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Merge branch 'develop' into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2023-08-09 00:43:29 -04:00
parent bddb19fda1 b6f7a27b09
commit b9afbf40a0
51 changed files with 806 additions and 304 deletions
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76
cmake/CMakeLists.txt
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@ -1,8 +1,9 @@
# -*- CMake -*- master configuration file for building LAMMPS
######################################## ########################################
# CMake build system # CMake build system
# This file is part of LAMMPS # This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger # Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.16)
######################################## ########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074) if(POLICY CMP0074)
@ -12,22 +13,11 @@ endif()
if(POLICY CMP0075) if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW) cmake_policy(SET CMP0075 NEW)
endif() endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW # set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135) if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD) cmake_policy(SET CMP0135 OLD)
endif() endif()
########################################
# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
if(CMAKE_VERSION VERSION_LESS 3.12)
unset(CONFIGURE_DEPENDS)
else()
set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
endif()
######################################## ########################################
project(lammps CXX) project(lammps CXX)
@ -203,8 +193,8 @@ else()
endif() endif()
include(GNUInstallDirs) include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp) file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES}) list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
add_library(lammps ${ALL_SOURCES}) add_library(lammps ${ALL_SOURCES})
@ -442,7 +432,7 @@ if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_T
find_package(BLAS) find_package(BLAS)
endif() endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG) if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp) file(GLOB LINALG_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
add_library(linalg STATIC ${LINALG_SOURCES}) add_library(linalg STATIC ${LINALG_SOURCES})
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE}) set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>") set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
@ -460,12 +450,7 @@ option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
if(WITH_JPEG) if(WITH_JPEG)
find_package(JPEG REQUIRED) find_package(JPEG REQUIRED)
target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG) target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG)
if(CMAKE_VERSION VERSION_LESS 3.12) target_link_libraries(lammps PRIVATE JPEG::JPEG)
target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE JPEG::JPEG)
endif()
endif() endif()
find_package(PNG QUIET) find_package(PNG QUIET)
@ -577,8 +562,8 @@ endforeach()
foreach(PKG ${STANDARD_PACKAGES}) foreach(PKG ${STANDARD_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp) file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h) file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system # check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -605,8 +590,8 @@ endforeach()
foreach(PKG ${SUFFIX_PACKAGES}) foreach(PKG ${SUFFIX_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp) file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h) file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system # check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -620,7 +605,7 @@ endforeach()
foreach(PKG_LIB POEMS ATC AWPMD H5MD) foreach(PKG_LIB POEMS ATC AWPMD H5MD)
if(PKG_${PKG_LIB}) if(PKG_${PKG_LIB})
string(TOLOWER "${PKG_LIB}" PKG_LIB) string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS} file(GLOB_RECURSE ${PKG_LIB}_SOURCES CONFIGURE_DEPENDS
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp) ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES}) add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE}) set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
@ -815,20 +800,11 @@ install(
# This is primarily for people that only want to use the Python wrapper. # This is primarily for people that only want to use the Python wrapper.
############################################################################### ###############################################################################
if(BUILD_SHARED_LIBS) if(BUILD_SHARED_LIBS)
if(CMAKE_VERSION VERSION_LESS 3.12) # backward compatibility
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake if(PYTHON_EXECUTABLE)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6) set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif() endif()
find_package(Python COMPONENTS Interpreter)
if(BUILD_IS_MULTI_CONFIG) if(BUILD_IS_MULTI_CONFIG)
set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>) set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
else() else()
@ -887,13 +863,23 @@ else()
endif() endif()
include(FeatureSummary) include(FeatureSummary)
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND) feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
OUTPUT_VARIABLE GIT_DESCRIBE
ERROR_QUIET
WORKING_DIRECTORY ${LAMMPS_DIR}
OUTPUT_STRIP_TRAILING_WHITESPACE)
endif()
message(STATUS "<<< Build configuration >>> message(STATUS "<<< Build configuration >>>
LAMMPS Version: ${PROJECT_VERSION} LAMMPS Version: ${PROJECT_VERSION} ${GIT_DESCRIBE}
Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION} Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
CMake Version: ${CMAKE_VERSION} CMake Version: ${CMAKE_VERSION}
Build type: ${LAMMPS_BUILD_TYPE} Build type: ${LAMMPS_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX} Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}") Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
if(CMAKE_CROSSCOMPILING)
message(STATUS "Cross compiling on ${CMAKE_HOST_SYSTEM}")
endif()
############################################################################### ###############################################################################
# Print package summary # Print package summary
############################################################################### ###############################################################################
@ -937,11 +923,9 @@ if(_index GREATER -1)
endif() endif()
message(STATUS "<<< Linker flags: >>>") message(STATUS "<<< Linker flags: >>>")
message(STATUS "Executable name: ${LAMMPS_BINARY}") message(STATUS "Executable name: ${LAMMPS_BINARY}")
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) get_target_property(OPTIONS lammps LINK_OPTIONS)
get_target_property(OPTIONS lammps LINK_OPTIONS) if(OPTIONS)
if(OPTIONS) message(STATUS "Linker options: ${OPTIONS}")
message(STATUS "Linker options: ${OPTIONS}")
endif()
endif() endif()
if(CMAKE_EXE_LINKER_FLAGS) if(CMAKE_EXE_LINKER_FLAGS)
message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}") message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")

18
cmake/Modules/CodingStandard.cmake
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@ -1,19 +1,11 @@
if(CMAKE_VERSION VERSION_LESS 3.12) # use default (or custom) Python executable, if version is sufficient
find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12 if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
if(PYTHONINTERP_FOUND) set(Python3_EXECUTABLE ${Python_EXECUTABLE})
set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
set(Python3_VERSION ${PYTHON_VERSION_STRING})
endif()
else()
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.5)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 COMPONENTS Interpreter QUIET)
endif() endif()
find_package(Python3 COMPONENTS Interpreter)
if(Python3_EXECUTABLE) if(Python3_EXECUTABLE)
if(Python3_VERSION VERSION_GREATER_EQUAL 3.5) if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
add_custom_target( add_custom_target(
check-whitespace check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py . ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .

