/lal_coul_debye_ext.cpp index af9156c24c8339089143310c751370072a38d186..af54746defca665a6a6a8ce0f98ff04028f55260 100644 --- a/lib/gpu/lal_coul_debye_ext.cpp +++ b/lib/gpu/lal_coul_debye_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_coul_debye.h" diff --git a/lib/gpu/lal_coul_dsf_ext.cpp b/lib/gpu/lal_coul_dsf_ext.cpp index 026dd924c9c49f786231088835bd4e7719ef9d7e..2d18f9f94d65c723aeb0833791659b72a374d9a6 100644 --- a/lib/gpu/lal_coul_dsf_ext.cpp +++ b/lib/gpu/lal_coul_dsf_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_coul_dsf.h" diff --git a/lib/gpu/lal_coul_ext.cpp b/lib/gpu/lal_coul_ext.cpp index f03d8fcdfcd91c063bba63713bbfbf3ec960bc9d..9779526d62aeac9b2a55d079d0ba3da296d689d6 100644 --- a/lib/gpu/lal_coul_ext.cpp +++ b/lib/gpu/lal_coul_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_coul.h" diff --git a/lib/gpu/lal_coul_long.h b/lib/gpu/lal_coul_long.h index d12198fccc48fe37e262d1dfa63cdfea0b7ae844..ae25b91dc77a9322449fbcc5c1f96d994710838c 100644 --- a/lib/gpu/lal_coul_long.h +++ b/lib/gpu/lal_coul_long.h @@ -72,7 +72,7 @@ class CoulLong : public BaseCharge { numtyp _cut_coulsq, _qqrd2e, _g_ewald; - private: + protected: bool _allocated; void loop(const bool _eflag, const bool _vflag); }; diff --git a/lib/gpu/lal_coul_long_cs.cpp b/lib/gpu/lal_coul_long_cs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..7afa0ae5d21bfb95bbf5c18315907250e7155318 --- /dev/null +++ b/lib/gpu/lal_coul_long_cs.cpp @@ -0,0 +1,78 @@ +/*************************************************************************** + coul_long_cs.cpp + ------------------- + Trung Nguyen (Northwestern) + + Class for acceleration of the coul/long pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : June 2018 + email : ndactrung@gmail.com + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "coul_long_cs_cl.h" +#elif defined(USE_CUDART) +const char *coul_long_cs=0; +#else +#include "coul_long_cs_cubin.h" +#endif + +#include "lal_coul_long_cs.h" +#include +using namespace LAMMPS_AL; +#define CoulLongCST CoulLongCS + +extern Device pair_gpu_device; + +template +int CoulLongCST::init(const int ntypes, double **host_scale, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size, + gpu_split,_screen,coul_long_cs,"k_coul_long_cs"); + if (success!=0) + return success; + + int lj_types=ntypes; + this->shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + this->shared_types=true; + } + this->_lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iscale.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack1(ntypes,lj_types,this->scale,host_write,host_scale); + + this->sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_coul[i]; + } + ucl_copy(this->sp_cl,host_write,4,false); + + this->_cut_coulsq=host_cut_coulsq; + this->_qqrd2e=qqrd2e; + this->_g_ewald=g_ewald; + + this->_allocated=true; + this->_max_bytes=this->scale.row_bytes()+this->sp_cl.row_bytes(); + return 0; +} + +template class CoulLongCS; diff --git a/lib/gpu/lal_coul_long_cs.cu b/lib/gpu/lal_coul_long_cs.cu new file mode 100644 index 0000000000000000000000000000000000000000..3c34666131d2d363c03bc6f684bd9b573b54c043 --- /dev/null +++ b/lib/gpu/lal_coul_long_cs.cu @@ -0,0 +1,367 @@ +// ************************************************************************** +// coul_long_cs.cu +// ------------------- +// Trung Nguyen (Northwestern) +// +// Device code for acceleration of the coul/long/cs pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : June 2018 +// email : ndactrung@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL + +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +#else +texture pos_tex; +texture q_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#endif + +// Note: EWALD_P is different from that in lal_preprocessor.h +// acctyp is needed for these parameters +#define CS_EWALD_P (acctyp)9.95473818e-1 +#define B0 (acctyp)-0.1335096380159268 +#define B1 (acctyp)-2.57839507e-1 +#define B2 (acctyp)-1.37203639e-1 +#define B3 (acctyp)-8.88822059e-3 +#define B4 (acctyp)-5.80844129e-3 +#define B5 (acctyp)1.14652755e-1 + +#define EPSILON (acctyp)(1.0e-20) +#define EPS_EWALD (acctyp)(1.0e-6) +#define EPS_EWALD_SQR (acctyp)(1.0e-12) + +#if (ARCH < 300) + +#define store_answers_lq(f, e_coul, virial, ii, inum, tid, \ + t_per_atom, offset, eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + __local acctyp red_acc[6][BLOCK_PAIR]; \ + \ + red_acc[0][tid]=f.x; \ + red_acc[1][tid]=f.y; \ + red_acc[2][tid]=f.z; \ + red_acc[3][tid]=e_coul; \ + \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<4; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + \ + f.x=red_acc[0][tid]; \ + f.y=red_acc[1][tid]; \ + f.z=red_acc[2][tid]; \ + e_coul=red_acc[3][tid]; \ + \ + if (vflag>0) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid]=virial[r]; \ + \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + \ + for (int r=0; r<6; r++) \ + virial[r]=red_acc[r][tid]; \ + } \ + } \ + \ + if (offset==0) { \ + __global acctyp *ap1=engv+ii; \ + if (eflag>0) { \ + *ap1=(acctyp)0; \ + ap1+=inum; \ + *ap1=e_coul*(acctyp)0.5; \ + ap1+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + *ap1=virial[i]*(acctyp)0.5; \ + ap1+=inum; \ + } \ + } \ + ans[ii]=f; \ + } + +#else + +#define store_answers_lq(f, e_coul, virial, ii, inum, tid, \ + t_per_atom, offset, eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + f.x += shfl_xor(f.x, s, t_per_atom); \ + f.y += shfl_xor(f.y, s, t_per_atom); \ + f.z += shfl_xor(f.z, s, t_per_atom); \ + e_coul += shfl_xor(e_coul, s, t_per_atom); \ + } \ + if (vflag>0) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + for (int r=0; r<6; r++) \ + virial[r] += shfl_xor(virial[r], s, t_per_atom); \ + } \ + } \ + } \ + if (offset==0) { \ + __global acctyp *ap1=engv+ii; \ + if (eflag>0) { \ + *ap1=(acctyp)0; \ + ap1+=inum; \ + *ap1=e_coul*(acctyp)0.5; \ + ap1+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + *ap1=virial[i]*(acctyp)0.5; \ + ap1+=inum; \ + } \ + } \ + ans[ii]=f; \ + } + +#endif + +__kernel void k_coul_long_cs(const __global numtyp4 *restrict x_, + const __global numtyp *restrict scale, + const int lj_types, + const __global numtyp *restrict sp_cl_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_cl[4]; + sp_cl[0]=sp_cl_in[0]; + sp_cl[1]=sp_cl_in[1]; + sp_cl[2]=sp_cl_in[2]; + sp_cl[3]=sp_cl_in[3]; + + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_lq(f,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_coul_long_cs_fast(const __global numtyp4 *restrict x_, + const __global numtyp *restrict scale_in, + const __global numtyp *restrict sp_cl_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp scale[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_cl[4]; + if (tid<4) + sp_cl[tid]=sp_cl_in[tid]; + if (tid0) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_lq(f,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_coul_long_cs.h b/lib/gpu/lal_coul_long_cs.h new file mode 100644 index 0000000000000000000000000000000000000000..3cfcb80fc86c9ab3f3066e086533cad795a378be --- /dev/null +++ b/lib/gpu/lal_coul_long_cs.h @@ -0,0 +1,50 @@ +/*************************************************************************** + coul_long_cs.h + ------------------- + Trung Nguyen (Northwestern) + + Class for acceleration of the coul/long/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : June 2018 + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_COUL_LONG_CS_H +#define LAL_COUL_LONG_CS_H + +#include "lal_coul_long.h" + +namespace LAMMPS_AL { + +template +class CoulLongCS : public CoulLong { + public: + CoulLongCS() {} + ~CoulLongCS() {} + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **scale, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); +}; + +} + +#endif diff --git a/lib/gpu/lal_coul_long_cs_ext.cpp b/lib/gpu/lal_coul_long_cs_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..ae57eb20382a0e47e1d987921e521d84a169dfb3 --- /dev/null +++ b/lib/gpu/lal_coul_long_cs_ext.cpp @@ -0,0 +1,145 @@ +/*************************************************************************** + coul_long_cs_ext.cpp + ------------------- + Trung Nguyen (Northwestern) + + Functions for LAMMPS access to coul/long/cs acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : June 2018 + email : ndactrung@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_coul_long_cs.h" + +using namespace std; +using namespace LAMMPS_AL; + +static CoulLongCS CLCSMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int clcs_gpu_init(const int ntypes, double **host_scale, + const int inum, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, int &gpu_mode, + FILE *screen, double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald) { + CLCSMF.clear(); + gpu_mode=CLCSMF.device->gpu_mode(); + double gpu_split=CLCSMF.device->particle_split(); + int first_gpu=CLCSMF.device->first_device(); + int last_gpu=CLCSMF.device->last_device(); + int world_me=CLCSMF.device->world_me(); + int gpu_rank=CLCSMF.device->gpu_rank(); + int procs_per_gpu=CLCSMF.device->procs_per_gpu(); + + CLCSMF.device->init_message(screen,"coul/long/cs",first_gpu,last_gpu); + + bool message=false; + if (CLCSMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=CLCSMF.init(ntypes, host_scale, inum, nall, 300, maxspecial, + cell_size, gpu_split, screen, host_cut_coulsq, + host_special_coul, qqrd2e, g_ewald); + + CLCSMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + CLCSMF.estimate_gpu_overhead(); + return init_ok; +} + +// --------------------------------------------------------------------------- +// Copy updated coeffs from host to device +// --------------------------------------------------------------------------- +void clcs_gpu_reinit(const int ntypes, double **host_scale) { + int world_me=CLCSMF.device->world_me(); + int gpu_rank=CLCSMF.device->gpu_rank(); + int procs_per_gpu=CLCSMF.device->procs_per_gpu(); + + if (world_me==0) + CLCSMF.reinit(ntypes, host_scale); + + CLCSMF.device->world_barrier(); + + for (int i=0; igpu_barrier(); + } +} + +void clcs_gpu_clear() { + CLCSMF.clear(); +} + +int** clcs_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd) { + return CLCSMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, boxlo, prd); +} + +void clcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd) { + CLCSMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success, + host_q,nlocal,boxlo,prd); +} + +double clcs_gpu_bytes() { + return CLCSMF.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_coul_long_ext.cpp b/lib/gpu/lal_coul_long_ext.cpp index 06c102b2d19f16917ca3d0f1a9ef86da47f4e0a0..653b4be4f322ec70bb1388aaa3cfa22498070ec9 100644 --- a/lib/gpu/lal_coul_long_ext.cpp +++ b/lib/gpu/lal_coul_long_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_coul_long.h" diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index e95f2b30efcc0356646fc0fdf5035034ccb8c996..6b4d0ab2a504e404a72af7bf35d3bc436f9fdd8a 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -16,7 +16,7 @@ #include "lal_device.h" #include "lal_precision.h" #include -#include +#include #ifdef _OPENMP #include #endif @@ -34,8 +34,8 @@ using namespace LAMMPS_AL; template DeviceT::Device() : _init_count(0), _device_init(false), - _gpu_mode(GPU_FORCE), _first_device(0), - _last_device(0), _compiled(false) { + _gpu_mode(GPU_FORCE), _first_device(0), + _last_device(0), _platform_id(-1), _compiled(false) { } template @@ -67,6 +67,17 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, _particle_split=p_split; _cell_size=cell_size; _block_pair=block_pair; + // support selecting platform though "package device" keyword. + // "0:generic" will select platform 0 and tune for generic device + // "1:fermi" will select platform 1 and tune for Nvidia Fermi gpu + if (ocl_vendor) { + char *sep = NULL; + if ((sep = strstr(ocl_vendor,":"))) { + *sep = '\0'; + _platform_id = atoi(ocl_vendor); + ocl_vendor = sep+1; + } + } // Get the rank/size within the world MPI_Comm_rank(_comm_world,&_world_me); @@ -78,9 +89,9 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, // Get the names of all nodes int name_length; char node_name[MPI_MAX_PROCESSOR_NAME]; - char node_names[MPI_MAX_PROCESSOR_NAME*_world_size]; + char *node_names = new char[MPI_MAX_PROCESSOR_NAME*_world_size]; MPI_Get_processor_name(node_name,&name_length); - MPI_Allgather(&node_name,MPI_MAX_PROCESSOR_NAME,MPI_CHAR,&node_names, + MPI_Allgather(&node_name,MPI_MAX_PROCESSOR_NAME,MPI_CHAR,&node_names[0], MPI_MAX_PROCESSOR_NAME,MPI_CHAR,_comm_world); std::string node_string=std::string(node_name); @@ -104,6 +115,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, split_id=split_num; split_num++; } + delete[] node_names; // Set up a per node communicator and find rank within MPI_Comm node_comm; @@ -118,8 +130,16 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, // Time on the device only if 1 proc per gpu _time_device=true; + +#if 0 + // XXX: the following setting triggers a memory leak with OpenCL and MPI + // setting _time_device=true for all processes doesn't seem to be a + // problem with either (no segfault, no (large) memory leak. + // thus keeping this disabled for now. may need to review later. + // 2018-07-23 if (_procs_per_gpu>1) _time_device=false; +#endif // Set up a per device communicator MPI_Comm_split(node_comm,my_gpu,0,&_comm_gpu); @@ -134,6 +154,9 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, return -7; #endif + if (gpu->set_platform_accelerator(_platform_id)!=UCL_SUCCESS) + return -12; + if (gpu->set(my_gpu)!=UCL_SUCCESS) return -6; @@ -190,13 +213,15 @@ int DeviceT::set_ocl_params(char *ocl_vendor) { _ocl_vendor_string="-DUSE_OPENCL"; int token_count=0; std::string params[13]; - char *pch = strtok(ocl_vendor,"\" "); + char *pch = strtok(ocl_vendor,","); + pch = strtok(NULL,","); + if (pch == NULL) return -11; while (pch != NULL) { if (token_count==13) return -11; params[token_count]=pch; token_count++; - pch = strtok(NULL,"\" "); + pch = strtok(NULL,","); } _ocl_vendor_string+=" -DMEM_THREADS="+params[0]+ " -DTHREADS_PER_ATOM="+params[1]+ @@ -655,7 +680,7 @@ int DeviceT::compile_kernels() { dev_program=new UCL_Program(*gpu); int success=dev_program->load_string(device,compile_string().c_str()); if (success!