diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index c003901199..911b6f0f15 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -87,7 +87,8 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) # 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 ${LAMMPS_SOURCE_DIR}/lmpgitversion.h) +file(GLOB SRC_AUTOGEN_PACKAGES ${LAMMPS_SOURCE_DIR}/packages_*.h) +list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h) foreach(_SRC ${SRC_AUTOGEN_FILES}) get_filename_component(FILENAME "${_SRC}" NAME) if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME}) @@ -172,21 +173,17 @@ set(LAMMPS_LINK_LIBS) set(LAMMPS_DEPS) set(LAMMPS_API_DEFINES) -set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR - KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI 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-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS - USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK - USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) +set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE + GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ + REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI + 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-PLUMED USER-PTM USER-QTB USER-REAXC + USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF + USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) 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}) +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) endforeach() @@ -203,7 +200,6 @@ endif() include_directories(${LAMMPS_SOURCE_DIR}) - if(PKG_USER-ADIOS) # The search for ADIOS2 must come before MPI because # it includes its own MPI search with the latest FindMPI.cmake @@ -213,7 +209,6 @@ if(PKG_USER-ADIOS) list(APPEND LAMMPS_LINK_LIBS adios2::adios2) 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}) @@ -233,7 +228,6 @@ else() list(APPEND LAMMPS_LINK_LIBS mpi_stubs) endif() - set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) @@ -320,10 +314,26 @@ pkg_depends(USER-LB MPI) pkg_depends(USER-PHONON KSPACE) pkg_depends(USER-SCAFACOS MPI) +include(CheckIncludeFileCXX) find_package(OpenMP QUIET) -option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) -if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL) + +# TODO: this is a temporary workaround until a better solution is found. AK 2019-05-30 +# GNU GCC 9.x uses settings incompatible with our use of 'default(none)' in OpenMP pragmas +# where we assume older GCC semantics. For the time being, we disable OpenMP by default +# for GCC 9.x and beyond. People may manually turn it on, but need to run the script +# src/USER-OMP/hack_openmp_for_pgi_gcc9.sh on all sources to make it compatible with gcc 9. +if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9)) + option(BUILD_OMP "Build with OpenMP support" OFF) +else() + option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) +endif() + +if(BUILD_OMP) find_package(OpenMP REQUIRED) + check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE) + if(NOT HAVE_OMP_H_INCLUDE) + message(FATAL_ERROR "Cannot find required 'omp.h' header file") + endif() set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") endif() @@ -367,7 +377,7 @@ if(PKG_KSPACE) endif() endif() -if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) +if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE) find_package(LAPACK) find_package(BLAS) if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) @@ -441,9 +451,14 @@ else() set(CUDA_REQUEST_PIC) endif() - if(PKG_VORONOI) - option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF) + find_package(VORO) + if(VORO_FOUND) + set(DOWNLOAD_VORO_DEFAULT OFF) + else() + set(DOWNLOAD_VORO_DEFAULT ON) + endif() + option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT}) if(DOWNLOAD_VORO) message(STATUS "Voro++ download requested - we will build our own") include(ExternalProject) @@ -476,7 +491,13 @@ if(PKG_VORONOI) endif() if(PKG_LATTE) - option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF) + find_package(LATTE) + if(LATTE_FOUND) + set(DOWNLOAD_LATTE_DEFAULT OFF) + else() + set(DOWNLOAD_LATTE_DEFAULT ON) + endif() + option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT}) if(DOWNLOAD_LATTE) if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7") @@ -488,6 +509,9 @@ if(PKG_LATTE) URL_MD5 85ac414fdada2d04619c8f936344df14 SOURCE_SUBDIR cmake CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= ${CMAKE_REQUEST_PIC} + -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES} + -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS} + -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} ) ExternalProject_get_property(latte_build INSTALL_DIR) set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a) @@ -503,7 +527,15 @@ endif() if(PKG_USER-SCAFACOS) find_package(GSL REQUIRED) - option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF) + find_package(PkgConfig QUIET) + set(DOWNLOAD_SCAFACOS_DEFAULT ON) + if(PKG_CONFIG_FOUND) + pkg_check_modules(SCAFACOS QUIET scafacos) + if(SCAFACOS_FOUND) + set(DOWNLOAD_SCAFACOS_DEFAULT