28
cmake/Modules/Documentation.cmake
View File

@ -5,24 +5,18 @@ option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC) if(BUILD_DOC)
# Current Sphinx versions require at least Python 3.8 # Current Sphinx versions require at least Python 3.8
if(CMAKE_VERSION VERSION_LESS 3.12) # use default (or custom) Python executable, if version is sufficient
find_package(PythonInterp 3.8 REQUIRED) if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv) set(Python3_EXECUTABLE ${Python_EXECUTABLE})
else()
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.8)
message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
endif() endif()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.8)
message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
find_package(Doxygen 1.8.10 REQUIRED) find_package(Doxygen 1.8.10 REQUIRED)
file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
add_custom_command( add_custom_command(
OUTPUT docenv OUTPUT docenv
@ -80,7 +74,7 @@ if(BUILD_DOC)
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz") message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif() endif()
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*) file(GLOB MATHJAX_VERSION_DIR CONFIGURE_DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax) execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
endif() endif()

10
cmake/Modules/FindCythonize.cmake
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@ -7,15 +7,7 @@
# adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake # adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
#============================================================================= #=============================================================================
if(CMAKE_VERSION VERSION_LESS 3.12) find_package(Python 3.6 COMPONENTS Interpreter QUIET)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python 3.6 COMPONENTS Interpreter QUIET)
endif()
# Use the Cython executable that lives next to the Python executable # Use the Cython executable that lives next to the Python executable
# if it is a local installation. # if it is a local installation.

2
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -63,7 +63,7 @@ endfunction(validate_option)
# helper function for getting the most recently modified file or folder from a glob pattern # helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable) function(get_newest_file path variable)
file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path}) file(GLOB _dirs CONFIGURE_DEPENDS ${path})
set(_besttime 2000-01-01T00:00:00) set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>") set(_bestfile "<unknown>")
foreach(_dir ${_dirs}) foreach(_dir ${_dirs})

6
cmake/Modules/LAMMPSUtils.cmake
View File

@ -41,7 +41,7 @@ endfunction()
# helper function for getting the most recently modified file or folder from a glob pattern # helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable) function(get_newest_file path variable)
file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path}) file(GLOB _dirs CONFIGURE_DEPENDS ${path})
set(_besttime 2000-01-01T00:00:00) set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>") set(_bestfile "<unknown>")
foreach(_dir ${_dirs}) foreach(_dir ${_dirs})
@ -80,8 +80,8 @@ endfunction()
function(check_for_autogen_files source_dir) function(check_for_autogen_files source_dir)
message(STATUS "Running check for auto-generated files from make-based build system") message(STATUS "Running check for auto-generated files from make-based build system")
file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h) file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h) file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h) list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp) list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
foreach(_SRC ${SRC_AUTOGEN_FILES}) foreach(_SRC ${SRC_AUTOGEN_FILES})

2
cmake/Modules/Packages/COLVARS.cmake
View File

@ -1,6 +1,6 @@
set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars) set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp) file(GLOB COLVARS_SOURCES CONFIGURE_DEPENDS ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF) option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)

14
cmake/Modules/Packages/GPU.cmake
View File

@ -39,7 +39,7 @@ if (PKG_AMOEBA)
${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp) ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
endif() endif()
file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp) file(GLOB GPU_LIB_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu) file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA") if(GPU_API STREQUAL "CUDA")
@ -70,7 +70,7 @@ if(GPU_API STREQUAL "CUDA")
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)") set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h) file(GLOB GPU_LIB_OLD_CUBIN_HEADERS CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if(GPU_LIB_OLD_CUBIN_HEADERS) if(GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n" message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n" "Found file(s) generated by the make-based build system in lib/gpu\n"
@ -80,15 +80,15 @@ if(GPU_API STREQUAL "CUDA")
"########################################################################") "########################################################################")
endif() endif()
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu) file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${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) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu) cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT) if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini) cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp) file(GLOB GPU_LIB_CUDPP_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu) file(GLOB GPU_LIB_CUDPP_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif() endif()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
@ -205,7 +205,7 @@ elseif(GPU_API STREQUAL "OPENCL")
include(OpenCLUtils) include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h) 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 ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu) file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU list(REMOVE_ITEM GPU_LIB_CU
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@ -335,7 +335,7 @@ elseif(GPU_API STREQUAL "HIP")
endif() endif()
endif() endif()
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu) file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${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) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
set(GPU_LIB_CU_HIP "") set(GPU_LIB_CU_HIP "")

7
cmake/Modules/Packages/KIM.cmake
View File

@ -1,12 +1,7 @@
set(KIM-API_MIN_VERSION 2.1.3) set(KIM-API_MIN_VERSION 2.1.3)
find_package(CURL) find_package(CURL)
if(CURL_FOUND) if(CURL_FOUND)
if(CMAKE_VERSION VERSION_LESS 3.12) target_link_libraries(lammps PRIVATE CURL::libcurl)
target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE CURL::libcurl)
endif()
target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL) target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.") set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
mark_as_advanced(LMP_DEBUG_CURL) mark_as_advanced(LMP_DEBUG_CURL)

2
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -156,7 +156,7 @@ if(PKG_ML-IAP)
# Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included # Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included
if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE) if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx) file(GLOB MLIAP_KOKKOS_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC}) foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE) get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h

4
cmake/Modules/Packages/LEPTON.cmake
View File

@ -4,7 +4,7 @@ if(LEPTON_SOURCE_DIR)
endif() endif()
set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton) set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp) file(GLOB LEPTON_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
@ -15,7 +15,7 @@ else()
endif() endif()
if(LEPTON_ENABLE_JIT) if(LEPTON_ENABLE_JIT)
file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp) file(GLOB ASMJIT_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
endif() endif()
add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES}) add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})