=UCL_SUCCESS) - return -4; + return -6; k_zero.set_function(*dev_program,"kernel_zero"); k_info.set_function(*dev_program,"kernel_info"); _compiled=true; diff --git a/lib/gpu/lal_device.h b/lib/gpu/lal_device.h index 4f7b594c7c9ae7f86e059cee98ffa33b3711be4f..695b0a62f9236f9f4e16119391ce05c6eafbf8e8 100644 --- a/lib/gpu/lal_device.h +++ b/lib/gpu/lal_device.h @@ -22,7 +22,7 @@ #include "lal_pppm.h" #include "mpi.h" #include -#include "stdio.h" +#include #include #include @@ -292,7 +292,7 @@ class Device { MPI_Comm _comm_world, _comm_replica, _comm_gpu; int _procs_per_gpu, _gpu_rank, _world_me, _world_size, _replica_me, _replica_size; - int _gpu_mode, _first_device, _last_device, _nthreads; + int _gpu_mode, _first_device, _last_device, _platform_id, _nthreads; double _particle_split; double _cpu_full; double _ptx_arch; diff --git a/lib/gpu/lal_dipole_lj_ext.cpp b/lib/gpu/lal_dipole_lj_ext.cpp index 76722a20b41c3b6992783ec80c5b141a184864ac..0a94969c8b3115952fa95b0f9b4cb7798854eecf 100644 --- a/lib/gpu/lal_dipole_lj_ext.cpp +++ b/lib/gpu/lal_dipole_lj_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_dipole_lj.h" diff --git a/lib/gpu/lal_dipole_lj_sf_ext.cpp b/lib/gpu/lal_dipole_lj_sf_ext.cpp index 68b935ff38f59add31f3a032a7907e629ec5a6f0..3626e8305ea36dd13844c7a9b9654c9d55bfac4a 100644 --- a/lib/gpu/lal_dipole_lj_sf_ext.cpp +++ b/lib/gpu/lal_dipole_lj_sf_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_dipole_lj_sf.h" diff --git a/lib/gpu/lal_dipole_long_lj.cpp b/lib/gpu/lal_dipole_long_lj.cpp new file mode 100644 index 0000000000000000000000000000000000000000..251e1def92972a9cfd317d0033a5b4e6893213a1 --- /dev/null +++ b/lib/gpu/lal_dipole_long_lj.cpp @@ -0,0 +1,173 @@ +/*************************************************************************** + dipole_lj.cpp + ------------------- + Trung Dac Nguyen (ORNL) + + Class for acceleration of the dipole/cut pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : nguyentd@ornl.gov + ***************************************************************************/ + +#ifdef USE_OPENCL +#include "dipole_long_lj_cl.h" +#elif defined(USE_CUDART) +const char *dipole_long_lj=0; +#else +#include "dipole_long_lj_cubin.h" +#endif + +#include "lal_dipole_long_lj.h" +#include +using namespace LAMMPS_AL; +#define DipoleLongLJT DipoleLongLJ + +extern Device device; + +template +DipoleLongLJT::DipoleLongLJ() : BaseDipole(), + _allocated(false) { +} + +template +DipoleLongLJT::~DipoleLongLJ() { + clear(); +} + +template +int DipoleLongLJT::bytes_per_atom(const int max_nbors) const { + return this->bytes_per_atom_atomic(max_nbors); +} + +template +int DipoleLongLJT::init(const int ntypes, + double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_cut_ljsq, const double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,dipole_long_lj,"k_dipole_long_lj"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + shared_types=true; + } + _lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2, + host_cut_ljsq); + + lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4, + host_offset); + + cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack1(ntypes,lj_types,cutsq,host_write,host_cutsq); + + sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_lj[i]; + host_write[i+4]=host_special_coul[i]; + } + ucl_copy(sp_lj,host_write,8,false); + + _cut_coulsq=host_cut_coulsq; + _qqrd2e=qqrd2e; + _g_ewald=g_ewald; + + _allocated=true; + this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+cutsq.row_bytes()+ + sp_lj.row_bytes(); + return 0; +} + +template +void DipoleLongLJT::clear() { + if (!_allocated) + return; + _allocated=false; + + lj1.clear(); + lj3.clear(); + cutsq.clear(); + sp_lj.clear(); + this->clear_atomic(); +} + +template +double DipoleLongLJT::host_memory_usage() const { + return this->host_memory_usage_atomic()+sizeof(DipoleLongLJ); +} + +// --------------------------------------------------------------------------- +// Calculate energies, forces, and torques +// --------------------------------------------------------------------------- +template +void DipoleLongLJT::loop(const bool _eflag, const bool _vflag) { + // Compute the block size and grid size to keep all cores busy + const int BX=this->block_size(); + int eflag, vflag; + if (_eflag) + eflag=1; + else + eflag=0; + + if (_vflag) + vflag=1; + else + vflag=0; + + int GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/this->_threads_per_atom))); + + int ainum=this->ans->inum(); + int nbor_pitch=this->nbor->nbor_pitch(); + this->time_pair.start(); + if (shared_types) { + this->k_pair_fast.set_size(GX,BX); + this->k_pair_fast.run(&this->atom->x, &lj1, &lj3, &sp_lj, + &this->nbor->dev_nbor, + &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, &vflag, + &ainum, &nbor_pitch, &this->atom->q, + &this->atom->quat, &cutsq, &_cut_coulsq, + &_qqrd2e, &_g_ewald, &this->_threads_per_atom); + } else { + this->k_pair.set_size(GX,BX); + this->k_pair.run(&this->atom->x, &lj1, &lj3, + &_lj_types, &sp_lj, &this->nbor->dev_nbor, + &this->_nbor_data->begin(), &this->ans->force, + &this->ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->atom->q, + &this->atom->quat, &cutsq, &_cut_coulsq, + &_qqrd2e, &_g_ewald, &this->_threads_per_atom); + } + this->time_pair.stop(); +} + +template class DipoleLongLJ; diff --git a/lib/gpu/lal_dipole_long_lj.cu b/lib/gpu/lal_dipole_long_lj.cu new file mode 100644 index 0000000000000000000000000000000000000000..f888dece9b513001b4af9309ebc76e7b30f060d2 --- /dev/null +++ b/lib/gpu/lal_dipole_long_lj.cu @@ -0,0 +1,640 @@ +// ************************************************************************** +// dipole_lj.cu +// ------------------- +// Trung Dac Nguyen (ORNL) +// +// Device code for acceleration of the dipole/cut pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : +// email : nguyentd@ornl.gov +// ***************************************************************************/ + +#ifdef NV_KERNEL +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +texture mu_tex; +#else +texture pos_tex; +texture q_tex; +texture mu_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#define mu_tex mu_ +#endif + +#if (ARCH < 300) + +#define store_answers_tq(f, tor, energy, ecoul, virial, ii, inum, tid, \ + t_per_atom, offset, eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + __local acctyp red_acc[8][BLOCK_PAIR]; \ + red_acc[0][tid]=f.x; \ + red_acc[1][tid]=f.y; \ + red_acc[2][tid]=f.z; \ + red_acc[3][tid]=tor.x; \ + red_acc[4][tid]=tor.y; \ + red_acc[5][tid]=tor.z; \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + f.x=red_acc[0][tid]; \ + f.y=red_acc[1][tid]; \ + f.z=red_acc[2][tid]; \ + tor.x=red_acc[3][tid]; \ + tor.y=red_acc[4][tid]; \ + tor.z=red_acc[5][tid]; \ + if (eflag>0 || vflag>0) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid]=virial[r]; \ + red_acc[6][tid]=energy; \ + red_acc[7][tid]=ecoul; \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<8; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + for (int r=0; r<6; r++) \ + virial[r]=red_acc[r][tid]; \ + energy=red_acc[6][tid]; \ + ecoul=red_acc[7][tid]; \ + } \ + } \ + if (offset==0) { \ + int ei=ii; \ + if (eflag>0) { \ + engv[ei]=energy*(acctyp)0.5; \ + ei+=inum; \ + engv[ei]=e_coul*(acctyp)0.5; \ + ei+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + engv[ei]=virial[i]*(acctyp)0.5; \ + ei+=inum; \ + } \ + } \ + ans[ii]=f; \ + ans[ii+inum]=tor; \ + } + +#else + +#define store_answers_tq(f, tor, energy, e_coul, virial, ii, inum, tid, \ + t_per_atom, offset, eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + f.x += shfl_xor(f.x, s, t_per_atom); \ + f.y += shfl_xor(f.y, s, t_per_atom); \ + f.z += shfl_xor(f.z, s, t_per_atom); \ + tor.x += shfl_xor(tor.x, s, t_per_atom); \ + tor.y += shfl_xor(tor.y, s, t_per_atom); \ + tor.z += shfl_xor(tor.z, s, t_per_atom); \ + energy += shfl_xor(energy, s, t_per_atom); \ + e_coul += shfl_xor(e_coul, s, t_per_atom); \ + } \ + if (vflag>0) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + for (int r=0; r<6; r++) \ + virial[r] += shfl_xor(virial[r], s, t_per_atom); \ + } \ + } \ + } \ + if (offset==0) { \ + int ei=ii; \ + if (eflag>0) { \ + engv[ei]=energy*(acctyp)0.5; \ + ei+=inum; \ + engv[ei]=e_coul*(acctyp)0.5; \ + ei+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + engv[ei]=virial[i]*(acctyp)0.5; \ + ei+=inum; \ + } \ + } \ + ans[ii]=f; \ + ans[ii+inum]=tor; \ + } + +#endif + +#define MY_PIS (acctyp)1.77245385090551602729 + +__kernel void k_dipole_long_lj(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict lj1, + const __global numtyp4 *restrict lj3, + const int lj_types, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict mu_, + const __global numtyp *restrict cutsq, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_lj[8]; + sp_lj[0]=sp_lj_in[0]; + sp_lj[1]=sp_lj_in[1]; + sp_lj[2]=sp_lj_in[2]; + sp_lj[3]=sp_lj_in[3]; + sp_lj[4]=sp_lj_in[4]; + sp_lj[5]=sp_lj_in[5]; + sp_lj[6]=sp_lj_in[6]; + sp_lj[7]=sp_lj_in[7]; + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp4 tor; + tor.x=(acctyp)0; + tor.y=(acctyp)0; + tor.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + numtyp pre1 = numtyp(2.0) * g_ewald / MY_PIS; + numtyp pre2 = numtyp(4.0) * (g_ewald*g_ewald*g_ewald) / MY_PIS; + numtyp pre3 = numtyp(8.0) * (g_ewald*g_ewald*g_ewald*g_ewald*g_ewald) / MY_PIS; + + if (ii (numtyp)0.0) { + b0 = _erfc * rinv; + b1 = (b0 + pre1*expm2) * r2inv; + b2 = ((numtyp)3.0*b1 + pre2*expm2) * r2inv; + b3 = ((numtyp)5.0*b2 + pre3*expm2) * r2inv; + + g0b1_g1b2_g2b3 = g0*b1 + g1*b2 + g2*b3; + fdx = delx * g0b1_g1b2_g2b3 - + b1 * (qtmp*muj.x - qj*mui.x) + + b2 * (pjdotr*mui.x + pidotr*muj.x); + fdy = dely * g0b1_g1b2_g2b3 - + b1 * (qtmp*muj.y - qj*mui.y) + + b2 * (pjdotr*mui.y + pidotr*muj.y); + fdz = delz * g0b1_g1b2_g2b3 - + b1 * (qtmp*muj.z - qj*mui.z) + + b2 * (pjdotr*mui.z + pidotr*muj.z); + + zdix = delx * (qj*b1 + b2*pjdotr) - b1*muj.x; + zdiy = dely * (qj*b1 + b2*pjdotr) - b1*muj.y; + zdiz = delz * (qj*b1 + b2*pjdotr) - b1*muj.z; + zdjx = delx * (-qtmp*b1 + b2*pidotr) - b1*mui.x; + zdjy = dely * (-qtmp*b1 + b2*pidotr) - b1*mui.y; + zdjz = delz * (-qtmp*b1 + b2*pidotr) - b1*mui.z; + + if (factor_coul < (numtyp)1.0) { + fdx *= factor_coul; + fdy *= factor_coul; + fdz *= factor_coul; + zdix *= factor_coul; + zdiy *= factor_coul; + zdiz *= factor_coul; + zdjx *= factor_coul; + zdjy *= factor_coul; + zdjz *= factor_coul; + } + } else { + fdx = fdy = fdz = (numtyp)0.0; + zdix = zdiy = zdiz = (numtyp)0.0; + zdjx = zdjy = zdjz = (numtyp)0.0; + } + + if (factor_coul < (numtyp)1.0) { + d0 = (_erfc - (numtyp)1.0) * rinv; + d1 = (d0 + pre1*expm2) * r2inv; + d2 = ((numtyp)3.0*d1 + pre2*expm2) * r2inv; + d3 = ((numtyp)5.0*d2 + pre3*expm2) * r2inv; + + g0d1_g1d2_g2d3 = g0*d1 + g1*d2 + g2*d3; + fax = delx * g0d1_g1d2_g2d3 - + d1 * (qtmp*muj.x - qj*mui.x) + + d2 * (pjdotr*mui.x + pidotr*muj.x); + fay = dely * g0d1_g1d2_g2d3 - + d1 * (qtmp*muj.y - qj*mui.y) + + d2 * (pjdotr*mui.y + pidotr*muj.y); + faz = delz * g0d1_g1d2_g2d3 - + d1 * (qtmp*muj.z - qj*mui.z) + + d2 * (pjdotr*mui.z + pidotr*muj.z); + + zaix = delx * (qj*d1 + d2*pjdotr) - d1*muj.x; + zaiy = dely * (qj*d1 + d2*pjdotr) - d1*muj.y; + zaiz = delz * (qj*d1 + d2*pjdotr) - d1*muj.z; + zajx = delx * (-qtmp*d1 + d2*pidotr) - d1*mui.x; + zajy = dely * (-qtmp*d1 + d2*pidotr) - d1*mui.y; + zajz = delz * (-qtmp*d1 + d2*pidotr) - d1*mui.z; + + if (factor_coul > (numtyp)0.0) { + facm1 = (numtyp)1.0 - factor_coul; + fax *= facm1; + fay *= facm1; + faz *= facm1; + zaix *= facm1; + zaiy *= facm1; + zaiz *= facm1; + zajx *= facm1; + zajy *= facm1; + zajz *= facm1; + } + } else { + fax = fay = faz = (numtyp)0.0; + zaix = zaiy = zaiz = (numtyp)0.0; + zajx = zajy = zajz = (numtyp)0.0; + } + + forcecoul.x = fdx + fax; + forcecoul.y = fdy + fay; + forcecoul.z = fdz + faz; + + ticoul.x = mui.y*(zdiz + zaiz) - mui.z*(zdiy + zaiy); + ticoul.y = mui.z*(zdix + zaix) - mui.x*(zdiz + zaiz); + ticoul.z = mui.x*(zdiy + zaiy) - mui.y*(zdix + zaix); + + } else { + forcecoul.x = forcecoul.y = forcecoul.z = (numtyp)0.0; + ticoul.x = ticoul.y = ticoul.z = (numtyp)0.0; + } + + force.x = qqrd2e*forcecoul.x + delx*force_lj; + force.y = qqrd2e*forcecoul.y + dely*force_lj; + force.z = qqrd2e*forcecoul.z + delz*force_lj; + f.x+=force.x; + f.y+=force.y; + f.z+=force.z; + tor.x+=qqrd2e*ticoul.x; + tor.y+=qqrd2e*ticoul.y; + tor.z+=qqrd2e*ticoul.z; + + if (eflag>0) { + acctyp e = (acctyp)0.0; + if (rsq < cut_coulsq && factor_coul > (numtyp)0.0) { + e = qqrd2e*(b0*g0 + b1*g1 + b2*g2); + if (factor_coul < (numtyp)1.0) { + e_coul *= factor_coul; + e_coul += ((numtyp)1.0-factor_coul) * qqrd2e * (d0*g0 + d1*g1 + d2*g2); + } + } else e = (acctyp)0.0; + e_coul += e; + + if (rsq < lj1[mtype].z) { + e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y); + energy+=factor_lj*(e-lj3[mtype].z); + } + } + if (vflag>0) { + virial[0] += delx*force.x; + virial[1] += dely*force.y; + virial[2] += delz*force.z; + virial[3] += delx*force.y; + virial[4] += delx*force.z; + virial[5] += dely*force.z; + } + } + + } // for nbor + store_answers_tq(f,tor,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_dipole_long_lj_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict lj1_in, + const __global numtyp4 *restrict lj3_in, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict mu_, + const __global numtyp *restrict _cutsq, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 lj1[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 lj3[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[8]; + if (tid<8) + sp_lj[tid]=sp_lj_in[tid]; + if (tid0) + lj3[tid]=lj3_in[tid]; + } + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp4 tor; + tor.x=(acctyp)0; + tor.y=(acctyp)0; + tor.