OFF) + endif() + endif() + option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT}) if(DOWNLOAD_SCAFACOS) message(STATUS "ScaFaCoS download requested - we will build our own") include(ExternalProject) @@ -543,8 +575,8 @@ if(PKG_USER-SCAFACOS) 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) + find_package(PkgConfig REQUIRED) + pkg_check_modules(SCAFACOS REQUIRED scafacos) list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS}) endif() include_directories(${SCAFACOS_INCLUDE_DIRS}) @@ -558,29 +590,53 @@ if(PKG_USER-PLUMED) validate_option(PLUMED_MODE PLUMED_MODE_VALUES) string(TOUPPER ${PLUMED_MODE} PLUMED_MODE) - option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF) + find_package(PkgConfig QUIET) + set(DOWNLOAD_PLUMED_DEFAULT ON) + if(PKG_CONFIG_FOUND) + pkg_check_modules(PLUMED QUIET plumed) + if(PLUMED_FOUND) + set(DOWNLOAD_PLUMED_DEFAULT OFF) + endif() + endif() + + option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT}) if(DOWNLOAD_PLUMED) + if(BUILD_MPI) + set(PLUMED_CONFIG_MPI "--enable-mpi") + set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER}) + set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER}) + else() + set(PLUMED_CONFIG_MPI "--disable-mpi") + set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER}) + set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER}) + endif() + if(BUILD_OMP) + set(PLUMED_CONFIG_OMP "--enable-openmp") + else() + set(PLUMED_CONFIG_OMP "--disable-openmp") + endif() message(STATUS "PLUMED download requested - we will build our own") include(ExternalProject) ExternalProject_Add(plumed_build - URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz - URL_MD5 71ed465bdc7c2059e282dbda8d564e71 + URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz + URL_MD5 c2a7b519e32197a120cdf47e0f194f81 BUILD_IN_SOURCE 1 CONFIGURE_COMMAND /configure --prefix= ${CONFIGURE_REQUEST_PIC} - --enable-modules=all - CXX=${CMAKE_MPI_CXX_COMPILER} - CC=${CMAKE_MPI_C_COMPILER} + --enable-modules=all + ${PLUMED_CONFIG_MPI} + ${PLUMED_CONFIG_OMP} + CXX=${PLUMED_CONFIG_CXX} + CC=${PLUMED_CONFIG_CC} ) ExternalProject_get_property(plumed_build INSTALL_DIR) set(PLUMED_INSTALL_DIR ${INSTALL_DIR}) list(APPEND LAMMPS_DEPS plumed_build) if(PLUMED_MODE STREQUAL "STATIC") add_definitions(-D__PLUMED_WRAPPER_CXX=1) - list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o - "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS}) + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS}) elseif(PLUMED_MODE STREQUAL "SHARED") - list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS}) + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS}) elseif(PLUMED_MODE STREQUAL "RUNTIME") add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so) list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS}) @@ -588,7 +644,7 @@ if(PKG_USER-PLUMED) set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include") else() find_package(PkgConfig REQUIRED) - pkg_check_modules(PLUMED plumed REQUIRED) + pkg_check_modules(PLUMED REQUIRED plumed) if(PLUMED_MODE STREQUAL "STATIC") add_definitions(-D__PLUMED_WRAPPER_CXX=1) include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static) @@ -607,7 +663,10 @@ if(PKG_USER-MOLFILE) set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers") add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS}) - target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) + # no need to link with -ldl on windows + if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) + endif() list(APPEND LAMMPS_LINK_LIBS molfile) endif() @@ -619,7 +678,13 @@ if(PKG_USER-NETCDF) endif() if(PKG_USER-SMD) - option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF) + find_package(Eigen3 NO_MODULE) + if(EIGEN3_FOUND) + set(DOWNLOAD_EIGEN3_DEFAULT OFF) + else() + set(DOWNLOAD_EIGEN3_DEFAULT ON) + endif() + option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT}) if(DOWNLOAD_EIGEN3) message(STATUS "Eigen3 download requested - we will build our own") include(ExternalProject) @@ -667,7 +732,13 @@ if(PKG_KIM) list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES}) add_definitions(-DLMP_KIM_CURL) endif() - option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" OFF) + find_package(KIM-API QUIET) + if(KIM-API_FOUND) + set(DOWNLOAD_KIM_DEFAULT OFF) + else() + set(DOWNLOAD_KIM_DEFAULT ON) + endif() + option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT}) if(DOWNLOAD_KIM) message(STATUS "KIM-API download requested - we will build our own") enable_language(C) @@ -688,10 +759,7 @@ if(PKG_KIM) set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}) list(APPEND LAMMPS_DEPS kim_build) else() - find_package(KIM-API) - if(NOT KIM-API_FOUND) - message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it") - endif() + find_package(KIM-API REQUIRED) endif() list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}") include_directories(${KIM-API_INCLUDE_DIRS}) @@ -709,6 +777,7 @@ if(PKG_MESSAGE) set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi") else() target_compile_definitions(cslib PRIVATE -DMPI_NO) + target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI) set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi") endif() @@ -728,7 +797,13 @@ endif() if(PKG_MSCG) find_package(GSL REQUIRED) - option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF) + find_package(MSCG QUIET) + if(MSGC_FOUND) + set(DOWNLOAD_MSCG_DEFAULT OFF) + else() + set(DOWNLOAD_MSCG_DEFAULT ON) + endif() + option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT}) if(DOWNLOAD_MSCG) if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7") @@ -777,7 +852,6 @@ endif() ######################################################################## # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## -include(CheckIncludeFileCXX) foreach(HEADER cmath) check_include_file_cxx(${HEADER} FOUND_${HEADER}) if(NOT FOUND_${HEADER}) @@ -825,6 +899,8 @@ foreach(PKG ${DEFAULT_PACKAGES}) list(APPEND LIB_SOURCES ${${PKG}_SOURCES}) include_directories(${${PKG}_SOURCES_DIR}) endif() + + RegisterPackages(${${PKG}_SOURCES_DIR}) endforeach() # packages that need defines set @@ -843,6 +919,8 @@ foreach(PKG ${ACCEL_PACKAGES}) # check for package files in src directory due to old make system DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) + + RegisterPackages(${${PKG}_SOURCES_DIR}) endforeach() ############################################## @@ -891,7 +969,6 @@ if(PKG_USER-H5MD) include_directories(${HDF5_INCLUDE_DIRS}) endif() - ###################################################################### # packages which selectively include variants based on enabled styles # e.g. accelerator packages @@ -944,7 +1021,7 @@ if(PKG_USER-OMP) # detects styles which have USER-OMP version RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) - RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h") + RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h) get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) @@ -1057,37 +1134,82 @@ if(PKG_OPT) endif() if(PKG_USER-INTEL) - find_package(TBB REQUIRED) - find_package(MKL REQUIRED) + include(CheckIncludeFile) + check_include_file(immintrin.h FOUND_IMMINTRIN) + if(NOT FOUND_IMMINTRIN) + message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it") + endif() - if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler") - endif() + add_definitions(-DLMP_USER_INTEL) - if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) - message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") - endif() + set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") + set(INTEL_ARCH_VALUES cpu knl) + set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES}) + validate_option(INTEL_ARCH INTEL_ARCH_VALUES) + string(TOUPPER ${INTEL_ARCH} INTEL_ARCH) - if(NOT BUILD_OMP) - message(FATAL_ERROR "USER-INTEL requires OpenMP") - endif() - - if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64") - message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64") - endif() - - set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") - set(INTEL_ARCH_VALUES cpu knl) - set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES}) - validate_option(INTEL_ARCH INTEL_ARCH_VALUES) - string(TOUPPER ${INTEL_ARCH} INTEL_ARCH) - - if(INTEL_ARCH STREQUAL "KNL") - set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload") - set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"") - add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS}) - add_definitions(-DLMP_INTEL_OFFLOAD) + find_package(Threads QUIET) + if(Threads_FOUND) + set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)") + else() + set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)") + endif() + set(INTEL_LRT_VALUES none threads c++11) + set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES}) + validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES) + string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE) + if(INTEL_LRT_MODE STREQUAL "THREADS") + if(Threads_FOUND) + add_definitions(-DLMP_INTEL_USELRT) + list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT}) else() + message(FATAL_ERROR "Must have working threads library for Long-range thread support") + endif() + endif() + if(INTEL_LRT_MODE STREQUAL "C++11") + add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11) + endif() + + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) + message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") + endif() + else() + message(WARNING "USER-INTEL gives best performance with Intel compilers") + endif() + + find_package(TBB QUIET) + if(TBB_FOUND) + list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES}) + else() + add_definitions(-DLMP_INTEL_NO_TBB) + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries") + endif() + endif() + + find_package(MKL QUIET) + if(MKL_FOUND) + add_definitions(-DLMP_USE_MKL_RNG) + list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES}) + else() + message(STATUS "Pair style dpd/intel will be faster with MKL libraries") + endif() + + if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256")) + message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform") + endif() + + if(INTEL_ARCH STREQUAL "KNL") + if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture") + endif() + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload") + set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"") + add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS}) + add_definitions(-DLMP_INTEL_OFFLOAD) + else() + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512") else() @@ -1100,33 +1222,35 @@ if(PKG_USER-INTEL) add_compile_options(${_FLAG}) endif() endforeach() + else() + add_compile_options(-O3 -ffast-math) endif() + endif() - add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG) + # collect sources + set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL) + set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp + ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp + ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp + ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp + ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp) - list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES}) + set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}") - 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 - ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp - ${USER-INTEL_SOURCES_DIR}/math_extra_intel.h - ${USER-INTEL_SOURCES_DIR}/nbin_intel.h - ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp - ${USER-INTEL_SOURCES_DIR}/npair_intel.h - ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp - ${USER-INTEL_SOURCES_DIR}/intel_simd.h - ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h) + # detect styles which have a USER-INTEL version + RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES) + RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h) + RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h) + RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h) - set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}") + get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES) + if(PKG_KSPACE) + list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) + RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h) + endif() - # detects styles which have USER-INTEL version - RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES) - - get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES) - - list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES}) - include_directories(${USER-INTEL_SOURCES_DIR}) + list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES}) + include_directories(${USER-INTEL_SOURCES_DIR}) endif() if(PKG_GPU) @@ -1168,6 +1292,10 @@ if(PKG_GPU) message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.") endif() option(CUDPP_OPT "Enable CUDPP_OPT" ON) + option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF) + if(CUDA_MPS_SUPPORT) + set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY") + endif() set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)") @@ -1231,7 +1359,7 @@ if(PKG_GPU) add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS}) target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY}) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS}) - target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT) + target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS}) if(CUDPP_OPT) target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) target_compile_definitions(gpu PRIVATE -DUSE_CUDPP) @@ -1257,7 +1385,15 @@ if(PKG_GPU) set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h) file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu) - list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu) + list(REMOVE_ITEM GPU_LIB_CU + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu + ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu + ) foreach(GPU_KERNEL ${GPU_LIB_CU}) get_filename_component(basename ${GPU_KERNEL} NAME_WE) @@ -1268,7 +1404,21 @@ if(PKG_GPU) GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu) GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu) - list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h) + GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu) + GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu) + GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu) + GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu) + GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu) + + list(APPEND GPU_LIB_SOURCES + ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h + ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h + ) add_library(gpu STATIC ${GPU_LIB_SOURCES}) target_link_libraries(gpu ${OpenCL_LIBRARIES}) @@ -1301,10 +1451,12 @@ endif() ###################################################### # Generate style headers based on global list of # styles registered during package selection +# Generate packages headers from all packages ###################################################### set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles) GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR}) +GeneratePackagesHeaders(${LAMMPS_STYLE_HEADERS_DIR}) include_directories(${LAMMPS_STYLE_HEADERS_DIR}) @@ -1313,7 +1465,7 