34
cmake/Modules/Packages/MDI.cmake
View File

@ -26,29 +26,9 @@ if(DOWNLOAD_MDI)
# detect if we have python development support and thus can enable python plugins # detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF) set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12) find_package(Python QUIET COMPONENTS Development)
if(NOT PYTHON_VERSION_STRING) if(Python_Development_FOUND)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6) set(MDI_USE_PYTHON_PLUGINS ON)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()
find_package(Python QUIET COMPONENTS Development)
if(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif() endif()
# python plugins are not supported and thus must be always off on Windows # python plugins are not supported and thus must be always off on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows") if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
@ -102,13 +82,9 @@ if(DOWNLOAD_MDI)
# if compiling with python plugins we need # if compiling with python plugins we need
# to add python libraries as dependency. # to add python libraries as dependency.
if(MDI_USE_PYTHON_PLUGINS) if(MDI_USE_PYTHON_PLUGINS)
if(CMAKE_VERSION VERSION_LESS 3.12) list(APPEND MDI_DEP_LIBS Python::Python)
list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
else()
list(APPEND MDI_DEP_LIBS Python::Python)
endif()
endif() endif()
# need to add support for dlopen/dlsym, except when compiling for Windows. # need to add support for dlopen/dlsym, except when compiling for Windows.
if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows")) if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}") list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")

23
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -2,12 +2,7 @@
set(MLIAP_ENABLE_PYTHON_DEFAULT OFF) set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
if(PKG_PYTHON) if(PKG_PYTHON)
find_package(Cythonize QUIET) find_package(Cythonize QUIET)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14) find_package(Python COMPONENTS NumPy QUIET)
find_package(Python COMPONENTS NumPy QUIET)
else()
# assume we have NumPy
set(Python_NumPy_FOUND ON)
endif()
if(Cythonize_FOUND AND Python_NumPy_FOUND) if(Cythonize_FOUND AND Python_NumPy_FOUND)
set(MLIAP_ENABLE_PYTHON_DEFAULT ON) set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
endif() endif()
@ -17,24 +12,16 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
if(MLIAP_ENABLE_PYTHON) if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED) find_package(Cythonize REQUIRED)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14) find_package(Python COMPONENTS NumPy REQUIRED)
find_package(Python COMPONENTS NumPy REQUIRED)
endif()
if(NOT PKG_PYTHON) if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP") message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif() endif()
if(CMAKE_VERSION VERSION_LESS 3.12) if(Python_VERSION VERSION_LESS 3.6)
if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6) message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
else()
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
endif() endif()
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython) set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx) file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR}) file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC}) foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE) get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)

34
cmake/Modules/Packages/PYTHON.cmake
View File

@ -1,29 +1,11 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING) if(NOT Python_INTERPRETER)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6) # backward compatibility
# search for interpreter first, so we have a consistent library if(PYTHON_EXECUTABLE)
find_package(PythonInterp) # Deprecated since version 3.12 set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif() endif()
# search for the library matching the selected interpreter find_package(Python COMPONENTS Interpreter)
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
else()
if(NOT Python_INTERPRETER)
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
endif() endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
target_compile_definitions(lammps PRIVATE -DLMP_PYTHON) target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

4
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -1,5 +1,5 @@
function(FindStyleHeaders path style_class file_pattern headers) function(FindStyleHeaders path style_class file_pattern headers)
file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h") file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
get_property(hlist GLOBAL PROPERTY ${headers}) get_property(hlist GLOBAL PROPERTY ${headers})
foreach(file_name ${files}) foreach(file_name ${files})
@ -187,7 +187,7 @@ endfunction(DetectBuildSystemConflict)
function(FindPackagesHeaders path style_class file_pattern headers) function(FindPackagesHeaders path style_class file_pattern headers)
file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h") file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
get_property(plist GLOBAL PROPERTY ${headers}) get_property(plist GLOBAL PROPERTY ${headers})
foreach(file_name ${files}) foreach(file_name ${files})

28
cmake/Modules/Testing.cmake
View File

@ -6,7 +6,7 @@ if(ENABLE_TESTING)
find_program(VALGRIND_BINARY NAMES valgrind) find_program(VALGRIND_BINARY NAMES valgrind)
# generate custom suppression file # generate custom suppression file
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n") file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp) file(GLOB VALGRIND_SUPPRESSION_FILES CONFIGURE_DEPENDS ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
foreach(SUPP ${VALGRIND_SUPPRESSION_FILES}) foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
file(READ ${SUPP} SUPPRESSIONS) file(READ ${SUPP} SUPPRESSIONS)
file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}") file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
@ -19,7 +19,7 @@ if(ENABLE_TESTING)
# we need to build and link a LOT of tester executables, so it is worth checking if # we need to build and link a LOT of tester executables, so it is worth checking if
# a faster linker is available. requires GNU or Clang compiler, newer CMake. # a faster linker is available. requires GNU or Clang compiler, newer CMake.
# also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails) # also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))) AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04))) ((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
@ -66,16 +66,8 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF) option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE) mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE) if(ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13) target_compile_options(lammps PUBLIC --coverage)
if(CMAKE_CXX_FLAGS) target_link_options(lammps PUBLIC --coverage)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
else()
target_compile_options(lammps PUBLIC --coverage)
target_link_options(lammps PUBLIC --coverage)
endif()
endif() endif()
endif() endif()
@ -118,16 +110,8 @@ validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER) string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
if(NOT ENABLE_SANITIZER STREQUAL "none") if(NOT ENABLE_SANITIZER STREQUAL "none")
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
if(CMAKE_VERSION VERSION_LESS 3.13) target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
if(CMAKE_CXX_FLAGS) target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
endif()
else()
target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
else() else()
message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.") message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
set(ENABLE_SANITIZER "none") set(ENABLE_SANITIZER "none")