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + numtyp pre1 = numtyp(2.0) * g_ewald / MY_PIS; + numtyp pre2 = numtyp(4.0) * (g_ewald*g_ewald*g_ewald) / MY_PIS; + numtyp pre3 = numtyp(8.0) * (g_ewald*g_ewald*g_ewald*g_ewald*g_ewald) / MY_PIS; + + if (ii (numtyp)0.0) { + b0 = _erfc * rinv; + b1 = (b0 + pre1*expm2) * r2inv; + b2 = ((numtyp)3.0*b1 + pre2*expm2) * r2inv; + b3 = ((numtyp)5.0*b2 + pre3*expm2) * r2inv; + + g0b1_g1b2_g2b3 = g0*b1 + g1*b2 + g2*b3; + fdx = delx * g0b1_g1b2_g2b3 - + b1 * (qtmp*muj.x - qj*mui.x) + + b2 * (pjdotr*mui.x + pidotr*muj.x); + fdy = dely * g0b1_g1b2_g2b3 - + b1 * (qtmp*muj.y - qj*mui.y) + + b2 * (pjdotr*mui.y + pidotr*muj.y); + fdz = delz * g0b1_g1b2_g2b3 - + b1 * (qtmp*muj.z - qj*mui.z) + + b2 * (pjdotr*mui.z + pidotr*muj.z); + + zdix = delx * (qj*b1 + b2*pjdotr) - b1*muj.x; + zdiy = dely * (qj*b1 + b2*pjdotr) - b1*muj.y; + zdiz = delz * (qj*b1 + b2*pjdotr) - b1*muj.z; + zdjx = delx * (-qtmp*b1 + b2*pidotr) - b1*mui.x; + zdjy = dely * (-qtmp*b1 + b2*pidotr) - b1*mui.y; + zdjz = delz * (-qtmp*b1 + b2*pidotr) - b1*mui.z; + + if (factor_coul < (numtyp)1.0) { + fdx *= factor_coul; + fdy *= factor_coul; + fdz *= factor_coul; + zdix *= factor_coul; + zdiy *= factor_coul; + zdiz *= factor_coul; + zdjx *= factor_coul; + zdjy *= factor_coul; + zdjz *= factor_coul; + } + } else { + fdx = fdy = fdz = (numtyp)0.0; + zdix = zdiy = zdiz = (numtyp)0.0; + zdjx = zdjy = zdjz = (numtyp)0.0; + } + + if (factor_coul < (numtyp)1.0) { + d0 = (_erfc - (numtyp)1.0) * rinv; + d1 = (d0 + pre1*expm2) * r2inv; + d2 = ((numtyp)3.0*d1 + pre2*expm2) * r2inv; + d3 = ((numtyp)5.0*d2 + pre3*expm2) * r2inv; + + g0d1_g1d2_g2d3 = g0*d1 + g1*d2 + g2*d3; + fax = delx * g0d1_g1d2_g2d3 - + d1 * (qtmp*muj.x - qj*mui.x) + + d2 * (pjdotr*mui.x + pidotr*muj.x); + fay = dely * g0d1_g1d2_g2d3 - + d1 * (qtmp*muj.y - qj*mui.y) + + d2 * (pjdotr*mui.y + pidotr*muj.y); + faz = delz * g0d1_g1d2_g2d3 - + d1 * (qtmp*muj.z - qj*mui.z) + + d2 * (pjdotr*mui.z + pidotr*muj.z); + + zaix = delx * (qj*d1 + d2*pjdotr) - d1*muj.x; + zaiy = dely * (qj*d1 + d2*pjdotr) - d1*muj.y; + zaiz = delz * (qj*d1 + d2*pjdotr) - d1*muj.z; + zajx = delx * (-qtmp*d1 + d2*pidotr) - d1*mui.x; + zajy = dely * (-qtmp*d1 + d2*pidotr) - d1*mui.y; + zajz = delz * (-qtmp*d1 + d2*pidotr) - d1*mui.z; + + if (factor_coul > (numtyp)0.0) { + facm1 = (numtyp)1.0 - factor_coul; + fax *= facm1; + fay *= facm1; + faz *= facm1; + zaix *= facm1; + zaiy *= facm1; + zaiz *= facm1; + zajx *= facm1; + zajy *= facm1; + zajz *= facm1; + } + } else { + fax = fay = faz = (numtyp)0.0; + zaix = zaiy = zaiz = (numtyp)0.0; + zajx = zajy = zajz = (numtyp)0.0; + } + + forcecoul.x = fdx + fax; + forcecoul.y = fdy + fay; + forcecoul.z = fdz + faz; + + ticoul.x = mui.y*(zdiz + zaiz) - mui.z*(zdiy + zaiy); + ticoul.y = mui.z*(zdix + zaix) - mui.x*(zdiz + zaiz); + ticoul.z = mui.x*(zdiy + zaiy) - mui.y*(zdix + zaix); + + } else { + forcecoul.x = forcecoul.y = forcecoul.z = (numtyp)0.0; + ticoul.x = ticoul.y = ticoul.z = (numtyp)0.0; + } + + force.x = qqrd2e*forcecoul.x + delx*force_lj; + force.y = qqrd2e*forcecoul.y + dely*force_lj; + force.z = qqrd2e*forcecoul.z + delz*force_lj; + f.x+=force.x; + f.y+=force.y; + f.z+=force.z; + tor.x+=qqrd2e*ticoul.x; + tor.y+=qqrd2e*ticoul.y; + tor.z+=qqrd2e*ticoul.z; + + if (eflag>0) { + acctyp e = (acctyp)0.0; + if (rsq < cut_coulsq && factor_coul > (numtyp)0.0) { + e = qqrd2e*(b0*g0 + b1*g1 + b2*g2); + if (factor_coul < (numtyp)1.0) { + e_coul *= factor_coul; + e_coul += ((numtyp)1.0-factor_coul) * qqrd2e * (d0*g0 + d1*g1 + d2*g2); + } + } else e = (acctyp)0.0; + e_coul += e; + + if (rsq < lj1[mtype].z) { + e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y); + energy+=factor_lj*(e-lj3[mtype].z); + } + } + if (vflag>0) { + virial[0] += delx*force.x; + virial[1] += dely*force.y; + virial[2] += delz*force.z; + virial[3] += delx*force.y; + virial[4] += delx*force.z; + virial[5] += dely*force.z; + } + } + + } // for nbor + store_answers_tq(f,tor,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_dipole_long_lj.h b/lib/gpu/lal_dipole_long_lj.h new file mode 100644 index 0000000000000000000000000000000000000000..1381e243267bcc548d7eef6da409b29f3da36931 --- /dev/null +++ b/lib/gpu/lal_dipole_long_lj.h @@ -0,0 +1,85 @@ +/*************************************************************************** + dipole_long_lj.h + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the lj/cut/dipole/long pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_DIPOLE_LONG_LJ_H +#define LAL_DIPOLE_LONG_LJ_H + +#include "lal_base_dipole.h" + +namespace LAMMPS_AL { + +template +class DipoleLongLJ : public BaseDipole { + public: + DipoleLongLJ(); + ~DipoleLongLJ(); + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **host_offset, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, double **host_cut_ljsq, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); + + /// Clear all host and device data + /** \note This is called at the beginning of the init() routine **/ + void clear(); + + /// Returns memory usage on device per atom + int bytes_per_atom(const int max_nbors) const; + + /// Total host memory used by library for pair style + double host_memory_usage() const; + + // --------------------------- TYPE DATA -------------------------- + + /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq_vdw, lj1.w = cutsq_coul + UCL_D_Vec lj1; + /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset + UCL_D_Vec lj3; + /// cutsq + UCL_D_Vec cutsq; + /// Special LJ values [0-3] and Special Coul values [4-7] + UCL_D_Vec sp_lj; + + /// If atom type constants fit in shared memory, use fast kernels + bool shared_types; + + /// Number of atom types + int _lj_types; + + numtyp _cut_coulsq, _qqrd2e, _g_ewald; + + private: + bool _allocated; + void loop(const bool _eflag, const bool _vflag); +}; + +} + +#endif diff --git a/lib/gpu/lal_dipole_long_lj_ext.cpp b/lib/gpu/lal_dipole_long_lj_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..b2751e8a8221a1620a1ebb61211158eee8f455ad --- /dev/null +++ b/lib/gpu/lal_dipole_long_lj_ext.cpp @@ -0,0 +1,129 @@ +/*************************************************************************** + dipole_long_lj_ext.cpp + ------------------- + Trung Dac Nguyen (ORNL) + + Functions for LAMMPS access to dipole/cut acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : nguyentd@ornl.gov + ***************************************************************************/ + +#include +#include +#include + +#include "lal_dipole_long_lj.h" + +using namespace std; +using namespace LAMMPS_AL; + +static DipoleLongLJ DPLJMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int dplj_gpu_init(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double *special_lj, const int inum, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double **host_cut_ljsq, const double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + DPLJMF.clear(); + gpu_mode=DPLJMF.device->gpu_mode(); + double gpu_split=DPLJMF.device->particle_split(); + int first_gpu=DPLJMF.device->first_device(); + int last_gpu=DPLJMF.device->last_device(); + int world_me=DPLJMF.device->world_me(); + int gpu_rank=DPLJMF.device->gpu_rank(); + int procs_per_gpu=DPLJMF.device->procs_per_gpu(); + + DPLJMF.device->init_message(screen,"lj/cut/dipole/long",first_gpu,last_gpu); + + bool message=false; + if (DPLJMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=DPLJMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, + host_lj4, offset, special_lj, inum, nall, 300, + maxspecial, cell_size, gpu_split, screen, host_cut_ljsq, + host_cut_coulsq, host_special_coul, qqrd2e, g_ewald); + + DPLJMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + DPLJMF.estimate_gpu_overhead(); + return init_ok; +} + +void dplj_gpu_clear() { + DPLJMF.clear(); +} + +int** dplj_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double **host_mu, + double *boxlo, double *prd) { + return DPLJMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, host_mu, boxlo, prd); +} + +void dplj_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + double **host_mu, const int nlocal, double *boxlo, double *prd) { + DPLJMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj,firstneigh,eflag, + vflag,eatom,vatom,host_start,cpu_time,success,host_q,host_mu, + nlocal,boxlo,prd); +} + +double dplj_gpu_bytes() { + return DPLJMF.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_dpd_ext.cpp b/lib/gpu/lal_dpd_ext.cpp index 26bbb660b840d48d2439dbf3963325cb65aa1e96..33b4beddb03849448943a96a0133d1489b1a11f1 100644 --- a/lib/gpu/lal_dpd_ext.cpp +++ b/lib/gpu/lal_dpd_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_dpd.h" diff --git a/lib/gpu/lal_eam_alloy_ext.cpp b/lib/gpu/lal_eam_alloy_ext.cpp index 9209ed5c2602769b034802a1ae26428abdec0d93..e5f1010e76dae225718deb446993183e69f846b7 100644 --- a/lib/gpu/lal_eam_alloy_ext.cpp +++ b/lib/gpu/lal_eam_alloy_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_eam.h" diff --git a/lib/gpu/lal_eam_ext.cpp b/lib/gpu/lal_eam_ext.cpp index 1b5602f808fc4a97f5fe6516d1cd01eb43f16cdc..78f2e3c1f834e5c6ed4bd53fb7dd777e70a14d0c 100644 --- a/lib/gpu/lal_eam_ext.cpp +++ b/lib/gpu/lal_eam_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_eam.h" diff --git a/lib/gpu/lal_eam_fs_ext.cpp b/lib/gpu/lal_eam_fs_ext.cpp index b9e25466aaa71c8c82a5b6511b96b0fea3c320c4..37208e54f8c4cf245bdcc4297455e03d72ed26e5 100644 --- a/lib/gpu/lal_eam_fs_ext.cpp +++ b/lib/gpu/lal_eam_fs_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_eam.h" diff --git a/lib/gpu/lal_gauss_ext.cpp b/lib/gpu/lal_gauss_ext.cpp index 7fa4b68870ea9ff4f6bb797e6904b99cd612e622..a2804ce3cf9b20994246c5077cc73de63c27dc55 100644 --- a/lib/gpu/lal_gauss_ext.cpp +++ b/lib/gpu/lal_gauss_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_gauss.h" diff --git a/lib/gpu/lal_gayberne_ext.cpp b/lib/gpu/lal_gayberne_ext.cpp index 451550e7efca8023f78397ca499dc459e4d3fb53..56aad61632f3c86a0531528ff6109d81f6edd973 100644 --- a/lib/gpu/lal_gayberne_ext.cpp +++ b/lib/gpu/lal_gayberne_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_gayberne.h" diff --git a/lib/gpu/lal_lj96_ext.cpp b/lib/gpu/lal_lj96_ext.cpp index 5c4a58c5e8a272541e8b95e80e4fad40c72dae5a..f68b35de57b283e9fb4039a3dacc1d13c9809909 100644 --- a/lib/gpu/lal_lj96_ext.cpp +++ b/lib/gpu/lal_lj96_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj96.h" diff --git a/lib/gpu/lal_lj_class2_long_ext.cpp b/lib/gpu/lal_lj_class2_long_ext.cpp index 6ed15126d99d08633f7b9677b69c24bf683a6cc7..f669a811898f9d06fc61be16bff3805434cde248 100644 --- a/lib/gpu/lal_lj_class2_long_ext.cpp +++ b/lib/gpu/lal_lj_class2_long_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_class2_long.h" diff --git a/lib/gpu/lal_lj_coul_debye_ext.cpp b/lib/gpu/lal_lj_coul_debye_ext.cpp index 3a0a3593e7bf89a3e0ef83589251ecfda5a3f3f5..95588eb95ad6eb0442b9260ef7192304c4439d4c 100644 --- a/lib/gpu/lal_lj_coul_debye_ext.cpp +++ b/lib/gpu/lal_lj_coul_debye_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_coul_debye.h" diff --git a/lib/gpu/lal_lj_coul_ext.cpp b/lib/gpu/lal_lj_coul_ext.cpp index b803101b9e49193ad7569205ce34d3da7fd5abf4..060088a7cbef707e275851f5701a1f671e784ce5 100644 --- a/lib/gpu/lal_lj_coul_ext.cpp +++ b/lib/gpu/lal_lj_coul_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_coul.h" diff --git a/lib/gpu/lal_lj_coul_long_ext.cpp b/lib/gpu/lal_lj_coul_long_ext.cpp index 6f8b5c9fe12451773586e9b6c4b079adf9fa8bb6..33771af53c59e68dabf7e11857b0c744c88da7cc 100644 --- a/lib/gpu/lal_lj_coul_long_ext.cpp +++ b/lib/gpu/lal_lj_coul_long_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_coul_long.h" diff --git a/lib/gpu/lal_lj_coul_msm_ext.cpp b/lib/gpu/lal_lj_coul_msm_ext.cpp index bf520e4dc55fd5a804e03cb6f454a24ed30e7a5b..d957cbe37670e449b18ec3db006531e1efe95c31 100644 --- a/lib/gpu/lal_lj_coul_msm_ext.cpp +++ b/lib/gpu/lal_lj_coul_msm_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_coul_msm.h" diff --git a/lib/gpu/lal_lj_cubic_ext.cpp b/lib/gpu/lal_lj_cubic_ext.cpp index efbcee0a9f4db2dc78df16422c5f047b5c6344e7..f02ce0f184bca4fe1b507eb53f1541bf66d48661 100644 --- a/lib/gpu/lal_lj_cubic_ext.cpp +++ b/lib/gpu/lal_lj_cubic_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_cubic.h" diff --git a/lib/gpu/lal_lj_dsf_ext.cpp b/lib/gpu/lal_lj_dsf_ext.cpp index 25802e75447d6b70c600495f069079e498ec57bc..6d53896a1181f32b33eb1f4f11a1def1159c83ad 100644 --- a/lib/gpu/lal_lj_dsf_ext.cpp +++ b/lib/gpu/lal_lj_dsf_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_dsf.h" diff --git a/lib/gpu/lal_lj_expand_coul_long.cpp b/lib/gpu/lal_lj_expand_coul_long.cpp new file mode 100644 index 0000000000000000000000000000000000000000..32a4f8120e2e42d40ae6f67bcf960515182b3ca0 --- /dev/null +++ b/lib/gpu/lal_lj_expand_coul_long.cpp @@ -0,0 +1,183 @@ +/*************************************************************************** + lj_expand_coul_long.cpp + -------------------------- + Trung Nguyen (Northwestern) + + Class for acceleration of the lj/expand/coul/long pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "lj_expand_coul_long_cl.h" +#elif defined(USE_CUDART) +const char *lj_expand_coul_long=0; +#else +#include "lj_expand_coul_long_cubin.h" +#endif + +#include "lal_lj_expand_coul_long.h" +#include +using namespace LAMMPS_AL; +#define LJExpandCoulLongT LJExpandCoulLong + +extern Device device; + +template +LJExpandCoulLongT::LJExpandCoulLong() : BaseCharge(), + _allocated(false) { +} + +template +LJExpandCoulLongT::~LJExpandCoulLong() { + clear(); +} + +template +int LJExpandCoulLongT::bytes_per_atom(const int max_nbors) const { + return this->bytes_per_atom_atomic(max_nbors); +} + +template +int LJExpandCoulLongT::init(const int ntypes, + double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, double **host_shift, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_cut_ljsq, const double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,lj_expand_coul_long,"k_lj_expand_coul_long"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + shared_types=true; + } + _lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj1,host_write,host_lj1,host_lj2, + host_cutsq, host_cut_ljsq); + + lj3.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,lj3,host_write,host_lj3,host_lj4, + host_offset,host_shift); + + sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_lj[i]; + host_write[i+4]=host_special_coul[i]; + } + ucl_copy(sp_lj,host_write,8,false); + + _cut_coulsq=host_cut_coulsq; + _qqrd2e=qqrd2e; + _g_ewald=g_ewald; + + _allocated=true; + this->_max_bytes=lj1.row_bytes()+lj3.row_bytes()+sp_lj.row_bytes(); + return 0; +} + +template +void LJExpandCoulLongT::reinit(const int ntypes, double **host_cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **host_offset, double **host_shift, double **host_cut_ljsq) { + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(_lj_types*_lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; i<_lj_types*_lj_types; i++) + host_write[i]=0.0; + + this->atom->type_pack4(ntypes,_lj_types,lj1,host_write,host_lj1,host_lj2, + host_cutsq, host_cut_ljsq); + this->atom->type_pack4(ntypes,_lj_types,lj3,host_write,host_lj3,host_lj4, + host_offset,host_shift); +} + +template +void LJExpandCoulLongT::clear() { + if (!