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR}) ###################################### set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n") set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n") -set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) +set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) list(SORT temp_PKG_LIST) foreach(PKG ${temp_PKG_LIST}) if(PKG_${PKG}) @@ -1381,8 +1533,16 @@ if(BUILD_EXE) if(ENABLE_TESTING) add_test(ShowHelp ${LAMMPS_BINARY} -help) endif() -endif() + enable_language(C) + get_filename_component(MSI2LMP_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools/msi2lmp/src ABSOLUTE) + file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c) + add_executable(msi2lmp ${MSI2LMP_SOURCES}) + target_link_libraries(msi2lmp m) + install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) + install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) + +endif() ############################################################################### # Build documentation @@ -1445,11 +1605,14 @@ if(BUILD_DOC) endif() ############################################################################### -# Install potential files in data directory +# Install potential and force field files in data directory ############################################################################### set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR}) +set(LAMMPS_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files) +install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../tools/msi2lmp/frc_files/ DESTINATION ${LAMMPS_FRC_FILES_DIR}) + 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( @@ -1533,7 +1696,7 @@ endif() ############################################################################### # Print package summary ############################################################################### -foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) if(PKG_${PKG}) message(STATUS "Building package: ${PKG}") endif() diff --git a/cmake/Modules/FindKIM-API.cmake.in b/cmake/Modules/FindKIM-API.cmake similarity index 74% rename from cmake/Modules/FindKIM-API.cmake.in rename to cmake/Modules/FindKIM-API.cmake index d9397b9aba..5108b0f98c 100644 --- a/cmake/Modules/FindKIM-API.cmake.in +++ b/cmake/Modules/FindKIM-API.cmake @@ -36,14 +36,23 @@ # KIM-API-CMAKE_CXX_COMPILER # KIM-API-CMAKE_Fortran_COMPILER # -find_package(PkgConfig REQUIRED) + +if(KIM-API_FIND_QUIETLY) + set(REQ_OR_QUI "QUIET") +else() + set(REQ_OR_QUI "REQUIRED") +endif() + +find_package(PkgConfig ${REQ_OR_QUI}) include(FindPackageHandleStandardArgs) -pkg_check_modules(KIM-API REQUIRED libkim-api>=2.0) +pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0) -pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER) -pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER) -pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER) +if(KIM-API_FOUND) + pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER) + pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER) + pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER) +endif() # handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE # if all listed variables are TRUE diff --git a/cmake/Modules/OpenCLUtils.cmake b/cmake/Modules/OpenCLUtils.cmake index 5c147a685c..a9441ce518 100644 --- a/cmake/Modules/OpenCLUtils.cmake +++ b/cmake/Modules/OpenCLUtils.cmake @@ -6,7 +6,7 @@ function(GenerateOpenCLHeader varname outfile files) foreach(IDX RANGE 2 ${ARG_END}) list(GET ARGV ${IDX} filename) file(READ ${filename} content) - string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}") + string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}") string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}") string(REGEX REPLACE "\"" "\\\\\"" content "${content}") string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}") diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index a7b23b4cf1..04883d0292 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -91,6 +91,10 @@ function(RegisterFixStyle path) AddStyleHeader(${path} FIX) endfunction(RegisterFixStyle) +function(RegisterIntegrateStyle path) + AddStyleHeader(${path} INTEGRATE) +endfunction(RegisterIntegrateStyle) + function(RegisterStyles search_path) FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid @@ -177,3 +181,88 @@ function(DetectBuildSystemConflict lammps_src_dir) endforeach() endif() endfunction(DetectBuildSystemConflict) + + +function(FindPackagesHeaders path style_class file_pattern headers) + file(GLOB files "${path}/${file_pattern}*.h") + get_property(plist GLOBAL PROPERTY ${headers}) + + foreach(file_name ${files}) + file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class}) + if(is_style) + list(APPEND plist ${file_name}) + endif() + endforeach() + set_property(GLOBAL PROPERTY ${headers} "${plist}") +endfunction(FindPackagesHeaders) + +function(RegisterPackages search_path) + FindPackagesHeaders(${search_path} ANGLE_CLASS angle_ PKGANGLE ) # angle ) # force + FindPackagesHeaders(${search_path} ATOM_CLASS atom_vec_ PKGATOM_VEC ) # atom ) # atom atom_vec_hybrid + FindPackagesHeaders(${search_path} BODY_CLASS body_ PKGBODY ) # body ) # atom_vec_body + FindPackagesHeaders(${search_path} BOND_CLASS bond_ PKGBOND ) # bond ) # force + FindPackagesHeaders(${search_path} COMMAND_CLASS "[^.]" PKGCOMMAND ) # command ) # input + FindPackagesHeaders(${search_path} COMPUTE_CLASS compute_ PKGCOMPUTE ) # compute ) # modify + FindPackagesHeaders(${search_path} DIHEDRAL_CLASS dihedral_ PKGDIHEDRAL ) # dihedral ) # force + FindPackagesHeaders(${search_path} DUMP_CLASS dump_ PKGDUMP ) # dump ) # output write_dump + FindPackagesHeaders(${search_path} FIX_CLASS fix_ PKGFIX ) # fix ) # modify + FindPackagesHeaders(${search_path} IMPROPER_CLASS improper_ PKGIMPROPER ) # improper ) # force + FindPackagesHeaders(${search_path} INTEGRATE_CLASS "[^.]" PKGINTEGRATE ) # integrate ) # update + FindPackagesHeaders(${search_path} KSPACE_CLASS "[^.]" PKGKSPACE ) # kspace ) # force + FindPackagesHeaders(${search_path} MINIMIZE_CLASS min_ PKGMINIMIZE ) # minimize ) # update + FindPackagesHeaders(${search_path} NBIN_CLASS nbin_ PKGNBIN ) # nbin ) # neighbor + FindPackagesHeaders(${search_path} NPAIR_CLASS npair_ PKGNPAIR ) # npair ) # neighbor + FindPackagesHeaders(${search_path} NSTENCIL_CLASS nstencil_ PKGNSTENCIL ) # nstencil ) # neighbor + FindPackagesHeaders(${search_path} NTOPO_CLASS ntopo_ PKGNTOPO ) # ntopo ) # neighbor + FindPackagesHeaders(${search_path} PAIR_CLASS pair_ PKGPAIR ) # pair ) # force + FindPackagesHeaders(${search_path} READER_CLASS reader_ PKGREADER ) # reader ) # read_dump + FindPackagesHeaders(${search_path} REGION_CLASS region_ PKGREGION ) # region ) # domain +endfunction(RegisterPackages) + +function(CreatePackagesHeader path filename) + set(temp "") + if(ARGC GREATER 2) + list(REMOVE_AT ARGV 0 1) + foreach(FNAME ${ARGV}) + set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}") + get_filename_component(DNAME ${FNAME} DIRECTORY) + get_filename_component(DNAME ${DNAME} NAME) + get_filename_component(FNAME ${FNAME} NAME) + set(temp "${temp}#undef PACKAGE\n#define PACKAGE \"${DNAME}\"\n") + set(temp "${temp}#include \"${DNAME}/${FNAME}\"\n") + endforeach() + endif() + message(STATUS "Generating ${filename}...") + file(WRITE "${path}/${filename}.tmp" "${temp}" ) + execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}") + set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}") +endfunction(CreatePackagesHeader) + +function(GeneratePackagesHeader path property style) + get_property(files GLOBAL PROPERTY ${property}) + CreatePackagesHeader("${path}" "packages_${style}.h" ${files}) +endfunction(GeneratePackagesHeader) + +function(GeneratePackagesHeaders output_path) + GeneratePackagesHeader(${output_path} PKGANGLE angle ) # force + GeneratePackagesHeader(${output_path} PKGATOM_VEC atom ) # atom atom_vec_hybrid + GeneratePackagesHeader(${output_path} PKGBODY body ) # atom_vec_body + GeneratePackagesHeader(${output_path} PKGBOND bond ) # force + GeneratePackagesHeader(${output_path} PKGCOMMAND command ) # input + GeneratePackagesHeader(${output_path} PKGCOMPUTE compute ) # modify + GeneratePackagesHeader(${output_path} PKGDIHEDRAL dihedral ) # force + GeneratePackagesHeader(${output_path} PKGDUMP dump ) # output write_dump + GeneratePackagesHeader(${output_path} PKGFIX fix ) # modify + GeneratePackagesHeader(${output_path} PKGIMPROPER improper ) # force + GeneratePackagesHeader(${output_path} PKGINTEGRATE integrate ) # update + GeneratePackagesHeader(${output_path} PKGKSPACE kspace ) # force + GeneratePackagesHeader(${output_path} PKGMINIMIZE minimize ) # update + GeneratePackagesHeader(${output_path} PKGNBIN nbin ) # neighbor + GeneratePackagesHeader(${output_path} PKGNPAIR npair ) # neighbor + GeneratePackagesHeader(${output_path} PKGNSTENCIL nstencil ) # neighbor + GeneratePackagesHeader(${output_path} PKGNTOPO ntopo ) # neighbor + GeneratePackagesHeader(${output_path} PKGPAIR pair ) # force + GeneratePackagesHeader(${output_path} PKGREADER reader ) # read_dump + GeneratePackagesHeader(${output_path} PKGREGION region ) # domain +endfunction(GeneratePackagesHeaders) + diff --git a/cmake/README.md b/cmake/README.md index ce3b4502af..c11326f9d5 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -155,11 +155,13 @@ make 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 +`make yes-std` or `make no-lib`. Achieving a similar 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. +way. Since the cmake build process - contrary to the conventional build system - +includes the compilation of the bundled libraries into the standard build process, +the grouping of those presets is somewhat different. 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 @@ -171,10 +173,10 @@ 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 +# build LAMMPS with all packages enabled which don't use external libraries and enable GPU package mkdir build cd build -cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake +cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on ../cmake ``` # Reference @@ -209,7 +211,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake - + CMAKE_VERBOSE_MAKEFILE Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.