2
cmake/Modules/Tools.cmake
View File

@ -26,7 +26,7 @@ if(BUILD_TOOLS)
enable_language(C) enable_language(C)
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE) get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c) file(GLOB MSI2LMP_SOURCES CONFIGURE_DEPENDS ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES}) add_executable(msi2lmp ${MSI2LMP_SOURCES})
if(STANDARD_MATH_LIB) if(STANDARD_MATH_LIB)
target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB}) target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})

16
doc/src/Build_cmake.rst
View File

@ -16,8 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
.. note:: .. note::
LAMMPS currently requires that CMake version 3.10 or later is available; LAMMPS currently requires that CMake version 3.16 or later is available.
version 3.12 or later is preferred.
.. warning:: .. warning::
@ -34,19 +33,18 @@ Advantages of using CMake
^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^
CMake is an alternative to compiling LAMMPS in the traditional way CMake is an alternative to compiling LAMMPS in the traditional way
through :doc:`(manually customized) makefiles <Build_make>` and a recent through :doc:`(manually customized) makefiles <Build_make>`. Using
addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL) CMake has multiple advantages that are specifically helpful for
and Richard Berger (Temple U). Using CMake has multiple advantages that people with limited experience in compiling software or for people
are specifically helpful for people with limited experience in compiling that want to modify or extend LAMMPS.
software or for people that want to modify or extend LAMMPS.
- CMake can detect available hardware, tools, features, and libraries - CMake can detect available hardware, tools, features, and libraries
and adapt the LAMMPS default build configuration accordingly. and adapt the LAMMPS default build configuration accordingly.
- CMake can generate files for different build tools and integrated - CMake can generate files for different build tools and integrated
development environments (IDE). development environments (IDE).
- CMake supports customization of settings with a command line, text - CMake supports customization of settings with a command line, text
mode, or graphical user interface. No knowledge of file formats or mode, or graphical user interface. No manual editing of files,
complex command line syntax is required. knowledge of file formats or complex command line syntax is required.
- All enabled components are compiled in a single build operation. - All enabled components are compiled in a single build operation.
- Automated dependency tracking for all files and configuration options. - Automated dependency tracking for all files and configuration options.
- Support for true out-of-source compilation. Multiple configurations - Support for true out-of-source compilation. Multiple configurations

1
doc/src/Commands_compute.rst
View File

@ -91,6 +91,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>` * :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>` * :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>` * :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`local/comp/atom (k) <compute_local_comp_atom>`
* :doc:`mliap <compute_mliap>` * :doc:`mliap <compute_mliap>`
* :doc:`momentum <compute_momentum>` * :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>` * :doc:`msd <compute_msd>`

28
doc/src/Howto_cmake.rst
View File

@ -3,9 +3,9 @@ Using CMake with LAMMPS tutorial
The support for building LAMMPS with CMake is a recent addition to The support for building LAMMPS with CMake is a recent addition to
LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard
Berger (Temple U). One of the key strengths of CMake is that it is not Berger (LANL). One of the key strengths of CMake is that it is not
tied to a specific platform or build system and thus generate the files tied to a specific platform or build system and thus it generates the
necessary to build and develop for different build systems and on files necessary to build and develop for different build systems and on
different platforms. Note, that this applies to the build system itself different platforms. Note, that this applies to the build system itself
not the LAMMPS code. In other words, without additional porting effort, not the LAMMPS code. In other words, without additional porting effort,
it is not possible - for example - to compile LAMMPS with Visual C++ on it is not possible - for example - to compile LAMMPS with Visual C++ on
@ -14,7 +14,7 @@ necessary to program LAMMPS as a project in integrated development
environments (IDE) like Eclipse, Visual Studio, QtCreator, Xcode, environments (IDE) like Eclipse, Visual Studio, QtCreator, Xcode,
CodeBlocks, Kate and others. CodeBlocks, Kate and others.
A second important feature of CMake is, that it can detect and validate A second important feature of CMake is that it can detect and validate
available libraries, optimal settings, available support tools and so available libraries, optimal settings, available support tools and so
on, so that by default LAMMPS will take advantage of available tools on, so that by default LAMMPS will take advantage of available tools
without requiring to provide the details about how to enable/integrate without requiring to provide the details about how to enable/integrate
@ -32,8 +32,7 @@ program ``cmake`` (or ``cmake3``), a text mode interactive user
interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user
interface (GUI) program ``cmake-gui``. All of them are portable interface (GUI) program ``cmake-gui``. All of them are portable
software available on all supported platforms and can be used software available on all supported platforms and can be used
interchangeably. The minimum supported CMake version is 3.10 (3.12 or interchangeably. The minimum required CMake version is 3.16.
later is recommended).
All details about features and settings for CMake are in the `CMake All details about features and settings for CMake are in the `CMake
online documentation <https://cmake.org/documentation/>`_. We focus online documentation <https://cmake.org/documentation/>`_. We focus
@ -43,11 +42,20 @@ Prerequisites
------------- -------------
This tutorial assumes that you are operating in a command-line environment This tutorial assumes that you are operating in a command-line environment
using a shell like Bash. using a shell like Bash or Zsh.
- Linux: any Terminal window will work - Linux: any Terminal window will work or text console
- macOS: launch the Terminal application. - macOS: launch the Terminal application
- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>` - Windows 10 or 11: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
- other Unix-like operating systems like FreeBSD
.. note::
It is also possible to use CMake on Windows 10 or 11 through either the Microsoft
Visual Studio IDE with the bundled CMake or from the Windows command prompt using
a separately installed CMake package, both using the native Microsoft Visual C++
compilers and (optionally) the Microsoft MPI SDK. This tutorial, however, only
covers unix-like command line interfaces.
We also assume that you have downloaded and unpacked a recent LAMMPS source code package We also assume that you have downloaded and unpacked a recent LAMMPS source code package
or used Git to create a clone of the LAMMPS sources on your compilation machine. or used Git to create a clone of the LAMMPS sources on your compilation machine.

