Commit 84de0d38 authored by Stefan Paquay's avatar Stefan Paquay
Browse files

Replaced files with those from upstream.

parents c192236a a28990ed

cmake/CMakeLists.txt

+130 −33
Original line number Diff line number Diff line
@@ -136,6 +136,7 @@ if(BUILD_EXE) 
  if(LAMMPS_MACHINE)

    set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")

  endif()

  set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})

endif()



option(BUILD_LIB "Build LAMMPS library" OFF)
@@ -162,6 +163,34 @@ set(LAMMPS_LINK_LIBS) 
set(LAMMPS_DEPS)

set(LAMMPS_API_DEFINES)



set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR

  KSPACE MANYBODY MC MEAM MESSAGE 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-SCAFACOS 

  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(PKG_${PKG} "Build ${PKG} Package" OFF)

endforeach()

foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})

  option(PKG_${PKG} "Build ${PKG} Package" OFF)

endforeach()



######################################################

# packages with special compiler needs or external libs

######################################################

if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)

  enable_language(Fortran)

endif()



if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)

  enable_language(C)

endif()



# do MPI detection after language activation, if MPI for these language is required

find_package(MPI QUIET)

option(BUILD_MPI "Build MPI version" ${MPI_FOUND})

if(BUILD_MPI)
@@ -206,25 +235,52 @@ endif() 
option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)



option(ENABLE_TESTING "Enable testing" OFF)

if(ENABLE_TESTING)

if(ENABLE_TESTING AND BUILD_EXE)

  enable_testing()

endif(ENABLE_TESTING)

  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")

  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")

  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)



set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR

  KSPACE MANYBODY MC MEAM MESSAGE 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(PKG_${PKG} "Build ${PKG} Package" OFF)

endforeach()

foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})

  option(PKG_${PKG} "Build ${PKG} Package" OFF)

  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)

    include(FetchContent)



    FetchContent_Declare(lammps-testing

      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git

      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}

    )



    FetchContent_GetProperties(lammps-testing)

    if(NOT lammps-testing_POPULATED)

      message(STATUS "Downloading tests...")

      FetchContent_Populate(lammps-testing)

    endif()



    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})

  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)

    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"

                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")

  endif()



  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})

    message(STATUS "Running test discovery...")



    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)

    foreach(script_path ${TEST_SCRIPTS})

      get_filename_component(TEST_NAME ${script_path} EXT)

      get_filename_component(SCRIPT_NAME ${script_path} NAME)

      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)

      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)

      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})

      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})

      set(TEST_NAME "test_core_${TEST_NAME}_serial")

      add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})

      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})

    endforeach()

    list(LENGTH TEST_SCRIPTS NUM_TESTS)



    message(STATUS "Found ${NUM_TESTS} tests.")

  endif()

endif()



macro(pkg_depends PKG1 PKG2)

  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
@@ -238,17 +294,7 @@ pkg_depends(MPIIO MPI) 
pkg_depends(USER-ATC MANYBODY)

pkg_depends(USER-LB MPI)

pkg_depends(USER-PHONON KSPACE)



######################################################

# packages with special compiler needs or external libs

######################################################

if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)

  enable_language(Fortran)

endif()



if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)

  enable_language(C)

endif()

pkg_depends(USER-SCAFACOS MPI)



find_package(OpenMP QUIET)

option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
@@ -426,6 +472,57 @@ if(PKG_LATTE) 
  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})

endif()



if(PKG_USER-SCAFACOS)

  find_package(GSL REQUIRED)

  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF)

  if(DOWNLOAD_SCAFACOS)

    include(ExternalProject)

    ExternalProject_Add(scafacos_build

      URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz

      URL_MD5 bd46d74e3296bd8a444d731bb10c1738

      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> 

                                               --disable-doc 

                                               --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m

                                               --with-internal-fftw

                                               --with-internal-pfft

                                               --with-internal-pnfft

                                               $<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>                                               

                                               FC=${CMAKE_MPI_Fortran_COMPILER} 

                                               CXX=${CMAKE_MPI_CXX_COMPILER} 

                                               CC=${CMAKE_MPI_C_COMPILER}

                                               F77=

      )

    ExternalProject_get_property(scafacos_build INSTALL_DIR)

    set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})

    set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)

    list(APPEND LAMMPS_DEPS scafacos_build)

    # list and order from pkg_config file of ScaFaCoS build

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)

    list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)

    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})

    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})

  else()

    FIND_PACKAGE(PkgConfig REQUIRED)

    PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED)

    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})

  endif()

  include_directories(${SCAFACOS_INCLUDE_DIRS})

endif()



if(PKG_USER-MOLFILE)

  add_library(molfile INTERFACE)

  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
@@ -435,8 +532,8 @@ endif() 


if(PKG_USER-NETCDF)

  find_package(NetCDF REQUIRED)

  include_directories(NETCDF_INCLUDE_DIR)

  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})

  include_directories(${NETCDF_INCLUDE_DIRS})

  list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})

  add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)

endif()
@@ -1119,11 +1216,11 @@ if(BUILD_EXE) 
    endif()

  endif()