_allocated) + return; + _allocated=false; + + lj1.clear(); + lj3.clear(); + sp_lj.clear(); + this->clear_atomic(); +} + +template +double LJExpandCoulLongT::host_memory_usage() const { + return this->host_memory_usage_atomic()+sizeof(LJExpandCoulLong); +} + +// --------------------------------------------------------------------------- +// Calculate energies, forces, and torques +// --------------------------------------------------------------------------- +template +void LJExpandCoulLongT::loop(const bool _eflag, const bool _vflag) { + // Compute the block size and grid size to keep all cores busy + const int BX=this->block_size(); + int eflag, vflag; + if (_eflag) + eflag=1; + else + eflag=0; + + if (_vflag) + vflag=1; + else + vflag=0; + + int GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/this->_threads_per_atom))); + + int ainum=this->ans->inum(); + int nbor_pitch=this->nbor->nbor_pitch(); + this->time_pair.start(); + if (shared_types) { + this->k_pair_fast.set_size(GX,BX); + this->k_pair_fast.run(&this->atom->x, &lj1, &lj3, &sp_lj, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, + &vflag, &ainum, &nbor_pitch, &this->atom->q, + &_cut_coulsq, &_qqrd2e, &_g_ewald, + &this->_threads_per_atom); + } else { + this->k_pair.set_size(GX,BX); + this->k_pair.run(&this->atom->x, &lj1, &lj3, + &_lj_types, &sp_lj, &this->nbor->dev_nbor, + &this->_nbor_data->begin(), &this->ans->force, + &this->ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->atom->q, &_cut_coulsq, + &_qqrd2e, &_g_ewald, &this->_threads_per_atom); + } + this->time_pair.stop(); +} + +template class LJExpandCoulLong; diff --git a/lib/gpu/lal_lj_expand_coul_long.cu b/lib/gpu/lal_lj_expand_coul_long.cu new file mode 100644 index 0000000000000000000000000000000000000000..aa8f02be8c521134f80201e873ad5636b33783e4 --- /dev/null +++ b/lib/gpu/lal_lj_expand_coul_long.cu @@ -0,0 +1,272 @@ +// ************************************************************************** +// lj_coul_long.cu +// ------------------- +// Trung Nguyen (Northwestern) +// +// Device code for acceleration of the lj/expand/coul/long pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : +// email : ndactrung@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL + +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +#else +texture pos_tex; +texture q_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#endif + +__kernel void k_lj_expand_coul_long(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict lj1, + const __global numtyp4 *restrict lj3, + const int lj_types, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_lj[8]; + sp_lj[0]=sp_lj_in[0]; + sp_lj[1]=sp_lj_in[1]; + sp_lj[2]=sp_lj_in[2]; + sp_lj[3]=sp_lj_in[3]; + sp_lj[4]=sp_lj_in[4]; + sp_lj[5]=sp_lj_in[5]; + sp_lj[6]=sp_lj_in[6]; + sp_lj[7]=sp_lj_in[7]; + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + if (rsq < cut_coulsq) + e_coul += prefactor*(_erfc-factor_coul); + if (rsq < lj1[mtype].w) { + numtyp e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y); + energy+=factor_lj*(e-lj3[mtype].z); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_lj_expand_coul_long_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict lj1_in, + const __global numtyp4 *restrict lj3_in, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, + const int inum, const int nbor_pitch, + const __global numtyp *restrict q_, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 lj1[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 lj3[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[8]; + if (tid<8) + sp_lj[tid]=sp_lj_in[tid]; + if (tid0) { + if (rsq < cut_coulsq) + e_coul += prefactor*(_erfc-factor_coul); + if (rsq < lj1[mtype].w) { + numtyp e=r6inv*(lj3[mtype].x*r6inv-lj3[mtype].y); + energy+=factor_lj*(e-lj3[mtype].z); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_lj_expand_coul_long.h b/lib/gpu/lal_lj_expand_coul_long.h new file mode 100644 index 0000000000000000000000000000000000000000..64fd9df1abdcb88725e021db9a8bfb5dd96d94d3 --- /dev/null +++ b/lib/gpu/lal_lj_expand_coul_long.h @@ -0,0 +1,88 @@ +/*************************************************************************** + lj_expand_coul_long.h + ------------------- + Trung Nguyen (Northwestern) + + Class for acceleration of the lj/expand/coul/long pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_LJ_EXPAND_COUL_LONG_H +#define LAL_LJ_EXPAND_COUL_LONG_H + +#include "lal_base_charge.h" + +namespace LAMMPS_AL { + +template +class LJExpandCoulLong : public BaseCharge { + public: + LJExpandCoulLong(); + ~LJExpandCoulLong(); + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, + double **host_lj1, double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, double **host_shift, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, double **host_cut_ljsq, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); + + /// Send updated coeffs from host to device (to be compatible with fix adapt) + void reinit(const int ntypes, double **host_cutsq, + double **host_lj1, double **host_lj2, double **host_lj3, + double **host_lj4, double **host_offset, double **host_shift, double **host_cut_ljsq); + + /// Clear all host and device data + /** \note This is called at the beginning of the init() routine **/ + void clear(); + + /// Returns memory usage on device per atom + int bytes_per_atom(const int max_nbors) const; + + /// Total host memory used by library for pair style + double host_memory_usage() const; + + // --------------------------- TYPE DATA -------------------------- + + /// lj1.x = lj1, lj1.y = lj2, lj1.z = cutsq, lj1.w = cutsq_vdw + UCL_D_Vec lj1; + /// lj3.x = lj3, lj3.y = lj4, lj3.z = offset, lj3.w = shift + UCL_D_Vec lj3; + /// Special LJ values [0-3] and Special Coul values [4-7] + UCL_D_Vec sp_lj; + + /// If atom type constants fit in shared memory, use fast kernels + bool shared_types; + + /// Number of atom types + int _lj_types; + + numtyp _cut_coulsq, _qqrd2e, _g_ewald; + + private: + bool _allocated; + void loop(const bool _eflag, const bool _vflag); +}; + +} + +#endif diff --git a/lib/gpu/lal_lj_expand_coul_long_ext.cpp b/lib/gpu/lal_lj_expand_coul_long_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..3ff1bef70128c20122c1d3c28e800a43e98c56fd --- /dev/null +++ b/lib/gpu/lal_lj_expand_coul_long_ext.cpp @@ -0,0 +1,152 @@ +/*************************************************************************** + lj_expand_coul_long_ext.cpp + ------------------------ + Trung Nguyen (Northwestern) + + Functions for LAMMPS access to lj/expand/coul/long acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_lj_expand_coul_long.h" + +using namespace std; +using namespace LAMMPS_AL; + +static LJExpandCoulLong LJECLMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int ljecl_gpu_init(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double **shift, double *special_lj, const int inum, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double **host_cut_ljsq, double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + LJECLMF.clear(); + gpu_mode=LJECLMF.device->gpu_mode(); + double gpu_split=LJECLMF.device->particle_split(); + int first_gpu=LJECLMF.device->first_device(); + int last_gpu=LJECLMF.device->last_device(); + int world_me=LJECLMF.device->world_me(); + int gpu_rank=LJECLMF.device->gpu_rank(); + int procs_per_gpu=LJECLMF.device->procs_per_gpu(); + + LJECLMF.device->init_message(screen,"lj/expand/coul/long",first_gpu,last_gpu); + + bool message=false; + if (LJECLMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=LJECLMF.init(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, + offset, shift, special_lj, inum, nall, 300, maxspecial, + cell_size, gpu_split, screen, host_cut_ljsq, + host_cut_coulsq, host_special_coul, qqrd2e, g_ewald); + + LJECLMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + LJECLMF.estimate_gpu_overhead(); + return init_ok; +} + +// --------------------------------------------------------------------------- +// Copy updated coeffs from host to device +// --------------------------------------------------------------------------- +void ljecl_gpu_reinit(const int ntypes, double **cutsq, double **host_lj1, + double **host_lj2, double **host_lj3, double **host_lj4, + double **offset, double **shift, double **host_cut_ljsq) { + int world_me=LJECLMF.device->world_me(); + int gpu_rank=LJECLMF.device->gpu_rank(); + int procs_per_gpu=LJECLMF.device->procs_per_gpu(); + + if (world_me==0) + LJECLMF.reinit(ntypes, cutsq, host_lj1, host_lj2, host_lj3, host_lj4, + offset, shift, host_cut_ljsq); + LJECLMF.device->world_barrier(); + + for (int i=0; igpu_barrier(); + } +} + +void ljecl_gpu_clear() { + LJECLMF.clear(); +} + +int** ljecl_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd) { + return LJECLMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, boxlo, prd); +} + +void ljecl_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd) { + LJECLMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success, + host_q,nlocal,boxlo,prd); +} + +double ljecl_gpu_bytes() { + return LJECLMF.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_lj_expand_ext.cpp b/lib/gpu/lal_lj_expand_ext.cpp index a9c791803b11f3ff5343f10cfb433f0dd1d9924e..603e425d3f99c9f8b2927f2ea1f7e66e619eaa28 100644 --- a/lib/gpu/lal_lj_expand_ext.cpp +++ b/lib/gpu/lal_lj_expand_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_expand.h" diff --git a/lib/gpu/lal_lj_ext.cpp b/lib/gpu/lal_lj_ext.cpp index 8124556d40394a5d2a2b3d78f61f41df9e5539ae..124cf46c8c18be346132e16f7603726eedc4c02b 100644 --- a/lib/gpu/lal_lj_ext.cpp +++ b/lib/gpu/lal_lj_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj.h" diff --git a/lib/gpu/lal_lj_gromacs_ext.cpp b/lib/gpu/lal_lj_gromacs_ext.cpp index 53b93bfdff306d8ad4eb993458ee6daad8ad8569..99d32ab09a5131681c909a162eabeb32c6a72acc 100644 --- a/lib/gpu/lal_lj_gromacs_ext.cpp +++ b/lib/gpu/lal_lj_gromacs_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_gromacs.h" diff --git a/lib/gpu/lal_lj_sdk_ext.cpp b/lib/gpu/lal_lj_sdk_ext.cpp index 386106161e1b33a4ca11391e9470089d482ebeaf..de0c5fef4f224951e3533e48f20a8bfd91ec9430 100644 --- a/lib/gpu/lal_lj_sdk_ext.cpp +++ b/lib/gpu/lal_lj_sdk_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_sdk.h" diff --git a/lib/gpu/lal_lj_sdk_long_ext.cpp b/lib/gpu/lal_lj_sdk_long_ext.cpp index 08390d3eeb8f1e011324e394f6b5b2281409746b..f29348728211644ee599f599380f0ac32c0cf472 100644 --- a/lib/gpu/lal_lj_sdk_long_ext.cpp +++ b/lib/gpu/lal_lj_sdk_long_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_lj_sdk_long.h" diff --git a/lib/gpu/lal_mie_ext.cpp b/lib/gpu/lal_mie_ext.cpp index 9b03903c4f027070a8048941beb42d69d3de3e45..f612de4336779c511ac3e5ef4f2013d0046ba3fb 100644 --- a/lib/gpu/lal_mie_ext.cpp +++ b/lib/gpu/lal_mie_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_mie.h" diff --git a/lib/gpu/lal_morse_ext.cpp b/lib/gpu/lal_morse_ext.cpp index 0338bc07a835a8716afd622b72563b3717c40aef..3b62d10305a2e6d1897846b70b87b52018a205fe 100644 --- a/lib/gpu/lal_morse_ext.cpp +++ b/lib/gpu/lal_morse_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_morse.h" diff --git a/lib/gpu/lal_neighbor.cpp b/lib/gpu/lal_neighbor.cpp index 0a9933a6c02982bce3a2521756d246341f826638..3e128bcf57349d39399f5cf625e5f863186a3630 100644 --- a/lib/gpu/lal_neighbor.cpp +++ b/lib/gpu/lal_neighbor.cpp @@ -17,7 +17,7 @@ #include "lal_precision.h" #include "lal_neighbor.h" #include "lal_device.h" -#include "math.h" +#include using namespace LAMMPS_AL; int Neighbor::bytes_per_atom(const int max_nbors) const { @@ -127,10 +127,10 @@ void Neighbor::alloc(bool &success) { dev_packed.clear(); success=success && (dev_packed.alloc((_max_nbors+2)*_max_atoms,*dev, _packed_permissions)==UCL_SUCCESS); - dev_acc.clear(); - success=success && (dev_acc.alloc(_max_atoms,*dev, + dev_ilist.clear(); + success=success && (dev_ilist.alloc(_max_atoms,*dev, UCL_READ_WRITE)==UCL_SUCCESS); - _c_bytes+=dev_packed.row_bytes()+dev_acc.row_bytes(); + _c_bytes+=dev_packed.row_bytes()+dev_ilist.row_bytes(); } if (_max_host>0) { nbor_host.clear(); @@ -197,7 +197,7 @@ void Neighbor::clear() { host_packed.clear(); host_acc.clear(); - dev_acc.clear(); + dev_ilist.clear(); dev_nbor.clear(); nbor_host.clear(); dev_packed.clear(); @@ -281,7 +281,7 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj, } UCL_D_Vec acc_view; acc_view.view_offset(inum,dev_nbor,inum*2); - ucl_copy(acc_view,host_acc,true); + ucl_copy(acc_view,host_acc,inum*2,true); UCL_H_Vec host_view; host_view.alloc(_max_atoms,*dev,UCL_READ_WRITE); @@ -289,7 +289,7 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj, int i=ilist[ii]; host_view[i] = ii; } - ucl_copy(dev_acc,host_view,true); + ucl_copy(dev_ilist,host_view,true); time_nbor.stop(); @@ -364,7 +364,7 @@ void Neighbor::get_host3(const int inum, const int nlist, int *ilist, int *numj, } UCL_D_Vec acc_view; acc_view.view_offset(inum,dev_nbor,inum*2); - ucl_copy(acc_view,host_acc,true); + ucl_copy(acc_view,host_acc,inum*2,true); time_nbor.stop(); if (_use_packing==false) { diff --git a/lib/gpu/lal_neighbor.h b/lib/gpu/lal_neighbor.h index 05168834c6034a3cc336ef429242d441a63c9945..996deaff6d12bbbfa6789ac12dae0910b7f7f699 100644 --- a/lib/gpu/lal_neighbor.h +++ b/lib/gpu/lal_neighbor.h @@ -110,7 +110,7 @@ class Neighbor { } if (_time_device) { time_nbor.add_to_total(); - time_kernel.add_to_total(); + if (_use_packing==false) time_kernel.add_to_total(); if (_gpu_nbor==2) { time_hybrid1.add_to_total(); time_hybrid2.add_to_total(); @@ -200,7 +200,7 @@ class Neighbor { /// Host storage for nbor counts (row 1) & accumulated neighbor counts (row2) UCL_H_Vec host_acc; /// Device storage for accessing atom indices from the neighbor list (3-body) - UCL_D_Vec dev_acc; + UCL_D_Vec dev_ilist; // ----------------- Data for GPU Neighbor Calculation --------------- diff --git a/lib/gpu/lal_neighbor_gpu.cu b/lib/gpu/lal_neighbor_gpu.cu index b0b3cfb90c958c5c7e7f0c84816be3b03ba73d04..83692a24e4c04bfd9d1441c2a49b5da01fc9813e 100644 --- a/lib/gpu/lal_neighbor_gpu.cu +++ b/lib/gpu/lal_neighbor_gpu.cu @@ -118,24 +118,24 @@ __kernel void transpose(__global tagint *restrict out, const __global tagint *restrict in, int columns_in, int rows_in) { - __local tagint block[BLOCK_CELL_2D][BLOCK_CELL_2D+1]; + __local tagint block[BLOCK_CELL_2D][BLOCK_CELL_2D+1]; - unsigned ti=THREAD_ID_X; - unsigned tj=THREAD_ID_Y; - unsigned bi=BLOCK_ID_X; - unsigned bj=BLOCK_ID_Y; + unsigned ti=THREAD_ID_X; + unsigned tj=THREAD_ID_Y; + unsigned bi=BLOCK_ID_X; + unsigned bj=BLOCK_ID_Y; - unsigned i=bi*BLOCK_CELL_2D+ti; - unsigned j=bj*BLOCK_CELL_2D+tj; - if ((i 1e-5) { + if (r2 < cell_size*cell_size && pid_j != pid_i) { // && r2 > 1e-5 cnt++; if (cnt <= neigh_bin_size) { *neigh_list = pid_j; @@ -243,8 +243,8 @@ __kernel void calc_neigh_list_cell(const __global numtyp4 *restrict x_, } } } - __syncthreads(); - } // for (k) + __syncthreads(); + } // for (k) } } } diff --git a/lib/gpu/lal_pppm_ext.cpp b/lib/gpu/lal_pppm_ext.cpp index 7e07d6c87b393190d3dbd342c0bc6ebfa1ead468..a75536eb19aa805a32c0fd307bc055896f7a80df 100644 --- a/lib/gpu/lal_pppm_ext.cpp +++ b/lib/gpu/lal_pppm_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_pppm.h" diff --git a/lib/gpu/lal_re_squared_ext.cpp b/lib/gpu/lal_re_squared_ext.cpp index b719dfe05f689ffcca81b7c8f93305b1b5998a41..e1eb8a45b01f7d2adc3bd7b8aad02aec03f2f2b6 100644 --- a/lib/gpu/lal_re_squared_ext.cpp +++ b/lib/gpu/lal_re_squared_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_re_squared.h" diff --git a/lib/gpu/lal_soft_ext.cpp b/lib/gpu/lal_soft_ext.cpp index d3b3fa25984cae7225ce70244771ee5a394ecb76..7c0cbe79731a9b204237ea6950a7020582d88662 100644 --- a/lib/gpu/lal_soft_ext.cpp +++ b/lib/gpu/lal_soft_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_soft.h" diff --git a/lib/gpu/lal_sw.cpp b/lib/gpu/lal_sw.cpp index 24984e48785d665c63ad9cae54dc45812846a5f2..46b6382a6097aeaab518a2cc509b6eeb5d92e41b 100644 --- a/lib/gpu/lal_sw.cpp +++ b/lib/gpu/lal_sw.cpp @@ -243,7 +243,7 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &sw1, &sw2, &sw3, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -252,7 +252,7 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &sw1, &sw2, &sw3, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); diff --git a/lib/gpu/lal_sw.cu b/lib/gpu/lal_sw.cu index 517de70691cd735cac9c9dab5cc849a257f5d373..3b6de5a683d603e74f53b8c2364942fd0f83f2cf 100644 --- a/lib/gpu/lal_sw.cu +++ b/lib/gpu/lal_sw.cu @@ -544,7 +544,7 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -614,13 +614,13 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -698,7 +698,7 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -768,13 +768,13 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/gpu/lal_sw_ext.cpp b/lib/gpu/lal_sw_ext.cpp index 4959650c90887d7a5aaaba42fe94452b5b890d88..1935ed615b1acf41697c68ea848f01354b98c180 100644 --- a/lib/gpu/lal_sw_ext.cpp +++ b/lib/gpu/lal_sw_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_sw.h" diff --git a/lib/gpu/lal_table_ext.cpp b/lib/gpu/lal_table_ext.cpp index a2b5c61e74bb9ea6db513f17c3808b52a325088a..f067881b882f5c4321d05d8b3067bfc891fa050a 100644 --- a/lib/gpu/lal_table_ext.cpp +++ b/lib/gpu/lal_table_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_table.h" diff --git a/lib/gpu/lal_tersoff.cpp b/lib/gpu/lal_tersoff.cpp index a63d286d9c16a9120ee9e300f16d9fda4e5ecdfc..ef55b98a2dba21347cc9830858f9663f0ff21b31 100644 --- a/lib/gpu/lal_tersoff.cpp +++ b/lib/gpu/lal_tersoff.cpp @@ -272,7 +272,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -311,7 +311,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -320,7 +320,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff.cu b/lib/gpu/lal_tersoff.cu index cec0ccc44341c10f9678e57b8de628d169980262..836f05660d7b066dcaf7398ed11e10e96eec7b07 100644 --- a/lib/gpu/lal_tersoff.cu +++ b/lib/gpu/lal_tersoff.cu @@ -696,7 +696,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, const __global acctyp4 *restrict zetaij, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -777,13 +777,13 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -941,7 +941,7 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, const __global acctyp4 *restrict zetaij, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -1022,13 +1022,13 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/gpu/lal_tersoff_ext.cpp b/lib/gpu/lal_tersoff_ext.cpp index e6dc5390354085e8b552a7eef683778795b8f2cc..749842864f958150170d534409d9fa12a03ac259 100644 --- a/lib/gpu/lal_tersoff_ext.cpp +++ b/lib/gpu/lal_tersoff_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_tersoff.h" diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp index c37c07f1a1234d1945cfefdac45d42f9be446458..3cbb488cab878c497c0f0cf7eede5f9c5ce9663c 100644 --- a/lib/gpu/lal_tersoff_mod.cpp +++ b/lib/gpu/lal_tersoff_mod.cpp @@ -272,7 +272,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -311,7 +311,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -320,7 +320,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff_mod.cu b/lib/gpu/lal_tersoff_mod.cu index 576359b5146246d74078b0deff98a700bbdcb533..dfb94c41451c4a553a244e14c2aa05710cf1ebe6 100644 --- a/lib/gpu/lal_tersoff_mod.cu +++ b/lib/gpu/lal_tersoff_mod.cu @@ -272,7 +272,7 @@ __kernel void k_tersoff_mod_zeta(const __global numtyp4 *restrict x_, if (ii #include -#include +#include #include "lal_tersoff_mod.h" diff --git a/lib/gpu/lal_tersoff_zbl.cpp b/lib/gpu/lal_tersoff_zbl.cpp index 341f663030f6330ec0ffbfd97526a24e5e59e87a..ebf67285eda47914ed06f3d0ec4abe3d4d4084aa 100644 --- a/lib/gpu/lal_tersoff_zbl.cpp +++ b/lib/gpu/lal_tersoff_zbl.cpp @@ -297,7 +297,7 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -337,7 +337,7 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -346,7 +346,7 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff_zbl.cu b/lib/gpu/lal_tersoff_zbl.cu index e8bb017f5901a9184b80403d8814aab50794500c..73ff51c70404cfea89fa7c9195e26ac12b6fbbcd 100644 --- a/lib/gpu/lal_tersoff_zbl.cu +++ b/lib/gpu/lal_tersoff_zbl.cu @@ -278,7 +278,7 @@ __kernel void k_tersoff_zbl_zeta(const __global numtyp4 *restrict x_, if (ii #include -#include +#include #include "lal_tersoff_zbl.h" diff --git a/lib/gpu/lal_ufm_ext.cpp b/lib/gpu/lal_ufm_ext.cpp index ae4a5fb8fc9fe11e658271154178610173541683..dd476ec3fa164c277716e431f08e77c1a31b8bec 100644 --- a/lib/gpu/lal_ufm_ext.cpp +++ b/lib/gpu/lal_ufm_ext.cpp @@ -17,7 +17,7 @@ #include #include -#include +#include #include "lal_ufm.h" diff --git a/lib/gpu/lal_vashishta.cpp b/lib/gpu/lal_vashishta.cpp index d03ac992bd468ea0677a6b537468016f56b7b3e0..5a01a9bd46f185938710ab65cfd75761b3f5fb1e 100644 --- a/lib/gpu/lal_vashishta.cpp +++ b/lib/gpu/lal_vashishta.cpp @@ -278,7 +278,7 @@ void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } else { @@ -286,7 +286,7 @@ void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_vashishta.cu b/lib/gpu/lal_vashishta.cu index d2e8bb1496abfd7355f88730cbb0d69c1c22339d..0da46c3b534cc29cba600851db0dda05a2cf38da 100644 --- a/lib/gpu/lal_vashishta.cu +++ b/lib/gpu/lal_vashishta.cu @@ -554,7 +554,7 @@ __kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -623,13 +623,13 @@ __kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -709,7 +709,7 @@ __kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -778,13 +778,13 @@ __kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/gpu/lal_vashishta_ext.cpp b/lib/gpu/lal_vashishta_ext.cpp index 22f530a7ed01dd580ad1122b06ac5785676f51a6..56dfd8a0ffb847c52baf7fd2108fc0e086df7a30 100644 --- a/lib/gpu/lal_vashishta_ext.cpp +++ b/lib/gpu/lal_vashishta_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_vashishta.h" using namespace LAMMPS_AL; diff --git a/lib/gpu/lal_yukawa_colloid_ext.cpp b/lib/gpu/lal_yukawa_colloid_ext.cpp index e2b0354d1046497a338d684d81fa3ba11d82df5e..988d33bdd663448da64437b720f39d6a8c06f036 100644 --- a/lib/gpu/lal_yukawa_colloid_ext.cpp +++ b/lib/gpu/lal_yukawa_colloid_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_yukawa_colloid.h" diff --git a/lib/gpu/lal_yukawa_ext.cpp b/lib/gpu/lal_yukawa_ext.cpp index 9d38387bc1b5611c44e4a97a1c95ca99ebd88371..995694bdfd9f3a2e7b854267977bfffa14af7a39 100644 --- a/lib/gpu/lal_yukawa_ext.cpp +++ b/lib/gpu/lal_yukawa_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_yukawa.h" diff --git a/lib/gpu/lal_zbl_ext.cpp b/lib/gpu/lal_zbl_ext.cpp index 37aa74351b63897f9c0979a9401f64db833b94e5..f15e814a50ae1b0c95b9907e1570e83dc7486356 100644 --- a/lib/gpu/lal_zbl_ext.cpp +++ b/lib/gpu/lal_zbl_ext.cpp @@ -15,7 +15,7 @@ #include #include -#include +#include #include "lal_zbl.h" diff --git a/lib/kim/Install.py b/lib/kim/Install.py index 0e873889546d198398f22d3fc2df37d0bc3fec06..d098250906bfabd19e74db7ad2a657d92a4c4ead 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -21,7 +21,7 @@ Syntax from lib dir: python Install.py -b -v version -a kim-name specify one or more options, order does not matter -v = version of KIM API library to use - default = kim-api-v1.9.2 (current as of Oct 2017) + default = kim-api-v1.9.5 (current as of May 2018) -b = download and build base KIM API library with example Models this will delete any previous installation in the current folder -n = do NOT download and build base KIM API library. @@ -109,7 +109,7 @@ nargs = len(args) if nargs == 0: error() thisdir = os.environ['PWD'] -version = "kim-api-v1.9.2" +version = "kim-api-v1.9.5" buildflag = False everythingflag = False @@ -166,9 +166,6 @@ if pathflag: mkfile.write("print_dir:\n") mkfile.write(" @printf $(KIM_INSTALL_DIR)\n") - with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile: - cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir) - print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir)) else: kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version) @@ -191,9 +188,6 @@ if buildflag: mkfile.write("print_dir:\n") mkfile.write(" @printf $(KIM_INSTALL_DIR)\n") - with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile: - cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir) - print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir)) # download entire kim-api tarball @@ -247,11 +241,16 @@ if buildflag: # add single OpenKIM model if addflag: + makefile_path = os.path.join(thisdir, "Makefile.KIM_DIR") + if os.path.isfile(makefile_path): + cmd = 'make --no-print-directory -f %s print_dir' % makefile_path + kimdir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if not os.path.isdir(kimdir): print("\nkim-api is not installed") error() # download single model - cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir, addmodelname) + cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname) txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) if verboseflag: print (txt.decode("UTF-8")) diff --git a/lib/kim/README b/lib/kim/README index 7a4230dc25e99a282b5ba9b8e439d0b0250da058..ce4ea1bdff42e55ad70b9101bdbea5b48ace61a6 100644 --- a/lib/kim/README +++ b/lib/kim/README @@ -20,47 +20,35 @@ Instructions: 1. Configure lammps for use with the kim-api library installed in this directory -$ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR -$ printf "include ${PWD}/lib/kim-api/Makefile.KIM_Config\n" > ./Makefile.KIM_Config +# replace X.Y.Z as appropriate here and below +$ printf "KIM_INSTALL_DIR=${PWD}/installed-kim-api-vX.Y.Z\n" > ./Makefile.KIM_DIR 2. Download and unpack the kim-api -# replace X.Y.Z as appropriate here and below -$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.tgz -$ tar zxvf kim-api-vX.Y.Z.tgz +$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.txz +$ tar zxvf kim-api-vX.Y.Z.txz # configure the kim-api $ cd kim-api-vX.Y.Z -$ ./configure --prefix=${PWD}/../ - -# setup the desired kim item -$ make add-Pair_Johnson_Fe__MO_857282754307_002 +$ ./configure --prefix=${PWD}/../installed-kim-api-vX.Y.Z 3. Build and install the kim-api and model $ make $ make install - -# replace X with the KIM API major version number -$ make install-set-default-to-vX -$ cd ../ +$ cd .. 4. Remove source and build files $ rm -rf kim-api-vX.Y.Z -$ rm -rf kim-api-vX.Y.Z.tgz +$ rm -rf kim-api-vX.Y.Z.txz -5. To add additional items do the following (replace the kim item name with your +5. To add items do the following (replace the kim item name with your desired value) -$ wget https://openkim.org/download/EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz -$ tar zxvf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz -$ cd EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001 -$ make -$ make install -$ cd .. -$ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001 -$ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz +$ source ${PWD}/kim-api-vX.Y.Z/bin/kim-api-v1-activate +$ kim-api-v1-collections-management install system Pair_Johnson_Fe__MO_857282754307_002 + ----------------- @@ -73,4 +61,4 @@ $ make g++ (or whatever target you wish) Note that the Makefile.lammps and Makefile.KIM_DIR files in this directory are required to allow the LAMMPS build to find the necessary KIM files. -You should not normally need to edit this file. +You should not normally need to edit these files. diff --git a/lib/kim/pair-kim.release.info b/lib/kim/pair-kim.release.info deleted file mode 100644 index f6c3c01c4e5ea5a1b61f0fc1e6900e391df57a66..0000000000000000000000000000000000000000 --- a/lib/kim/pair-kim.release.info +++ /dev/null @@ -1,6 +0,0 @@ -This package (pair-kim-v1.7.2+1) created from commit - -ced1275c5fd5b382cb9bd39e44ed1324c7c85e99 - -of the pair-kim git repository -By Ryan S. Elliott (relliott@umn.edu) on Mon Feb 22 14:59:53 CST 2016. diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index feb2bd547f034a5ef233667a3a9b5c3d0e02d3f8..145cc62706eea04fab0bb6e3fbcb676ee03b9ef8 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,58 @@ # Change Log +## [2.7.00](https://github.com/kokkos/kokkos/tree/2.7.00) (2018-05-24) +[Full Changelog](https://github.com/kokkos/kokkos/compare/2.6.00...2.7.00) + +**Part of the Kokkos C++ Performance Portability Programming EcoSystem 2.7** + +**Implemented enhancements:** + +- Deprecate team\_size auto adjusting to maximal value possible [\#1618](https://github.com/kokkos/kokkos/issues/1618) +- DynamicView - remove restrictions to std::is\_trivial types and value\_type is power of two [\#1586](https://github.com/kokkos/kokkos/issues/1586) +- Kokkos::StaticCrsGraph does not propagate memory traits \(e.g., Unmanaged\) [\#1581](https://github.com/kokkos/kokkos/issues/1581) +- Adding ETI for DeepCopy / ViewFill etc. [\#1578](https://github.com/kokkos/kokkos/issues/1578) +- Deprecate all the left over KOKKOS\_HAVE\_ Macros and Kokkos\_OldMacros.hpp [\#1572](https://github.com/kokkos/kokkos/issues/1572) +- Error if Kokkos\_ARCH set in CMake [\#1555](https://github.com/kokkos/kokkos/issues/1555) +- Deprecate ExecSpace::initialize / ExecSpace::finalize [\#1532](https://github.com/kokkos/kokkos/issues/1532) +- New API for TeamPolicy property setting [\#1531](https://github.com/kokkos/kokkos/issues/1531) +- clang 6.0 + cuda debug out-of-memory test failure [\#1521](https://github.com/kokkos/kokkos/issues/1521) +- Cuda UniqueToken interface not consistent with other backends [\#1505](https://github.com/kokkos/kokkos/issues/1505) +- Move Reducers out of Experimental namespace [\#1494](https://github.com/kokkos/kokkos/issues/1494) +- Provide scope guard for initialize/finalize [\#1479](https://github.com/kokkos/kokkos/issues/1479) +- Check Kokkos::is\_initialized in SharedAllocationRecord dtor [\#1465](https://github.com/kokkos/kokkos/issues/1465) +- Remove static list of allocations [\#1464](https://github.com/kokkos/kokkos/issues/1464) +- Makefiles: Support single compile/link line use case [\#1402](https://github.com/kokkos/kokkos/issues/1402) +- ThreadVectorRange with a range [\#1400](https://github.com/kokkos/kokkos/issues/1400) +- Exclusive scan + last value API [\#1358](https://github.com/kokkos/kokkos/issues/1358) +- Install kokkos\_generated\_settings.cmake [\#1348](https://github.com/kokkos/kokkos/issues/1348) +- Kokkos arrays \(not views!\) don't do bounds checking in debug mode [\#1342](https://github.com/kokkos/kokkos/issues/1342) +- Expose round-robin GPU assignment outside of initialize\(int, char\*\*\) [\#1318](https://github.com/kokkos/kokkos/issues/1318) +- DynamicView misses use\_count and label function [\#1298](https://github.com/kokkos/kokkos/issues/1298) +- View constructor should check arguments [\#1286](https://github.com/kokkos/kokkos/issues/1286) +- False Positive on Oversubscription Warning [\#1207](https://github.com/kokkos/kokkos/issues/1207) +- Allow \(require\) execution space for 1st arg of VerifyExecutionCanAccessMemorySpace [\#1192](https://github.com/kokkos/kokkos/issues/1192) +- ROCm: Add ROCmHostPinnedSpace [\#958](https://github.com/kokkos/kokkos/issues/958) +- power of two functions [\#656](https://github.com/kokkos/kokkos/issues/656) +- CUDA 8 has 64bit \_\_shfl [\#361](https://github.com/kokkos/kokkos/issues/361) +- Add TriBITS/CMake configure information about node types [\#243](https://github.com/kokkos/kokkos/issues/243) + +**Fixed bugs:** + +- CUDA atomic\_fetch\_sub for doubles is hitting CAS instead of intrinsic [\#1624](https://github.com/kokkos/kokkos/issues/1624) +- Bug: use of ballot on Volta [\#1612](https://github.com/kokkos/kokkos/issues/1612) +- Kokkos::deep\_copy memory access failures [\#1583](https://github.com/kokkos/kokkos/issues/1583) +- g++ -std option doubly set for cmake project [\#1548](https://github.com/kokkos/kokkos/issues/1548) +- ViewFill for 1D Views of larger 32bit entries fails [\#1541](https://github.com/kokkos/kokkos/issues/1541) +- CUDA Volta another warpsync bug [\#1520](https://github.com/kokkos/kokkos/issues/1520) +- triple\_nested\_parallelism fails with KOKKOS\_DEBUG and CUDA [\#1513](https://github.com/kokkos/kokkos/issues/1513) +- Jenkins errors in Kokkos\_SharedAlloc.cpp with debug build [\#1511](https://github.com/kokkos/kokkos/issues/1511) +- Kokkos::Sort out-of-bounds with empty bins [\#1504](https://github.com/kokkos/kokkos/issues/1504) +- Get rid of deprecated functions inside Kokkos [\#1484](https://github.com/kokkos/kokkos/issues/1484) +- get\_work\_partition casts int64\_t to int, causing a seg fault [\#1481](https://github.com/kokkos/kokkos/issues/1481) +- NVCC bug with \_\_device\_\_ on defaulted function [\#1470](https://github.com/kokkos/kokkos/issues/1470) +- CMake example broken with CUDA backend [\#1468](https://github.com/kokkos/kokkos/issues/1468) + + ## [2.6.00](https://github.com/kokkos/kokkos/tree/2.6.00) (2018-03-07) [Full Changelog](https://github.com/kokkos/kokkos/compare/2.5.00...2.6.00) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index cd1f4ea981339a5ff01095be9bca144cdb5d9064..9e5308f1c3245ea40a01079909cd9639cf22c82f 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -44,6 +44,7 @@ IF(NOT KOKKOS_HAS_TRILINOS) "${KOKKOS_SETTINGS} make -f ${KOKKOS_SRC_PATH}/cmake/Makefile.generate_cmake_settings CXX=${CMAKE_CXX_COMPILER} generate_build_settings") endif() include(${Kokkos_BINARY_DIR}/kokkos_generated_settings.cmake) + install(FILES ${Kokkos_BINARY_DIR}/kokkos_generated_settings.cmake DESTINATION lib/cmake/Kokkos) string(REPLACE " " ";" KOKKOS_TPL_INCLUDE_DIRS "${KOKKOS_GMAKE_TPL_INCLUDE_DIRS}") string(REPLACE " " ";" KOKKOS_TPL_LIBRARY_DIRS "${KOKKOS_GMAKE_TPL_LIBRARY_DIRS}") string(REPLACE " " ";" KOKKOS_TPL_LIBRARY_NAMES "${KOKKOS_GMAKE_TPL_LIBRARY_NAMES}") diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index a7bb63f190348405267c3ea50e0f55dcf20645a3..52cd3969f9f74d736fc9be99ad64114b8f5af6cf 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -1,7 +1,9 @@ # Default settings common options. #LAMMPS specific settings: -KOKKOS_PATH=../../lib/kokkos +ifndef KOKKOS_PATH + KOKKOS_PATH=../../lib/kokkos +endif CXXFLAGS=$(CCFLAGS) # Options: Cuda,ROCm,OpenMP,Pthreads,Qthreads,Serial @@ -21,8 +23,10 @@ KOKKOS_DEBUG ?