8
doc/src/Intro_portability.rst
View File

@ -25,7 +25,7 @@ LAMMPS can be compiled from source code using a (traditional) build
system based on shell scripts, a few shell utilities (grep, sed, cat, system based on shell scripts, a few shell utilities (grep, sed, cat,
tr) and the GNU make program. This requires running within a Bourne tr) and the GNU make program. This requires running within a Bourne
shell (``/bin/sh``). Alternatively, a build system with different back ends shell (``/bin/sh``). Alternatively, a build system with different back ends
can be created using CMake. CMake must be at least version 3.10. can be created using CMake. CMake must be at least version 3.16.
Operating systems Operating systems
^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^
@ -62,9 +62,9 @@ regularly tested.
Portability compliance Portability compliance
^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^
Only a subset of the LAMMPS source code is fully compliant to all of the Only a subset of the LAMMPS source code is *fully* compliant to *all*
above mentioned standards. This is rather typical for projects like of the above mentioned standards. This is rather typical for projects
LAMMPS that largely depend on contributions from the user community. like LAMMPS that largely depend on contributions from the user community.
Not all contributors are trained as programmers and not all of them have Not all contributors are trained as programmers and not all of them have
access to multiple platforms for testing. As part of the continuous access to multiple platforms for testing. As part of the continuous
integration process, however, all contributions are automatically tested integration process, however, all contributions are automatically tested

1
doc/src/compute.rst
View File

@ -245,6 +245,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model * :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
* :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model * :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
* :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies * :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
* :doc:`local/comp/atom <compute_local_comp_atom>` - local composition for each atom
* :doc:`mliap <compute_mliap>` - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials * :doc:`mliap <compute_mliap>` - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials
* :doc:`momentum <compute_momentum>` - translational momentum * :doc:`momentum <compute_momentum>` - translational momentum
* :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms * :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms

118
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@ -0,0 +1,118 @@
.. index:: compute local/comp/atom
.. index:: compute local/comp/atom/kk
compute local/comp/atom command
===============================
Accelerator Variants: *local/comp/atom/kk*
Syntax
""""""
.. code-block:: LAMMPS
compute ID group-ID local/comp/atom keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* local/comp/atom = style name of this compute command
* one or more keyword/value pairs may be appended
.. parsed-literal::
keyword = *cutoff*
*cutoff* value = distance cutoff
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all local/comp/atom
compute 1 all local/comp/atom cutoff 9.0
comm_modify cutoff 9.0
Description
"""""""""""
.. versionadded:: TBD
Define a computation that calculates a local composition vector for each
atom. For a central atom with :math:`M` neighbors within the neighbor cutoff sphere,
composition is defined as the number of atoms of a given type
(including the central atom) divided by (:math:`M+1`). For a given central atom,
the sum of all compositions equals one.
.. note::
This compute uses the number of atom types, not chemical species, assigned in
:doc:`pair_coeff <pair_coeff>` command. If an interatomic potential has two
species (i.e., Cu and Ni) assigned to four different atom types in
:doc:`pair_coeff <pair_coeff>` (i.e., 'Cu Cu Ni Ni'), the compute will
output four fractional values. In those cases, the user may desire an extra
calculation step to consolidate per-type fractions into per-species fractions.
This calculation can be conducted within LAMMPS using another compute such as
:doc:`compute reduce <compute_reduce>`, an atom-style :doc:`variable`, or as a
post-processing step.
----------
The optional keyword *cutoff* defines the distance cutoff used when
searching for neighbors. The default value is the cutoff specified by
the pair style. If no pair style is defined, then a cutoff must be
defined using this keyword. If the specified cutoff is larger than
that of the pair_style plus neighbor skin (or no pair style is
defined), the *comm_modify cutoff* option must also be set to match
that of the *cutoff* keyword.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
.. note::
If you have a bonded system, then the settings of
:doc:`special_bonds <special_bonds>` command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral.
This is the default setting for the :doc:`special_bonds
<special_bonds>` command, and means those pairwise interactions do
not appear in the neighbor list. Because this compute uses the
neighbor list, it also means those pairs will not be included in
the order parameter. This difficulty can be circumvented by
writing a dump file, and using the :doc:`rerun <rerun>` command to
compute the order parameter for snapshots in the dump file. The
rerun script can use a :doc:`special_bonds <special_bonds>` command
that includes all pairs in the neighbor list.
----------
Output info
"""""""""""
This compute calculates a per-atom array with :math:`1 + N` columns, where :math:`N`
is the number of atom types. The first column is a count of the number of atoms
used to calculate composition (including the central atom), and each subsequent
column indicates the fraction of that atom type within the cutoff sphere.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>`
doc page for an overview of LAMMPS output options.
Restrictions
""""""""""""
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`comm_modify <comm_modify>`
Default
"""""""
The option defaults are *cutoff* = pair style cutoff.