@@ -1429,6 +1431,17 @@ TODO
+ + INTEL_LRT_MODE + How to support Long-range thread mode in Verlet integration + +
+
threads (default, if pthreads available)
+
none (default, if pthreads not available)
+
c++11
+
+ + @@ -1503,6 +1516,16 @@ target API. + + CUDA_MPS_SUPPORT (CUDA only) + Enable tweaks for running with Nvidia CUDA Multi-process services daemon + +
+
on
+
off (default)
+
+ + BIN2C (CUDA only) Path to bin2c executable, will automatically pick up the first one in your $PATH. diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in index def49bf75c..42f222d67c 100644 --- a/cmake/etc/profile.d/lammps.csh.in +++ b/cmake/etc/profile.d/lammps.csh.in @@ -1,2 +1,4 @@ -# set environment for LAMMPS executables to find potential files +# set environment for LAMMPS and msi2lmp executables +# to find potential and force field files if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ +if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@ diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in index acd75fa0cf..c1967cb5b2 100644 --- a/cmake/etc/profile.d/lammps.sh.in +++ b/cmake/etc/profile.d/lammps.sh.in @@ -1,2 +1,5 @@ -# set environment for LAMMPS executables to find potential files -export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} +# set environment for LAMMPS and msi2lmp executables +# to find potential and force field files +LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} +MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@} +export LAMMPS_POTENTIALS MSI2LMP_LIBRARY diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index b434796d7c..9d03be99ec 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -1,21 +1,17 @@ -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) +# preset that turns on all existing packages off. can be used to reset +# an existing package selection without losing any other settings -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-SDPD 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-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) +set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE + MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 3a1100f337..2ff107975a 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -1,21 +1,19 @@ -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) +# preset that turns on all existing packages. using the combination +# this preset followed by the nolib.cmake preset should configure a +# LAMMPS binary, with as many packages included, that can be compiled +# with just a working C++ compiler and an MPI library. -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-SDPD 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-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) +set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE + MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/clang.cmake b/cmake/presets/clang.cmake new file mode 100644 index 0000000000..828f359f54 --- /dev/null +++ b/cmake/presets/clang.cmake @@ -0,0 +1,17 @@ +# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes) + +set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE) +set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE) +set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE) +set(MPI_CXX "clang++" CACHE STRING "" FORCE) +set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE) +unset(HAVE_OMP_H_INCLUDE CACHE) + +set(OpenMP_C "clang" CACHE STRING "" FORCE) +set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE) +set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE) +set(OpenMP_CXX "clang++" CACHE STRING "" FORCE) +set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE) +set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE) +set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" FORCE) + diff --git a/cmake/presets/manual_selection.cmake b/cmake/presets/manual_selection.cmake deleted file mode 100644 index 6db41b708c..0000000000 --- a/cmake/presets/manual_selection.cmake +++ /dev/null @@ -1,71 +0,0 @@ -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-PHONON OFF CACHE BOOL "" FORCE) -set(PKG_USER-PLUMED 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-SDPD 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/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake new file mode 100644 index 0000000000..b53e5a7b93 --- /dev/null +++ b/cmake/presets/mingw-cross.cmake @@ -0,0 +1,17 @@ +set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ + REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD + USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION + USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD + USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP + USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD + USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF) + +foreach(PKG ${WIN_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() + +set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) +set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE) +set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE) +set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE) diff --git a/cmake/presets/minimal.cmake b/cmake/presets/minimal.cmake new file mode 100644 index 0000000000..e9ce6d6103 --- /dev/null +++ b/cmake/presets/minimal.cmake @@ -0,0 +1,8 @@ +# preset that turns on just a few, frequently used packages +# this will be compiled quickly and handle a lot of common inputs. + +set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake new file mode 100644 index 0000000000..35ad7ba55c --- /dev/null +++ b/cmake/presets/most.cmake @@ -0,0 +1,15 @@ +# preset that turns on a wide range of packages, some of which require +# external libraries. Compared to all_on.cmake some more unusual packages +# are removed. The resulting binary should be able to run most inputs. + +set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE + GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI + PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI + USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD + USER-DRUDE USER-FEP USER-MEAMC USER-MESO + USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC + USER-SPH USER-SMD USER-UEF