= "no" KOKKOS_USE_TPLS ?= "" # Options: c++11,c++1z KOKKOS_CXX_STANDARD ?= "c++11" -# Options: aggressive_vectorization,disable_profiling,disable_deprecated_code +# Options: aggressive_vectorization,disable_profiling,disable_deprecated_code,enable_large_mem_tests KOKKOS_OPTIONS ?= "" +# Option for setting ETI path +KOKKOS_ETI_PATH ?= ${KOKKOS_PATH}/core/src/eti # Default settings specific options. # Options: force_uvm,use_ldg,rdc,enable_lambda @@ -51,10 +55,12 @@ KOKKOS_INTERNAL_DISABLE_PROFILING := $(call kokkos_has_string,$(KOKKOS_OPTIONS), KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_deprecated_code) KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_dualview_modify_check) KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_profile_load_print) +KOKKOS_INTERNAL_ENABLE_LARGE_MEM_TESTS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_large_mem_tests) KOKKOS_INTERNAL_CUDA_USE_LDG := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),use_ldg) KOKKOS_INTERNAL_CUDA_USE_UVM := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),force_uvm) KOKKOS_INTERNAL_CUDA_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),rdc) KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_lambda) +KOKKOS_INTERNAL_ENABLE_ETI := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_eti) # Check for Kokkos Host Execution Spaces one of which must be on. @@ -78,7 +84,12 @@ KOKKOS_INTERNAL_USE_OPENMPTARGET := $(call kokkos_has_string,$(KOKKOS_DEVICES),O ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) KOKKOS_INTERNAL_NVCC_PATH := $(shell which nvcc) - CUDA_PATH ?= $(KOKKOS_INTERNAL_NVCC_PATH:/bin/nvcc=) + ifeq ($(origin CUDA_PATH), undefined) + CUDA_PATH = $(KOKKOS_INTERNAL_NVCC_PATH:/bin/nvcc=) + endif + ifeq ($(CUDA_PATH),) + CUDA_PATH = $(KOKKOS_INTERNAL_NVCC_PATH:/bin/nvcc=) + endif KOKKOS_INTERNAL_COMPILER_NVCC_VERSION := $(shell nvcc --version 2>&1 | grep release | cut -d' ' -f5 | cut -d',' -f1 | tr -d .) endif @@ -116,7 +127,7 @@ ifeq ($(KOKKOS_INTERNAL_COMPILER_HCC), 1) endif ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - KOKKOS_INTERNAL_COMPILER_CLANG_VERSION := $(shell clang --version | grep version | cut -d ' ' -f3 | tr -d '.') + KOKKOS_INTERNAL_COMPILER_CLANG_VERSION := $(shell $(CXX) --version | grep version | cut -d ' ' -f3 | tr -d '.') ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_CLANG_VERSION) -lt 400; echo $$?),0) @@ -323,12 +334,13 @@ endif # Generating the list of Flags. -KOKKOS_CPPFLAGS = -I./ -I$(KOKKOS_PATH)/core/src -I$(KOKKOS_PATH)/containers/src -I$(KOKKOS_PATH)/algorithms/src +#CPPFLAGS is now unused +KOKKOS_CPPFLAGS = +KOKKOS_CXXFLAGS = -I./ -I$(KOKKOS_PATH)/core/src -I$(KOKKOS_PATH)/containers/src -I$(KOKKOS_PATH)/algorithms/src -I$(KOKKOS_ETI_PATH) KOKKOS_TPL_INCLUDE_DIRS = KOKKOS_TPL_LIBRARY_DIRS = KOKKOS_TPL_LIBRARY_NAMES = -KOKKOS_CXXFLAGS = ifeq ($(KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS), 1) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_WARNINGS) endif @@ -336,6 +348,8 @@ endif KOKKOS_LIBS = -ldl KOKKOS_TPL_LIBRARY_NAMES += dl KOKKOS_LDFLAGS = -L$(shell pwd) +# CXXLDFLAGS is used together with CXXFLAGS in a combined compile/link command +KOKKOS_CXXLDFLAGS = -L$(shell pwd) KOKKOS_LINK_FLAGS = KOKKOS_SRC = KOKKOS_HEADERS = @@ -362,7 +376,7 @@ tmp := $(call kokkos_append_header,'\#endif') tmp := $(call kokkos_append_header,"/* Execution Spaces */") ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CUDA") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA") endif ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) @@ -374,19 +388,19 @@ ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) - tmp := $(call kokkos_append_header,'\#define KOKKOS_HAVE_OPENMP') + tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_OPENMP') endif ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_PTHREAD") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_THREADS") endif ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_QTHREADS") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_QTHREADS") endif ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_SERIAL") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_SERIAL") endif ifeq ($(KOKKOS_INTERNAL_USE_TM), 1) @@ -422,13 +436,13 @@ endif tmp := $(call kokkos_append_header,"/* General Settings */") ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX11), 1) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX11_FLAG) - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CXX11") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX11") endif ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Z), 1) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Z_FLAG) - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CXX11") - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_CXX1Z") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX11") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX1Z") endif ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1) @@ -437,9 +451,9 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1) endif KOKKOS_CXXFLAGS += -g - KOKKOS_LDFLAGS += -g -ldl + KOKKOS_LDFLAGS += -g tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK") - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_DEBUG") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG") ifeq ($(KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK), 0) tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK") endif @@ -451,14 +465,15 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) ifneq ($(HWLOC_PATH),) - KOKKOS_CPPFLAGS += -I$(HWLOC_PATH)/include + KOKKOS_CXXFLAGS += -I$(HWLOC_PATH)/include KOKKOS_LDFLAGS += -L$(HWLOC_PATH)/lib + KOKKOS_CXXLDFLAGS += -L$(HWLOC_PATH)/lib KOKKOS_TPL_INCLUDE_DIRS += $(HWLOC_PATH)/include KOKKOS_TPL_LIBRARY_DIRS += $(HWLOC_PATH)/lib endif KOKKOS_LIBS += -lhwloc KOKKOS_TPL_LIBRARY_NAMES += hwloc - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_HWLOC") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_HWLOC") endif ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1) @@ -469,14 +484,15 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) ifneq ($(MEMKIND_PATH),) - KOKKOS_CPPFLAGS += -I$(MEMKIND_PATH)/include + KOKKOS_CXXFLAGS += -I$(MEMKIND_PATH)/include KOKKOS_LDFLAGS += -L$(MEMKIND_PATH)/lib + KOKKOS_CXXLDFLAGS += -L$(MEMKIND_PATH)/lib KOKKOS_TPL_INCLUDE_DIRS += $(MEMKIND_PATH)/include KOKKOS_TPL_LIBRARY_DIRS += $(MEMKIND_PATH)/lib endif KOKKOS_LIBS += -lmemkind -lnuma KOKKOS_TPL_LIBRARY_NAMES += memkind numa - tmp := $(call kokkos_append_header,"\#define KOKKOS_HAVE_HBWSPACE") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_HBWSPACE") endif ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 0) @@ -486,6 +502,13 @@ endif ifeq ($(KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE), 0) tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEPRECATED_CODE") endif +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_ETI") +endif + +ifeq ($(KOKKOS_INTERNAL_ENABLE_LARGE_MEM_TESTS), 1) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_LARGE_MEM_TESTS") +endif tmp := $(call kokkos_append_header,"/* Optimization Settings */") @@ -497,27 +520,35 @@ tmp := $(call kokkos_append_header,"/* Cuda Settings */") ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LDG_INTRINSIC") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LDG_INTRINSIC") else ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LDG_INTRINSIC") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LDG_INTRINSIC") endif endif ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_UVM") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_UVM") endif ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE") KOKKOS_CXXFLAGS += --relocatable-device-code=true KOKKOS_LDFLAGS += --relocatable-device-code=true endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -ge 90; echo $$?),0) + # This diagnostic is just plain wrong in CUDA 9 + # See https://github.com/kokkos/kokkos/issues/1470 + KOKKOS_CXXFLAGS += -Xcudafe --diag_suppress=esa_on_defaulted_function_ignored + endif + endif + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1) ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0) - tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LAMBDA") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LAMBDA") KOKKOS_CXXFLAGS += -expt-extended-lambda else $(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.) @@ -525,12 +556,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) endif ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_USE_LAMBDA") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LAMBDA") endif endif ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - tmp := $(call kokkos_append_header,"\#define KOKKOS_CUDA_CLANG_WORKAROUND") + tmp := $(call kokkos_append_header,"\#define KOKKOS_IMPL_CUDA_CLANG_WORKAROUND") endif endif @@ -907,10 +938,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) KOKKOS_CXXFLAGS += $(shell $(ROCM_HCC_PATH)/bin/hcc-config --cxxflags) KOKKOS_LDFLAGS += $(shell $(ROCM_HCC_PATH)/bin/hcc-config --ldflags) -lhc_am -lm + KOKKOS_CXXLDFLAGS += $(shell $(ROCM_HCC_PATH)/bin/hcc-config --ldflags) -lhc_am -lm KOKKOS_TPL_LIBRARY_NAMES += hc_am m KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_ROCM_ARCH_FLAG) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/ROCm/*.cpp) +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/ROCm/*.cpp) +endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/ROCm/*.hpp) endif @@ -937,10 +972,14 @@ KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/containers/src/impl/*.cpp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp) +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/Cuda/*.cpp) +endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp) ifneq ($(CUDA_PATH),) - KOKKOS_CPPFLAGS += -I$(CUDA_PATH)/include + KOKKOS_CXXFLAGS += -I$(CUDA_PATH)/include KOKKOS_LDFLAGS += -L$(CUDA_PATH)/lib64 + KOKKOS_CXXLDFLAGS += -L$(CUDA_PATH)/lib64 KOKKOS_TPL_INCLUDE_DIRS += $(CUDA_PATH)/include KOKKOS_TPL_LIBRARY_DIRS += $(CUDA_PATH)/lib64 ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) @@ -964,6 +1003,9 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/OpenMP/*.cpp) +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/OpenMP/*.cpp) +endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/OpenMP/*.hpp) ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) @@ -978,6 +1020,9 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.cpp) +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/Threads/*.cpp) +endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.hpp) KOKKOS_LIBS += -lpthread KOKKOS_TPL_LIBRARY_NAMES += pthread @@ -987,8 +1032,9 @@ ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Qthreads/*.cpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Qthreads/*.hpp) ifneq ($(QTHREADS_PATH),) - KOKKOS_CPPFLAGS += -I$(QTHREADS_PATH)/include + KOKKOS_CXXFLAGS += -I$(QTHREADS_PATH)/include KOKKOS_LDFLAGS += -L$(QTHREADS_PATH)/lib + KOKKOS_CXXLDFLAGS += -L$(QTHREADS_PATH)/lib KOKKOS_TPL_INCLUDE_DIRS += $(QTHREADS_PATH)/include KOKKOS_TPL_LIBRARY_DIRS += $(QTHREADS_PATH)/lib64 endif @@ -1011,6 +1057,11 @@ endif # Don't include Kokkos_Serial.cpp or Kokkos_Serial_Task.cpp if not using Serial # device to avoid a link warning. +ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/Serial/*.cpp) +endif +endif ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial.cpp,$(KOKKOS_SRC)) KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial_Task.cpp,$(KOKKOS_SRC)) diff --git a/lib/kokkos/Makefile.targets b/lib/kokkos/Makefile.targets index a63598577c720a7b522a5f10192aa413046564b9..44da1e082ae12f6293a3fb925fb8b30e76e28248 100644 --- a/lib/kokkos/Makefile.targets +++ b/lib/kokkos/Makefile.targets @@ -31,6 +31,12 @@ Kokkos_SharedAlloc.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_ Kokkos_MemoryPool.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp +ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + include $(KOKKOS_ETI_PATH)/Serial/Makefile.eti_Serial +endif +endif + ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) Kokkos_Cuda_Impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Impl.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Impl.cpp @@ -40,6 +46,9 @@ Kokkos_Cuda_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cu $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp Kokkos_Cuda_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + include $(KOKKOS_ETI_PATH)/Cuda/Makefile.eti_Cuda +endif endif ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) @@ -51,6 +60,9 @@ Kokkos_ROCm_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_RO $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Task.cpp Kokkos_ROCm_Impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + include $(KOKKOS_ETI_PATH)/ROCm/Makefile.eti_ROCm +endif endif ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) @@ -58,6 +70,9 @@ Kokkos_ThreadsExec_base.