2
doc/utils/sphinx-config/false_positives.txt
View File

@ -3621,6 +3621,7 @@ Tk
Tkin Tkin
tloop tloop
tlsph tlsph
tm
tmax tmax
Tmax Tmax
tmd tmd
@ -4093,6 +4094,7 @@ zmq
zN zN
zs zs
zsc zsc
Zsh
zst zst
Zstandard Zstandard
zstd zstd

5
examples/COUPLE/plugin/CMakeLists.txt
View File

@ -1,9 +1,8 @@
########################################## # -*- CMake -*- file for example programs that use the LAMMPS library
# CMake build system for coupling to the LAMMPS library
# where the library is loaded dynamically at runtime. # where the library is loaded dynamically at runtime.
########################################## ##########################################
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.16)
# enforce out-of-source build # enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})

4
examples/COUPLE/simple/CMakeLists.txt
View File

@ -1,4 +1,6 @@
cmake_minimum_required(VERSION 3.10) # -*- CMake -*- file for simple examples using the LAMMPS library interface
cmake_minimum_required(VERSION 3.16)
# enforce out-of-source build # enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})

5
examples/PACKAGES/pace/plugin/CMakeLists.txt
View File

@ -1,10 +1,9 @@
########################################## # -*- CMake -*- build system for plugin examples.
# CMake build system for plugin examples.
# The is meant to be used as a template for plugins that are # The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package. # distributed independent from the LAMMPS package.
########################################## ##########################################
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.16)
project(paceplugin VERSION 1.0 LANGUAGES CXX) project(paceplugin VERSION 1.0 LANGUAGES CXX)

12
examples/kim/plugin/CMakeLists.txt
View File

@ -1,10 +1,9 @@
########################################## # -*- CMake -*- file for building plugins.
# CMake build system for plugin examples.
# The is meant to be used as a template for plugins that are # The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package. # distributed independent from the LAMMPS package.
########################################## ##########################################
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.16)
project(kimplugin VERSION 1.0 LANGUAGES CXX) project(kimplugin VERSION 1.0 LANGUAGES CXX)
@ -31,12 +30,7 @@ target_link_libraries(kimplugin PRIVATE KIM-API::kim-api)
# need libcurl # need libcurl
find_package(CURL) find_package(CURL)
if(CURL_FOUND) if(CURL_FOUND)
if(CMAKE_VERSION VERSION_LESS 3.12) target_link_libraries(kimplugin PRIVATE CURL::libcurl)
target_include_directories(kimplugin PRIVATE ${CURL_INCLUDE_DIRS})
target_link_libraries(kimplugin PRIVATE ${CURL_LIBRARIES})
else()
target_link_libraries(kimplugin PRIVATE CURL::libcurl)
endif()
target_compile_definitions(kimplugin PRIVATE -DLMP_KIM_CURL) target_compile_definitions(kimplugin PRIVATE -DLMP_KIM_CURL)
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.") set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
mark_as_advanced(LMP_DEBUG_CURL) mark_as_advanced(LMP_DEBUG_CURL)

5
examples/plugins/CMakeLists.txt
View File

@ -1,10 +1,9 @@
########################################## # -*- CMake -*- file for plugin examples.
# CMake build system for plugin examples.
# The is meant to be used as a template for plugins that are # The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package. # distributed independent from the LAMMPS package.
########################################## ##########################################
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.16)
# enforce out-of-source build # enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR}) if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})

2
src/.gitignore vendored
View File

@ -580,6 +580,8 @@
/compute_ke_eff.h /compute_ke_eff.h
/compute_ke_rigid.cpp /compute_ke_rigid.cpp
/compute_ke_rigid.h /compute_ke_rigid.h
/compute_local_comp_atom.cpp
/compute_local_comp_atom.h
/compute_meso_e_atom.cpp /compute_meso_e_atom.cpp
/compute_meso_e_atom.h /compute_meso_e_atom.h
/compute_meso_rho_atom.cpp /compute_meso_rho_atom.cpp

214
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@ -0,0 +1,214 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Megan McCarthy (SNL)
------------------------------------------------------------------------- */
#include "compute_local_comp_atom.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "pair.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
ComputeLocalCompAtom::ComputeLocalCompAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg), result(nullptr)
{
if (narg < 3 || narg > 5) error->all(FLERR, "Illegal compute local/comp/atom command");
cutoff = 0.0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg], "cutoff") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal compute local/comp/atom command");
cutoff = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
if (cutoff <= 0.0) error->all(FLERR, "Illegal compute local/comp/atom command");
iarg += 2;
} else
error->all(FLERR, "Illegal compute local/comp/atom command");
}
peratom_flag = 1;
ntypes = atom->ntypes;
size_peratom_cols = 1 + ntypes;
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputeLocalCompAtom::~ComputeLocalCompAtom()
{
if (copymode) return;
memory->destroy(result);
}
/* ---------------------------------------------------------------------- */
void ComputeLocalCompAtom::init()
{
if (!force->pair && cutoff == 0.0)
error->all(FLERR,
"Compute local/comp/atom requires a cutoff be specified "
"or a pair style be defined");
double skin = neighbor->skin;
if (cutoff != 0.0) {
double cutghost; // as computed by Neighbor and Comm
if (force->pair)
cutghost = MAX(force->pair->cutforce + skin, comm->cutghostuser);
else
cutghost = comm->cutghostuser;
if (cutoff > cutghost)
error->all(FLERR,
"Compute local/comp/atom cutoff exceeds ghost atom range - "
"use comm_modify cutoff command");
}
int cutflag = 1;
if (force->pair) {
if (cutoff == 0.0) { cutoff = force->pair->cutforce; }
if (cutoff <= force->pair->cutforce + skin) cutflag = 0;
}
cutsq = cutoff * cutoff;
// need an occasional full neighbor list
auto req = neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
if (cutflag) req->set_cutoff(cutoff);
}
/* ---------------------------------------------------------------------- */
void ComputeLocalCompAtom::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeLocalCompAtom::compute_peratom()
{
int i, j, ii, jj, inum, jnum;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
int *ilist, *jlist, *numneigh, **firstneigh;
int count, itype, jtype;
invoked_peratom = update->ntimestep;
// grow result array if necessary
if (atom->nmax > nmax) {
memory->destroy(result);
nmax = atom->nmax;
memory->create(result, nmax, size_peratom_cols, "local/comp/atom:result");
array_atom = result;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// compute properties for each atom in group
// use full neighbor list to count atoms less than cutoff
double **x = atom->x;
int *type = atom->type;
int *mask = atom->mask;
// get per-atom local compositions
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
// i atom contribution
count = 1;
itype = type[i];
result[i][itype]++;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
jtype = type[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
count++;
result[i][jtype]++;
}
}
// total count of atoms found in sampled radius range
result[i][0] = count;
// local comp fractions per element
double lfac = 1.0 / count;
for (int n = 1; n < size_peratom_cols; n++)
result[i][n+1] *= lfac;
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeLocalCompAtom::memory_usage()
{
double bytes = (double) 2 * nmax * sizeof(double);
return bytes;
}