USER-YAFF) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 4c02fb6210..c0968a8d82 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -1,21 +1,10 @@ -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) +# preset that turns off all packages that require some form of external +# library or special compiler (fortran or cuda) or equivalent. -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-SDPD 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-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON + VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB + USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP + USER-SCAFACOS USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/std.cmake b/cmake/presets/std.cmake deleted file mode 100644 index 4176aba44e..0000000000 --- a/cmake/presets/std.cmake +++ /dev/null @@ -1,22 +0,0 @@ -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-SDPD 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 deleted file mode 100644 index aa067f2ba0..0000000000 --- a/cmake/presets/std_nolib.cmake +++ /dev/null @@ -1,26 +0,0 @@ -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-SDPD 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 deleted file mode 100644 index af606203e9..0000000000 --- a/cmake/presets/user.cmake +++ /dev/null @@ -1,22 +0,0 @@ -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-SDPD 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-PLUMED 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/lammps.1 b/doc/lammps.1 index d49650bfaa..f4a801779a 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,40 +1,259 @@ -.TH LAMMPS "2018-08-22" +.TH LAMMPS "5 June 2019" "2019-06-05" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. .SH SYNOPSIS -.B lmp --in in.file +.B lmp +\-in [OPTIONS] ... or -mpirun \-np 2 -.B lmp --in in.file +mpirun \-np 2 +.B lmp + [OPTIONS] ... + +or + +.B lmp +\-r2data file.restart file.data .SH DESCRIPTION -.B LAMMPS -LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale -Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft -materials (biomolecules, polymers) and solid-state materials (metals, -semiconductors) and coarse-grained or mesoscopic systems. It can be used to -model atoms or, more generically, as a parallel particle simulator at the +.B LAMMPS +is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale +\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator. +.B LAMMPS +has potentials for soft +materials (bio-molecules, polymers) and solid-state materials (metals, +semiconductors) and coarse-grained or mesoscopic systems. It can be used to +model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. -See http://lammps.sandia.gov/ for documentation. +See https://lammps.sandia.gov/ for more information and documentation. + +.SH EXECUTABLE NAME +The +.B LAMMPS +executable can have different names depending on how it was configured, +compiled and installed. It will be either +.B lmp +or +.B lmp_. +The suffix corresponds to the (machine specific) makefile +used to compile +.B LAMMPS +when using the conventional build process. When building +.B LAMMPS +using +.B CMake +this parameter can be chosen arbitrarily at configuration +time, but more common is to just use +.B lmp +without a suffix. In this manpage we will use +.B lmp +to represent any of those names. .SH OPTIONS -See https://lammps.sandia.gov/doc/Run_options.html for details on -command-line options. -.SH COPYRIGHT -© 2003--2018 Sandia Corporation +.TP +\fB\-h\fR or \fB\-help\fR +Print a brief help summary and a list of settings and options compiled +into this executable. It also explicitly lists all LAMMPS styles +(atom_style, fix, compute, pair_style, bond_style, etc) available in +the specific executable. This can tell you if the command you want to +use was included via the appropriate package at compile time. +LAMMPS will print the info and immediately exit if this switch is used. +.TP +\fB\-e\fR or \fB\-echo\fR +Set the style of command echoing. The style can be +.B none +or +.B screen +or +.B log +or +.B both. +Depending on the style, each command read from the input script will +be echoed to the screen and/or logfile. This can be useful to figure +out which line of your script is causing an input error. +The default value is +.B log. +.TP +\fB\-i \fR or \fB\-in \fR +Specify a file to use as an input script. If it is not specified, +LAMMPS reads its script from standard input. This is a required +switch when running LAMMPS in multi-partition mode. +.TP +\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR +Enable or disable general KOKKOS support, as provided by the KOKKOS +package. Even if LAMMPS is built with this package, this switch must +be set to \fBon\fR to enable running with KOKKOS-enabled styles. More +details on this switch and its optional keyword value pairs are discussed +at: https://lammps.sandia.gov/doc/Run_options.html +.TP +\fB\-l \fR or \fB\-log \fR +Specify a log file for LAMMPS to write status information to. +The default value is "log.lammps". If the file name "none" is used, +\fBLAMMPS\fR will not write a log file. In multi-partition mode only +some high-level all-partition information is written to the "" +file, the remainder is written in a per-partition file ".N" +with "N" being the respective partition number, unless overridden +by the \-plog flag (see below). +.TP +\fB\-m \fR or \fB\-mpicolor \fR +If used, this must be the first command-line argument after the +.B LAMMPS +executable name. It is only used when +.B LAMMPS +is launched by an mpirun command which also launches one or more +other executable(s) at the same time. +.B LAMMPS +and the other executable(s) perform an MPI_Comm_split(), each with +their own different colors, to split the MPI_COMM_WORLD communicator +for each executable to the subset of processors they are supposed to +be actually running on. Currently, this is only used in +.B LAMMPS +to perform client/server messaging with another application. +.B LAMMPS +can act as either a client or server (or both). +.TP +\fB\-nc\fR or \fB\-nocite\fR +Disable writing the "log.cite" file which is normally written to +list references for specific cite-able features used during a +.B LAMMPS +run. +.TP +\fB\-pk