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec_base.cpp Kokkos_ThreadsExec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + include $(KOKKOS_ETI_PATH)/Threads/Makefile.eti_Threads +endif endif ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 1) @@ -72,6 +87,9 @@ Kokkos_OpenMP_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokko $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp Kokkos_OpenMP_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp +ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) + include $(KOKKOS_ETI_PATH)/OpenMP/Makefile.eti_OpenMP +endif endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index 1c659e44a45e5cd1d972f441f956ce4e47de2d2e..5f1d88bfffbfa90dd2a68361d8ef17e853a5bc8a 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -702,7 +702,11 @@ namespace Kokkos { } Random_XorShift64_Pool(uint64_t seed) { num_states_ = 0; +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE init(seed,DeviceType::max_hardware_threads()); +#else + init(seed,DeviceType::impl_max_hardware_threads()); +#endif } Random_XorShift64_Pool(const Random_XorShift64_Pool& src): @@ -751,7 +755,11 @@ namespace Kokkos { KOKKOS_INLINE_FUNCTION Random_XorShift64 get_state() const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE const int i = DeviceType::hardware_thread_id();; +#else + const int i = DeviceType::impl_hardware_thread_id();; +#endif return Random_XorShift64(state_(i),i); } @@ -957,7 +965,11 @@ namespace Kokkos { inline Random_XorShift1024_Pool(uint64_t seed){ num_states_ = 0; +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE init(seed,DeviceType::max_hardware_threads()); +#else + init(seed,DeviceType::impl_max_hardware_threads()); +#endif } Random_XorShift1024_Pool(const Random_XorShift1024_Pool& src): @@ -1012,7 +1024,11 @@ namespace Kokkos { KOKKOS_INLINE_FUNCTION Random_XorShift1024 get_state() const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE const int i = DeviceType::hardware_thread_id(); +#else + const int i = DeviceType::impl_hardware_thread_id(); +#endif return Random_XorShift1024(state_,p_(i),i); }; diff --git a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp index 888476045b8ee4a424e668a5da71567c408af934..c952b1e541af767d346ae2fdd2cea6c16c84a3eb 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp @@ -288,6 +288,7 @@ public: Kokkos::abort("BinSort::sort: values range length != permutation vector length"); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE scratch_view_type sorted_values("Scratch", len, @@ -298,6 +299,18 @@ public: values.extent(5), values.extent(6), values.extent(7)); +#else + scratch_view_type + sorted_values("Scratch", + values.rank_dynamic > 0 ? len : KOKKOS_IMPL_CTOR_DEFAULT_ARG, + values.rank_dynamic > 1 ? values.extent(1) : KOKKOS_IMPL_CTOR_DEFAULT_ARG , + values.rank_dynamic > 2 ? values.extent(2) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, + values.rank_dynamic > 3 ? values.extent(3) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, + values.rank_dynamic > 4 ? values.extent(4) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, + values.rank_dynamic > 5 ? values.extent(5) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, + values.rank_dynamic > 6 ? values.extent(6) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, + values.rank_dynamic > 7 ? values.extent(7) : KOKKOS_IMPL_CTOR_DEFAULT_ARG); +#endif { copy_permute_functor< scratch_view_type /* DstViewType */ @@ -362,8 +375,10 @@ public: KOKKOS_INLINE_FUNCTION void operator() (const bin_sort_bins_tag& tag, const int&i ) const { + auto bin_size = bin_count_const(i); + if (bin_size <= 1) return; + int upper_bound = bin_offsets(i)+bin_size; bool sorted = false; - int upper_bound = bin_offsets(i)+bin_count_const(i); while(!sorted) { sorted = true; int old_idx = sort_order(bin_offsets(i)); @@ -501,7 +516,7 @@ bool try_std_sort(ViewType view) { template struct min_max_functor { - typedef Kokkos::Experimental::MinMaxScalar minmax_scalar; + typedef Kokkos::MinMaxScalar minmax_scalar; ViewType view; min_max_functor(const ViewType& view_):view(view_) {} @@ -523,8 +538,8 @@ void sort( ViewType const & view , bool const always_use_kokkos_sort = false) } typedef BinOp1D CompType; - Kokkos::Experimental::MinMaxScalar result; - Kokkos::Experimental::MinMax reducer(result); + Kokkos::MinMaxScalar result; + Kokkos::MinMax reducer(result); parallel_reduce("Kokkos::Sort::FindExtent",Kokkos::RangePolicy(0,view.extent(0)), Impl::min_max_functor(view),reducer); if(result.min_val == result.max_val) return; @@ -542,8 +557,8 @@ void sort( ViewType view typedef Kokkos::RangePolicy range_policy ; typedef BinOp1D CompType; - Kokkos::Experimental::MinMaxScalar result; - Kokkos::Experimental::MinMax reducer(result); + Kokkos::MinMaxScalar result; + Kokkos::MinMax reducer(result); parallel_reduce("Kokkos::Sort::FindExtent", range_policy( begin , end ) , Impl::min_max_functor(view),reducer ); diff --git a/lib/kokkos/cmake/kokkos_build.cmake b/lib/kokkos/cmake/kokkos_build.cmake index 76d0655adb76753d09df3bbfd88ff6d98d7da013..94dd733ca33ecf4d0ea35957ffcf99b9e1dc00b6 100644 --- a/lib/kokkos/cmake/kokkos_build.cmake +++ b/lib/kokkos/cmake/kokkos_build.cmake @@ -76,7 +76,11 @@ IF(KOKKOS_SEPARATE_LIBS) ) foreach(lib IN LISTS KOKKOS_TPL_LIBRARY_NAMES) - find_library(LIB_${lib} ${lib} PATHS ${KOKKOS_TPL_LIBRARY_DIRS}) + if ("${lib}" STREQUAL "cuda") + set(LIB_cuda "-lcuda") + else() + find_library(LIB_${lib} ${lib} PATHS ${KOKKOS_TPL_LIBRARY_DIRS}) + endif() target_link_libraries(kokkoscore PUBLIC ${LIB_${lib}}) endforeach() @@ -154,7 +158,11 @@ ELSE() ) foreach(lib IN LISTS KOKKOS_TPL_LIBRARY_NAMES) - find_library(LIB_${lib} ${lib} PATHS ${KOKKOS_TPL_LIBRARY_DIRS}) + if ("${lib}" STREQUAL "cuda") + set(LIB_cuda "-lcuda") + else() + find_library(LIB_${lib} ${lib} PATHS ${KOKKOS_TPL_LIBRARY_DIRS}) + endif() target_link_libraries(kokkos PUBLIC ${LIB_${lib}}) endforeach() diff --git a/lib/kokkos/cmake/kokkos_options.cmake b/lib/kokkos/cmake/kokkos_options.cmake index 25eb8e86ced2e549eefa1d1c0788ffc41654cbd8..80a091bb98b1d57a24b50f0f22e902133062ecee 100644 --- a/lib/kokkos/cmake/kokkos_options.cmake +++ b/lib/kokkos/cmake/kokkos_options.cmake @@ -31,6 +31,7 @@ list(APPEND KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST Profiling_Load_Print Aggressive_Vectorization Deprecated_Code + Explicit_Instantiation ) #------------------------------------------------------------------------------- @@ -40,6 +41,7 @@ list(APPEND KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST foreach(opt ${KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST}) string(TOUPPER ${opt} OPT ) IF(DEFINED Kokkos_ENABLE_${opt}) + MESSAGE("Kokkos_ENABLE_${opt} is defined!") IF(DEFINED KOKKOS_ENABLE_${OPT}) IF(NOT ("${KOKKOS_ENABLE_${OPT}}" STREQUAL "${Kokkos_ENABLE_${opt}}")) IF(DEFINED KOKKOS_ENABLE_${OPT}_INTERNAL) @@ -57,18 +59,16 @@ foreach(opt ${KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST}) ENDIF() ELSE() SET(KOKKOS_INTERNAL_ENABLE_${OPT}_DEFAULT ${Kokkos_ENABLE_${opt}}) + MESSAGE("set KOKKOS_INTERNAL_ENABLE_${OPT}_DEFAULT!") ENDIF() ENDIF() endforeach() +IF(DEFINED Kokkos_ARCH) + MESSAGE(FATAL_ERROR "Defined Kokkos_ARCH, use KOKKOS_ARCH instead!") +ENDIF() IF(DEFINED Kokkos_Arch) - IF(DEFINED KOKKOS_ARCH) - IF(NOT (${KOKKOS_ARCH} STREQUAL "${Kokkos_Arch}")) - MESSAGE(FATAL_ERROR "Defined both Kokkos_Arch and KOKKOS_ARCH and they differ!") - ENDIF() - ELSE() - SET(KOKKOS_ARCH ${Kokkos_Arch}) - ENDIF() + MESSAGE(FATAL_ERROR "Defined Kokkos_Arch, use KOKKOS_ARCH instead!") ENDIF() #------------------------------------------------------------------------------- @@ -103,6 +103,8 @@ list(APPEND KOKKOS_ARCH_LIST Maxwell53 # (GPU) NVIDIA Maxwell generation CC 5.3 Pascal60 # (GPU) NVIDIA Pascal generation CC 6.0 Pascal61 # (GPU) NVIDIA Pascal generation CC 6.1 + Volta70 # (GPU) NVIDIA Volta generation CC 7.0 + Volta72 # (GPU) NVIDIA Volta generation CC 7.2 ) # List of possible device architectures. @@ -267,6 +269,8 @@ set(KOKKOS_ENABLE_PROFILING_LOAD_PRINT ${KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_P set_kokkos_default_default(DEPRECATED_CODE ON) set(KOKKOS_ENABLE_DEPRECATED_CODE ${KOKKOS_INTERNAL_ENABLE_DEPRECATED_CODE_DEFAULT} CACHE BOOL "Enable deprecated code.") +set_kokkos_default_default(EXPLICIT_INSTANTIATION ON) +set(KOKKOS_ENABLE_EXPLICIT_INSTANTIATION ${KOKKOS_INTERNAL_ENABLE_EXPLICIT_INSTANTIATION_DEFAULT} CACHE BOOL "Enable explicit template instantiation.") #------------------------------------------------------------------------------- #------------------------------- KOKKOS_USE_TPLS ------------------------------- diff --git a/lib/kokkos/cmake/kokkos_settings.cmake b/lib/kokkos/cmake/kokkos_settings.cmake index 579fab0c954c230d7690cda72a854d332d598be1..21c9d75a96aa52fd349c751aa0c2fa0f12316c91 100644 --- a/lib/kokkos/cmake/kokkos_settings.cmake +++ b/lib/kokkos/cmake/kokkos_settings.cmake @@ -74,6 +74,9 @@ endif() if(${KOKKOS_ENABLE_PROFILING_LOAD_PRINT}) list(APPEND KOKKOS_OPTIONSl enable_profile_load_print) endif() +if(${KOKKOS_ENABLE_EXPLICIT_INSTANTIATION}) + list(APPEND KOKKOS_OPTIONSl enable_eti) +endif() # List needs to be comma-delimitted string(REPLACE ";" "," KOKKOS_GMAKE_OPTIONS "${KOKKOS_OPTIONSl}") @@ -158,6 +161,19 @@ if (NOT "${KOKKOS_INTERNAL_ADDTOPATH}" STREQUAL "") set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} "PATH=\"${KOKKOS_INTERNAL_ADDTOPATH}:$ENV{PATH}\"") endif() +if (CMAKE_CXX_STANDARD) + if (CMAKE_CXX_STANDARD STREQUAL "98") + message(FATAL_ERROR "Kokkos requires C++11 or newer!") + endif() + set(KOKKOS_CXX_STANDARD "c++${CMAKE_CXX_STANDARD}") + if (CMAKE_CXX_EXTENSIONS) + if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU") + set(KOKKOS_CXX_STANDARD "gnu++${CMAKE_CXX_STANDARD}") + endif() + endif() + set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} "KOKKOS_CXX_STANDARD=\"${KOKKOS_CXX_STANDARD}\"") +endif() + # Final form that gets passed to make set(KOKKOS_SETTINGS env ${KOKKOS_SETTINGS}) diff --git a/lib/kokkos/cmake/tribits.cmake b/lib/kokkos/cmake/tribits.cmake index 1b5a7b2adb4572cf3b454af49ce7db13332fc7ce..f8eebc29f8b01dab2fe1baa831d30306b0eef376 100644 --- a/lib/kokkos/cmake/tribits.cmake +++ b/lib/kokkos/cmake/tribits.cmake @@ -300,7 +300,9 @@ FUNCTION(TRIBITS_ADD_EXECUTABLE EXE_NAME) ENDIF() ENDFUNCTION() -ADD_CUSTOM_TARGET(check COMMAND ${CMAKE_CTEST_COMMAND} -VV -C ${CMAKE_CFG_INTDIR}) +IF(NOT TARGET check) + ADD_CUSTOM_TARGET(check COMMAND ${CMAKE_CTEST_COMMAND} -VV -C ${CMAKE_CFG_INTDIR}) +ENDIF() FUNCTION(TRIBITS_ADD_TEST) ENDFUNCTION() diff --git a/lib/kokkos/config/test_all_sandia b/lib/kokkos/config/test_all_sandia index 28b4a64b10819538c7f5fc672ada210671343cf4..15e6049afbaf238d132a28335f811576d2d0c72d 100755 --- a/lib/kokkos/config/test_all_sandia +++ b/lib/kokkos/config/test_all_sandia @@ -22,30 +22,38 @@ if [[ "$HOSTNAME" =~ .*bowman.* ]]; then module load git fi -if [[ "$HOSTNAME" =~ n.* ]]; then # Warning: very generic name +if [[ "$HOSTNAME" == n* ]]; then # Warning: very generic name if [[ "$PROCESSOR" = "aarch64" ]]; then MACHINE=sullivan module load git fi fi -if [[ "$HOSTNAME" =~ node.* ]]; then # Warning: very generic name +if [[ "$HOSTNAME" == node* ]]; then # Warning: very generic name if [[ "$MACHINE" = "" ]]; then MACHINE=shepard module load git fi fi -if [[ "$HOSTNAME" =~ apollo ]]; then +if [[ "$HOSTNAME" == apollo\.* ]]; then MACHINE=apollo module load git fi -if [[ "$HOSTNAME" =~ sullivan ]]; then +if [[ "$HOSTNAME" == sullivan ]]; then MACHINE=sullivan module load git fi +if [[ "$HOSTNAME" == mayer\.* ]]; then + MACHINE=mayer +# module load git +fi +if [[ "$HOSTNAME" == cn* ]]; then # Warning: very generic name + MACHINE=mayer +fi + if [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then if [[ "$MACHINE" = "" ]]; then MACHINE=sems @@ -83,7 +91,7 @@ CUSTOM_BUILD_LIST="" QTHREADS_PATH="" DRYRUN=False BUILD_ONLY=False -declare -i NUM_JOBS_TO_RUN_IN_PARALLEL=3 +declare -i NUM_JOBS_TO_RUN_IN_PARALLEL=1 TEST_SCRIPT=False SKIP_HWLOC=False SPOT_CHECK=False @@ -142,6 +150,9 @@ do --with-cuda-options*) KOKKOS_CUDA_OPTIONS="--with-cuda-options=${key#*=}" ;; + --with-options*) + KOKKOS_OPTIONS="--with-options=enable_large_mem_tests,${key#*=}" + ;; --cxxflags-extra*) CXX_FLAGS_EXTRA="${key#*=}" ;; @@ -247,7 +258,7 @@ elif [ "$MACHINE" = "white" ]; then ARCH_FLAG="--arch=Power8,Kepler37" fi - NUM_JOBS_TO_RUN_IN_PARALLEL=2 + NUM_JOBS_TO_RUN_IN_PARALLEL=1 elif [ "$MACHINE" = "bowman" ]; then source /etc/profile.d/modules.sh @@ -268,7 +279,7 @@ elif [ "$MACHINE" = "bowman" ]; then ARCH_FLAG="--arch=KNL" fi - NUM_JOBS_TO_RUN_IN_PARALLEL=2 + NUM_JOBS_TO_RUN_IN_PARALLEL=1 elif [ "$MACHINE" = "sullivan" ]; then source /etc/profile.d/modules.sh @@ -284,7 +295,24 @@ elif [ "$MACHINE" = "sullivan" ]; then ARCH_FLAG="--arch=ARMv8-ThunderX" fi - NUM_JOBS_TO_RUN_IN_PARALLEL=2 + NUM_JOBS_TO_RUN_IN_PARALLEL=1 + +elif [ "$MACHINE" = "mayer" ]; then + SKIP_HWLOC=True + export SLURM_TASKS_PER_NODE=96 + + BASE_MODULE_LIST="/" + ARM_MODULE_LIST="/" + + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("gcc/7.2.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "arm/1.4.0 $ARM_MODULE_LIST $ARM_GCC_BUILD_LIST armclang++ $CLANG_WARNING_FLAGS") + + if [ -z "$ARCH_FLAG" ]; then + ARCH_FLAG="--arch=ARMv8-TX2" + fi + + NUM_JOBS_TO_RUN_IN_PARALLEL=1 elif [ "$MACHINE" = "shepard" ]; then source /etc/profile.d/modules.sh @@ -303,7 +331,7 @@ elif [ "$MACHINE" = "shepard" ]; then if [ -z "$ARCH_FLAG" ]; then ARCH_FLAG="--arch=HSW" fi - NUM_JOBS_TO_RUN_IN_PARALLEL=2 + NUM_JOBS_TO_RUN_IN_PARALLEL=1 elif [ "$MACHINE" = "apollo" ]; then source /projects/sems/modulefiles/utils/sems-modules-init.sh @@ -331,7 +359,7 @@ elif [ "$MACHINE" = "apollo" ]; then if [ "$SPOT_CHECK" = "True" ]; then # Format: (compiler module-list build-list exe-name warning-flag) COMPILERS=("gcc/4.8.4 $BASE_MODULE_LIST "OpenMP,Pthread" g++ $GCC_WARNING_FLAGS" - "gcc/5.1.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" + "gcc/5.3.