47
src/EXTRA-COMPUTE/compute_local_comp_atom.h Normal file
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@ -0,0 +1,47 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
// clang-format off
ComputeStyle(local/comp/atom,ComputeLocalCompAtom);
// clang-format on
#else
#ifndef LMP_COMPUTE_LOCAL_COMP_ATOM_H
#define LMP_COMPUTE_LOCAL_COMP_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeLocalCompAtom : public Compute {
public:
ComputeLocalCompAtom(class LAMMPS *, int, char **);
~ComputeLocalCompAtom() override;
void init() override;
void init_list(int, class NeighList *) override;
void compute_peratom() override;
double memory_usage() override;
protected:
int nmax, ntypes;
double cutoff; // global cutoff distance
double cutsq; // cutoff**2
class NeighList *list; // neighbor list
double **result; // peratom array of local compositions
};
} // namespace LAMMPS_NS
#endif
#endif

2
src/KOKKOS/Install.sh
View File

@ -96,6 +96,8 @@ action compute_coord_atom_kokkos.cpp
action compute_coord_atom_kokkos.h action compute_coord_atom_kokkos.h
action compute_erotate_sphere_kokkos.cpp action compute_erotate_sphere_kokkos.cpp
action compute_erotate_sphere_kokkos.h action compute_erotate_sphere_kokkos.h
action compute_local_comp_atom_kokkos.cpp compute_local_comp_atom.cpp
action compute_local_comp_atom_kokkos.h compute_local_comp_atom.h
action compute_orientorder_atom_kokkos.cpp action compute_orientorder_atom_kokkos.cpp
action compute_orientorder_atom_kokkos.h action compute_orientorder_atom_kokkos.h
action compute_temp_deform_kokkos.cpp action compute_temp_deform_kokkos.cpp

180
src/KOKKOS/compute_local_comp_atom_kokkos.cpp Normal file
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@ -0,0 +1,180 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU Gdirectoryeneral Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Megan McCarthy (SNL)
------------------------------------------------------------------------- */
#include "compute_local_comp_atom_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "memory_kokkos.h"
#include "modify.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor_kokkos.h"
#include "pair.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
template<class DeviceType>
ComputeLocalCompAtomKokkos<DeviceType>::ComputeLocalCompAtomKokkos(LAMMPS *lmp, int narg, char **arg) :
ComputeLocalCompAtom(lmp, narg, arg)
{
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = EMPTY_MASK;
datamask_modify = EMPTY_MASK;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
ComputeLocalCompAtomKokkos<DeviceType>::~ComputeLocalCompAtomKokkos()
{
if (copymode) return;
memoryKK->destroy_kokkos(k_result,result);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void ComputeLocalCompAtomKokkos<DeviceType>::init()
{
ComputeLocalCompAtom::init();
// adjust neighbor list request for KOKKOS
auto request = neighbor->find_request(this);
request->set_kokkos_host(std::is_same<DeviceType,LMPHostType>::value &&
!std::is_same<DeviceType,LMPDeviceType>::value);
request->set_kokkos_device(std::is_same<DeviceType,LMPDeviceType>::value);
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void ComputeLocalCompAtomKokkos<DeviceType>::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow result array if necessary
int size_peratom_cols = 1 + atom->ntypes;
if (atom->nmax > nmax) {
memoryKK->destroy_kokkos(k_result,result);
nmax = atom->nmax;
memoryKK->create_kokkos(k_result,result,nmax,size_peratom_cols,"local/comp/atom:result");
d_result = k_result.view<DeviceType>();
array_atom = result;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list);
int inum = list->inum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
// compute properties for each atom in group
// use full neighbor list to count atoms less than cutoff
atomKK->sync(execution_space,X_MASK|TYPE_MASK|MASK_MASK);
x = atomKK->k_x.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
ntypes = atom->ntypes;
Kokkos::deep_copy(d_result,0.0);
copymode = 1;
typename Kokkos::RangePolicy<DeviceType, TagComputeLocalCompAtom> policy(0,inum);
Kokkos::parallel_for("ComputeLocalComp",policy,*this);
copymode = 0;
k_result.modify<DeviceType>();
k_result.sync_host();
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void ComputeLocalCompAtomKokkos<DeviceType>::operator()(TagComputeLocalCompAtom, const int &ii) const
{
const int i = d_ilist[ii];
if (mask[i] & groupbit) {
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
// i atom contribution
int count = 1.0;
int itype = type[i];
d_result(i,itype)++;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
int jtype = type[j];
const F_FLOAT delx = x(j,0) - xtmp;
const F_FLOAT dely = x(j,1) - ytmp;
const F_FLOAT delz = x(j,2) - ztmp;
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
count++;
d_result(i,jtype) += 1.0;
}
}
// total count of atoms found in sampled radius range
d_result(i,0) = count;
// local comp fractions per atom type
double lfac = 1.0 / count;
for (int n = 1; n < size_peratom_cols; n++) {
d_result(i,n) *= lfac;
}
}
}
namespace LAMMPS_NS {
template class ComputeLocalCompAtomKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU
template class ComputeLocalCompAtomKokkos<LMPHostType>;
#endif
}