  

  set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})

  set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})

  install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})

  install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME lmp${LAMMPS_MACHINE}.1)

  install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)

  if(ENABLE_TESTING)

    add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)

    add_test(ShowHelp ${LAMMPS_BINARY} -help)

  endif()

endif()

doc/src/Build_extras.txt

+40 −0
Original line number Diff line number Diff line
@@ -48,6 +48,7 @@ This is the list of packages that may require additional steps. 
"USER-OMP"_#user-omp,

"USER-QMMM"_#user-qmmm,

"USER-QUIP"_#user-quip,

"USER-SCAFACOS"_#user-scafacos,

"USER-SMD"_#user-smd,

"USER-VTK"_#user-vtk :tb(c=6,ea=c,a=l)
@@ -928,6 +929,45 @@ successfully build on your system. 


:line



USER-SCAFACOS package :h4,link(user-scafacos)



To build with this package, you must download and build the "ScaFaCoS

Coulomb solver library"_scafacos_home



:link(scafacos_home,http://www.scafacos.de)



[CMake build]:



-D DOWNLOAD_SCAFACOS=value    # download ScaFaCoS for build, value = no (default) or yes

-D SCAFACOS_LIBRARY=path      # ScaFaCos library file (only needed if at custom location) 

-D SCAFACOS_INCLUDE_DIR=path  # ScaFaCoS include directory (only needed if at custom location) :pre



If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded

and built inside the CMake build directory.  If the ScaFaCoS library

is already on your system (in a location CMake cannot find it),

SCAFACOS_LIBRARY is the filename (plus path) of the ScaFaCoS library

file, not the directory the library file is in.  SCAFACOS_INCLUDE_DIR

is the directory the ScaFaCoS include file is in.



[Traditional make]:



You can download and build the ScaFaCoS library manually if you

prefer; follow the instructions in lib/scafacos/README.  You can also

do it in one step from the lammps/src dir, using a command like these,

which simply invoke the lib/scafacos/Install.py script with the

specified args:



make lib-scafacos                         # print help message

make lib-scafacos args="-b"               # download and build in lib/scafacos/scafacos-<version>

make lib-scafacos args="-p $HOME/scafacos  # use existing ScaFaCoS installation in $HOME/scafacos



Note that 2 symbolic (soft) links, "includelink" and "liblink", are

created in lib/scafacos to point to the ScaFaCoS src dir.  When LAMMPS

builds in src it will use these links.  You should not need to edit

the lib/scafacos/Makefile.lammps file.



:line



USER-SMD package :h4,link(user-smd)



To build with this package, you must download the Eigen3 library.

doc/src/Build_package.txt

+1 −0
Original line number Diff line number Diff line
@@ -59,6 +59,7 @@ packages: 
"USER-OMP"_Build_extras.html#user-omp,

"USER-QMMM"_Build_extras.html#user-qmmm,

"USER-QUIP"_Build_extras.html#user-quip,

"USER-SCAFACOS"_#Build_extras.html#user-scafacos,

"USER-SMD"_Build_extras.html#user-smd,

"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)

doc/src/Commands_kspace.txt

+2 −1
Original line number Diff line number Diff line
@@ -33,4 +33,5 @@ OPT. 
"pppm/disp (i)"_kspace_style.html,

"pppm/disp/tip4p"_kspace_style.html,

"pppm/stagger"_kspace_style.html,

"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
 
"pppm/tip4p (o)"_kspace_style.html,

"scafacos"_kspace_style.html :tb(c=4,ea=c)

doc/src/Packages_details.txt

+36 −0
Original line number Diff line number Diff line
@@ -92,6 +92,7 @@ as contained in the file name. 
"USER-QTB"_#PKG-USER-QTB,

"USER-QUIP"_#PKG-USER-QUIP,

"USER-REAXC"_#PKG-USER-REAXC,

"USER-SCAFACOS"_#USER-SCAFACOS,

"USER-SMD"_#PKG-USER-SMD,

"USER-SMTBQ"_#PKG-USER-SMTBQ,

"USER-SPH"_#PKG-USER-SPH,
@@ -1859,6 +1860,41 @@ examples/reax :ul 


:line



USER-SCAFACOS package :link(USER-SCAFACOS),h4



[Contents:]



A KSpace style which wraps the "ScaFaCoS Coulomb solver

library"_http://www.scafacos.de to compute long-range Coulombic

interactions.



To use this package you must have the ScaFaCoS library available on

your system.



[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.



ScaFaCoS itself was developed by a consortium of German research

facilities with a BMBF (German Ministry of Science and Education)

funded project in 2009-2012. Participants of the consortium were the

Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as

the Forschungszentrum Juelich.



[Install:]



This package has "specific installation

instructions"_Build_extras.html#user-scafacos on the "Build

extras"_Build_extras.html doc page.



[Supporting info:]



src/USER-SCAFACOS: filenames -> commands

src/USER-SCAFACOS/README

"kspace_style scafacos"_kspace_style.html

"kspace_modify"_kspace_modify.html

examples/USER/scafacos :ul



:line



USER-SMD package :link(PKG-USER-SMD),h4



[Contents:]

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