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" "clang/6.0 $CLANG_MODULE_LIST "Cuda_Pthread" clang++ $CUDA_WARNING_FLAGS" @@ -358,7 +386,7 @@ elif [ "$MACHINE" = "apollo" ]; then ARCH_FLAG="--arch=SNB,Volta70" fi - NUM_JOBS_TO_RUN_IN_PARALLEL=2 + NUM_JOBS_TO_RUN_IN_PARALLEL=1 else echo "Unhandled machine $MACHINE" >&2 @@ -627,6 +655,11 @@ single_build_and_test() { if [[ "$KOKKOS_CUDA_OPTIONS" != "" ]]; then local extra_args="$extra_args $KOKKOS_CUDA_OPTIONS" fi + if [[ "$KOKKOS_OPTIONS" != "" ]]; then + local extra_args="$extra_args $KOKKOS_OPTIONS" + else + local extra_args="$extra_args --with-options=enable_large_mem_tests" + fi echo " Starting job $desc" @@ -642,7 +675,7 @@ single_build_and_test() { else run_cmd ${KOKKOS_PATH}/generate_makefile.bash --with-devices=$build $ARCH_FLAG --compiler=$(which $compiler_exe) --cxxflags=\"$cxxflags\" --ldflags=\"$ldflags\" $extra_args &>> ${desc}.configure.log || { report_and_log_test_result 1 ${desc} configure && return 0; } local -i build_start_time=$(date +%s) - run_cmd make -j 32 build-test >& ${desc}.build.log || { report_and_log_test_result 1 ${desc} build && return 0; } + run_cmd make -j 48 build-test >& ${desc}.build.log || { report_and_log_test_result 1 ${desc} build && return 0; } local -i build_end_time=$(date +%s) comment="build_time=$(($build_end_time-$build_start_time))" @@ -682,6 +715,9 @@ run_in_background() { if [[ "$compiler" == cuda* ]]; then num_jobs=1 fi + if [[ "$compiler" == clang ]]; then + num_jobs=1 + fi # fi wait_for_jobs $num_jobs diff --git a/lib/kokkos/containers/performance_tests/TestCuda.cpp b/lib/kokkos/containers/performance_tests/TestCuda.cpp index 682f3f52f70a6d7c37ef1006267d3bddffc9cd70..351fb86df3d48836ff45286401e52a6f1f684fd7 100644 --- a/lib/kokkos/containers/performance_tests/TestCuda.cpp +++ b/lib/kokkos/containers/performance_tests/TestCuda.cpp @@ -70,13 +70,12 @@ protected: static void SetUpTestCase() { std::cout << std::setprecision(5) << std::scientific; - Kokkos::HostSpace::execution_space::initialize(); - Kokkos::Cuda::initialize( Kokkos::Cuda::SelectDevice(0) ); + Kokkos::InitArguments args(-1, -1, 0); + Kokkos::initialize(args); } static void TearDownTestCase() { - Kokkos::Cuda::finalize(); - Kokkos::HostSpace::execution_space::finalize(); + Kokkos::finalize(); } }; diff --git a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp index 66d497552e3de2dc09cd409bed204c35bc0ddb68..e6218074eafd965554c3ebe60136386c488fd882 100644 --- a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp +++ b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp @@ -70,13 +70,13 @@ protected: { std::cout << std::setprecision(5) << std::scientific; - Kokkos::OpenMP::initialize(); + Kokkos::initialize(); Kokkos::OpenMP::print_configuration( std::cout ); } static void TearDownTestCase() { - Kokkos::OpenMP::finalize(); + Kokkos::finalize(); } }; diff --git a/lib/kokkos/containers/performance_tests/TestThreads.cpp b/lib/kokkos/containers/performance_tests/TestThreads.cpp index a951a5ca56e4f30fcbe39d0ae797f6bd0d126882..6a02e67b252781f7320223ad8fb87cadfef3355e 100644 --- a/lib/kokkos/containers/performance_tests/TestThreads.cpp +++ b/lib/kokkos/containers/performance_tests/TestThreads.cpp @@ -81,12 +81,12 @@ protected: std::cout << "Threads: " << num_threads << std::endl; - Kokkos::Threads::initialize( num_threads ); + Kokkos::initialize( Kokkos::InitArguments(num_threads) ); } static void TearDownTestCase() { - Kokkos::Threads::finalize(); + Kokkos::finalize(); } }; diff --git a/lib/kokkos/containers/src/Kokkos_Bitset.hpp b/lib/kokkos/containers/src/Kokkos_Bitset.hpp index c48058d75d774feaf424cf196522dfceadf9e150..bfe8080f3b92ce9d11a0c040c123745acaf7e66b 100644 --- a/lib/kokkos/containers/src/Kokkos_Bitset.hpp +++ b/lib/kokkos/containers/src/Kokkos_Bitset.hpp @@ -271,7 +271,7 @@ private: block = Impl::rotate_right(block, offset); return ((( !(scan_direction & BIT_SCAN_REVERSE) ? Impl::bit_scan_forward(block) : - Impl::bit_scan_reverse(block) + ::Kokkos::log2(block) ) + offset ) & block_mask ) + block_start; diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 74fe4418f870854498cd65cfe8e346d7d183e716..548e96d251f13224f4b82e13dda1c233fe36a577 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -209,14 +209,14 @@ public: /// the first three integer arguments will be nonzero, and you may /// omit the integer arguments that follow. DualView (const std::string& label, - const size_t n0 = 0, - const size_t n1 = 0, - const size_t n2 = 0, - const size_t n3 = 0, - const size_t n4 = 0, - const size_t n5 = 0, - const size_t n6 = 0, - const size_t n7 = 0) + const size_t n0 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, + const size_t n1 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, + const size_t n2 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, + const size_t n3 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, + const size_t n4 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, + const size_t n5 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, + const size_t n6 = KOKKOS_IMPL_CTOR_DEFAULT_ARG, + const size_t n7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG) : d_view (label, n0, n1, n2, n3, n4, n5, n6, n7) , h_view (create_mirror_view (d_view)) // without UVM, host View mirrors , modified_device (View ("DualView::modified_device")) @@ -464,14 +464,14 @@ public: /// This discards any existing contents of the objects, and resets /// their modified flags. It does not copy the old contents /// of either View into the new View objects. - void realloc( const size_t n0 = 0 , - const size_t n1 = 0 , - const size_t n2 = 0 , - const size_t n3 = 0 , - const size_t n4 = 0 , - const size_t n5 = 0 , - const size_t n6 = 0 , - const size_t n7 = 0 ) { + void realloc( const size_t n0 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n1 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n2 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n3 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n4 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n5 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n6 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG ) { ::Kokkos::realloc(d_view,n0,n1,n2,n3,n4,n5,n6,n7); h_view = create_mirror_view( d_view ); @@ -483,14 +483,14 @@ public: /// /// This method only copies the old contents into the new View /// objects for the device which was last marked as modified. - void resize( const size_t n0 = 0 , - const size_t n1 = 0 , - const size_t n2 = 0 , - const size_t n3 = 0 , - const size_t n4 = 0 , - const size_t n5 = 0 , - const size_t n6 = 0 , - const size_t n7 = 0 ) { + void resize( const size_t n0 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n1 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n2 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n3 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n4 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n5 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n6 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , + const size_t n7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG ) { if(modified_device() >= modified_host()) { /* Resize on Device */ ::Kokkos::resize(d_view,n0,n1,n2,n3,n4,n5,n6,n7); @@ -533,10 +533,21 @@ public: //! \name Methods for getting capacity, stride, or dimension(s). //@{ +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE //! The allocation size (same as Kokkos::View::capacity). size_t capacity() const { return d_view.span(); } +#endif + + //! The allocation size (same as Kokkos::View::span). + KOKKOS_INLINE_FUNCTION constexpr size_t span() const { + return d_view.span(); + } + + KOKKOS_INLINE_FUNCTION bool span_is_contiguous() const { + return d_view.span_is_contiguous(); + } //! Get stride(s) for each dimension. template< typename iType> @@ -556,6 +567,11 @@ public: extent_int( const iType & r ) const { return static_cast(d_view.extent(r)); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + /* Deprecate all 'dimension' functions in favor of + * ISO/C++ vocabulary 'extent'. + */ + /* \brief return size of dimension 0 */ size_t dimension_0() const {return d_view.extent(0);} /* \brief return size of dimension 1 */ @@ -572,6 +588,7 @@ public: size_t dimension_6() const {return d_view.extent(6);} /* \brief return size of dimension 7 */ size_t dimension_7() const {return d_view.extent(7);} +#endif //@} }; diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index ccf53b3d5096574f4446d4cf9d7eee71b6e45c08..b30009a999e108235a1318431df08fd3115ec965 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -64,7 +64,7 @@ namespace Impl { template struct DynRankDimTraits { - enum : size_t{unspecified = ~size_t(0)}; + enum : size_t{unspecified =KOKKOS_INVALID_INDEX}; // Compute the rank of the view from the nonzero dimension arguments. KOKKOS_INLINE_FUNCTION @@ -192,14 +192,14 @@ struct DynRankDimTraits { static typename std::enable_if< (std::is_same::value || std::is_same::value) && std::is_integral::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank ) { - return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) - , dynrank > 1 ? layout.dimension[1] : ~size_t(0) - , dynrank > 2 ? layout.dimension[2] : ~size_t(0) - , dynrank > 3 ? layout.dimension[3] : ~size_t(0) - , dynrank > 4 ? layout.dimension[4] : ~size_t(0) - , dynrank > 5 ? layout.dimension[5] : ~size_t(0) - , dynrank > 6 ? layout.dimension[6] : ~size_t(0) - , dynrank > 7 ? layout.dimension[7] : ~size_t(0) + return Layout( dynrank > 0 ? layout.dimension[0] :KOKKOS_INVALID_INDEX + , dynrank > 1 ? layout.dimension[1] :KOKKOS_INVALID_INDEX + , dynrank > 2 ? layout.dimension[2] :KOKKOS_INVALID_INDEX + , dynrank > 3 ? layout.dimension[3] :KOKKOS_INVALID_INDEX + , dynrank > 4 ? layout.dimension[4] :KOKKOS_INVALID_INDEX + , dynrank > 5 ? layout.dimension[5] :KOKKOS_INVALID_INDEX + , dynrank > 6 ? layout.dimension[6] :KOKKOS_INVALID_INDEX + , dynrank > 7 ? layout.dimension[7] :KOKKOS_INVALID_INDEX ); } @@ -209,21 +209,21 @@ struct DynRankDimTraits { static typename std::enable_if< (std::is_same::value) && std::is_integral::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank ) { - return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) + return Layout( dynrank > 0 ? layout.dimension[0] :KOKKOS_INVALID_INDEX , dynrank > 0 ? layout.stride[0] : (0) - , dynrank > 1 ? layout.dimension[1] : ~size_t(0) + , dynrank > 1 ? layout.dimension[1] :KOKKOS_INVALID_INDEX , dynrank > 1 ? layout.stride[1] : (0) - , dynrank > 2 ? layout.dimension[2] : ~size_t(0) + , dynrank > 2 ? layout.dimension[2] :KOKKOS_INVALID_INDEX , dynrank > 2 ? layout.stride[2] : (0) - , dynrank > 3 ? layout.dimension[3] : ~size_t(0) + , dynrank > 3 ? layout.dimension[3] :KOKKOS_INVALID_INDEX , dynrank > 3 ? layout.stride[3] : (0) - , dynrank > 4 ? layout.dimension[4] : ~size_t(0) + , dynrank > 4 ? layout.dimension[4] :KOKKOS_INVALID_INDEX , dynrank > 4 ? layout.stride[4] : (0) - , dynrank > 5 ? layout.dimension[5] : ~size_t(0) + , dynrank > 5 ? layout.dimension[5] :KOKKOS_INVALID_INDEX , dynrank > 5 ? layout.stride[5] : (0) - , dynrank > 6 ? layout.dimension[6] : ~size_t(0) + , dynrank > 6 ? layout.dimension[6] :KOKKOS_INVALID_INDEX , dynrank > 6 ? layout.stride[6] : (0) - , dynrank > 7 ? layout.dimension[7] : ~size_t(0) + , dynrank > 7 ? layout.dimension[7] :KOKKOS_INVALID_INDEX , dynrank > 7 ? layout.stride[7] : (0) ); } @@ -501,6 +501,7 @@ public: * ISO/C++ vocabulary 'extent'. */ +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE template< typename iType > KOKKOS_INLINE_FUNCTION constexpr typename std::enable_if< std::is_integral::value , size_t >::type @@ -514,17 +515,18 @@ public: KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_map.dimension_5(); } KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_map.dimension_6(); } KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_map.dimension_7(); } +#endif //---------------------------------------- - KOKKOS_INLINE_FUNCTION constexpr size_t size() const { return m_map.dimension_0() * - m_map.dimension_1() * - m_map.dimension_2() * - m_map.dimension_3() * - m_map.dimension_4() * - m_map.dimension_5() * - m_map.dimension_6() * - m_map.dimension_7(); } + KOKKOS_INLINE_FUNCTION constexpr size_t size() const { return m_map.extent(0) * + m_map.extent(1) * + m_map.extent(2) * + m_map.extent(3) * + m_map.extent(4) * + m_map.extent(5) * + m_map.extent(6) * + m_map.extent(7); } KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_map.stride_0(); } KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_map.stride_1(); } @@ -547,15 +549,19 @@ public: enum { reference_type_is_lvalue_reference = std::is_lvalue_reference< reference_type >::value }; KOKKOS_INLINE_FUNCTION constexpr size_t span() const { return m_map.span(); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE // Deprecated, use 'span()' instead KOKKOS_INLINE_FUNCTION constexpr size_t capacity() const { return m_map.span(); } +#endif KOKKOS_INLINE_FUNCTION constexpr bool span_is_contiguous() const { return m_map.span_is_contiguous(); } KOKKOS_INLINE_FUNCTION constexpr pointer_type data() const { return m_map.data(); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE // Deprecated, use 'span_is_contigous()' instead KOKKOS_INLINE_FUNCTION constexpr bool is_contiguous() const { return m_map.span_is_contiguous(); } // Deprecated, use 'data()' instead KOKKOS_INLINE_FUNCTION constexpr pointer_type ptr_on_device() const { return m_map.data(); } +#endif //---------------------------------------- // Allow specializations to query their specialized map @@ -998,7 +1004,7 @@ public: //---------------------------------------- // Allocation according to allocation properties and array layout - // unused arg_layout dimensions must be set to ~size_t(0) so that rank deduction can properly take place + // unused arg_layout dimensions must be set toKOKKOS_INVALID_INDEX so that rank deduction can properly take place template< class ... P > explicit inline DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop @@ -1038,7 +1044,12 @@ public: , "View allocation constructor requires managed memory" ); if ( alloc_prop::initialize && - ! alloc_prop::execution_space::is_initialized() ) { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + ! alloc_prop::execution_space::is_initialized() +#else + ! alloc_prop::execution_space::impl_is_initialized() +#endif + ) { // If initializing view data then // the execution space must be initialized. Kokkos::Impl::throw_runtime_exception("Constructing DynRankView and initializing data with uninitialized execution space"); @@ -1104,14 +1115,14 @@ public: DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop , typename std::enable_if< ! Kokkos::Impl::ViewCtorProp< P... >::has_pointer , size_t - >::type const arg_N0 = ~size_t(0) - , const size_t arg_N1 = ~size_t(0) - , const size_t arg_N2 = ~size_t(0) - , const size_t arg_N3 = ~size_t(0) - , const size_t arg_N4 = ~size_t(0) - , const size_t arg_N5 = ~size_t(0) - , const size_t arg_N6 = ~size_t(0) - , const size_t arg_N7 = ~size_t(0) + >::type const arg_N0 =KOKKOS_INVALID_INDEX + , const size_t arg_N1 =KOKKOS_INVALID_INDEX + , const size_t arg_N2 =KOKKOS_INVALID_INDEX + , const size_t arg_N3 =KOKKOS_INVALID_INDEX + , const size_t arg_N4 =KOKKOS_INVALID_INDEX + , const size_t arg_N5 =KOKKOS_INVALID_INDEX + , const size_t arg_N6 =KOKKOS_INVALID_INDEX + , const size_t arg_N7 =KOKKOS_INVALID_INDEX ) : DynRankView( arg_prop , typename traits::array_layout @@ -1124,14 +1135,14 @@ public: DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop , typename std::enable_if< Kokkos::Impl::ViewCtorProp< P... >::has_pointer , size_t - >::type const arg_N0 = ~size_t(0) - , const size_t arg_N1 = ~size_t(0) - , const size_t arg_N2 = ~size_t(0) - , const size_t arg_N3 = ~size_t(0) - , const size_t arg_N4 = ~size_t(0) - , const size_t arg_N5 = ~size_t(0) - , const size_t arg_N6 = ~size_t(0) - , const size_t arg_N7 = ~size_t(0) + >::type const arg_N0 =KOKKOS_INVALID_INDEX + , const size_t arg_N1 =KOKKOS_INVALID_INDEX + , const size_t arg_N2 =KOKKOS_INVALID_INDEX + , const size_t arg_N3 =KOKKOS_INVALID_INDEX + , const size_t arg_N4 =KOKKOS_INVALID_INDEX + , const size_t arg_N5 =KOKKOS_INVALID_INDEX + , const size_t arg_N6 =KOKKOS_INVALID_INDEX + , const size_t arg_N7 =KOKKOS_INVALID_INDEX ) : DynRankView( arg_prop , typename traits::array_layout @@ -1156,14 +1167,14 @@ public: DynRankView( const Label & arg_label , typename std::enable_if< Kokkos::Impl::is_view_label