64
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@ -0,0 +1,64 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
// clang-format off
ComputeStyle(local/comp/atom/kk,ComputeLocalCompAtomKokkos<LMPDeviceType>);
ComputeStyle(local/comp/atom/kk/device,ComputeLocalCompAtomKokkos<LMPDeviceType>);
ComputeStyle(local/comp/atom/kk/host,ComputeLocalCompAtomKokkos<LMPHostType>);
// clang-format on
#else
#ifndef LMP_COMPUTE_LOCAL_COMP_ATOM_KOKKOS_H
#define LMP_COMPUTE_LOCAL_COMP_ATOM_KOKKOS_H
#include "compute_local_comp_atom.h"
#include "kokkos_type.h"
namespace LAMMPS_NS {
// clang-format off
struct TagComputeLocalCompAtom {};
// clang-format on
template <class DeviceType> class ComputeLocalCompAtomKokkos : public ComputeLocalCompAtom {
public:
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
ComputeLocalCompAtomKokkos(class LAMMPS *, int, char **);
~ComputeLocalCompAtomKokkos() override;
void init() override;
void compute_peratom() override;
KOKKOS_INLINE_FUNCTION
void operator()(TagComputeLocalCompAtom, const int &) const;
private:
typename AT::t_x_array x;
typename ArrayTypes<DeviceType>::t_int_1d type;
typename ArrayTypes<DeviceType>::t_int_1d mask;
typename AT::t_neighbors_2d d_neighbors;
typename AT::t_int_1d d_ilist;
typename AT::t_int_1d d_numneigh;
DAT::tdual_float_2d k_result;
typename AT::t_float_2d d_result;
};
} // namespace LAMMPS_NS
#endif
#endif

4
tools/phonon/CMakeLists.spglib
View File

@ -1,4 +1,5 @@
cmake_minimum_required(VERSION 3.10) # -*- CMake -*- file for building spglib for phana
cmake_minimum_required(VERSION 3.16)
project(spglib C) project(spglib C)
set(CMAKE_MACOSX_RPATH 1) set(CMAKE_MACOSX_RPATH 1)
set(CMAKE_C_FLAGS_RELEASE "-Wall -O2") set(CMAKE_C_FLAGS_RELEASE "-Wall -O2")
@ -10,7 +11,6 @@ message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
set(CMAKE_POSITION_INDEPENDENT_CODE ON) set(CMAKE_POSITION_INDEPENDENT_CODE ON)
# Version numbers # Version numbers
file(READ ${PROJECT_SOURCE_DIR}/src/version.h version_file) file(READ ${PROJECT_SOURCE_DIR}/src/version.h version_file)
string(REGEX MATCH "SPGLIB_MAJOR_VERSION ([0-9]+)" spglib_major_version ${version_file}) string(REGEX MATCH "SPGLIB_MAJOR_VERSION ([0-9]+)" spglib_major_version ${version_file})

1
tools/phonon/CMakeLists.txt
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@ -1,3 +1,4 @@
# -*- CMake -*- configuration for building the PHONON package analysis tool: phana
# Support Linux from Ubuntu 20.04LTS onward, CentOS 7.x (with EPEL), # Support Linux from Ubuntu 20.04LTS onward, CentOS 7.x (with EPEL),
# macOS, MSVC 2019 (=Version 16) # macOS, MSVC 2019 (=Version 16)

3
tools/phonon/tricubic/CMakeLists.txt
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@ -1,7 +1,8 @@
# -*- CMake -*- configuration for building the tricubic library
# Support Linux from Ubuntu 20.04LTS onward, CentOS 7.x (with EPEL), # Support Linux from Ubuntu 20.04LTS onward, CentOS 7.x (with EPEL),
# macOS, MSVC 2019 (=Version 16) # macOS, MSVC 2019 (=Version 16)
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.16)
# set up project # set up project
project(tricubic VERSION 1.1 DESCRIPTION "Tricubic library" LANGUAGES CXX) project(tricubic VERSION 1.1 DESCRIPTION "Tricubic library" LANGUAGES CXX)

4
tools/swig/CMakeLists.txt
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@ -1,7 +1,7 @@
# CMake configuration for generating script language interfaces with SWIG # -*- CMake -*- configuration for generating LAMMPS script language wrappers with SWIG
# set minimum CMake version required and switch to new policies for SWIG # set minimum CMake version required and switch to new policies for SWIG
cmake_minimum_required(VERSION 3.14) cmake_minimum_required(VERSION 3.16)
if(POLICY CMP0078) if(POLICY CMP0078)
cmake_policy(SET CMP0078 NEW) cmake_policy(SET CMP0078 NEW)
endif() endif()

11
unittest/CMakeLists.txt
View File

@ -1,10 +1,9 @@
######################################## # -*- CMake -*- build file for automated testing
# CMake build for automated testing
# This file is part of LAMMPS # This file is part of LAMMPS
# Created by Axel Kohlmeyer and Richard Berger # Created by Axel Kohlmeyer and Richard Berger
######################################## ########################################
# download and build googletest framework
# download and build googletest framework
# cannot compile googletest anymore with the default GCC on RHEL 7.x # cannot compile googletest anymore with the default GCC on RHEL 7.x
if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.0)) if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.0))
message(FATAL_ERROR "Need GNU C++ compiler version 6.x or later for unit testing") message(FATAL_ERROR "Need GNU C++ compiler version 6.x or later for unit testing")
@ -36,11 +35,7 @@ endforeach()
# must repeat handling coverage for older CMake # must repeat handling coverage for older CMake
if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND ENABLE_COVERAGE) if((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND ENABLE_COVERAGE)
if(CMAKE_VERSION VERSION_LESS 3.13) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
endif()
endif() endif()
######################################## ########################################

1
unittest/c-library/CMakeLists.txt
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@ -1,3 +1,4 @@
# -*- CMake -*- file for testing the c-library interface
add_executable(test_library_open test_library_open.cpp test_main.cpp) add_executable(test_library_open test_library_open.cpp test_main.cpp)
target_link_libraries(test_library_open PRIVATE lammps GTest::GMock) target_link_libraries(test_library_open PRIVATE lammps GTest::GMock)

1
unittest/commands/CMakeLists.txt
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@ -1,3 +1,4 @@
# -*- CMake -*- file for testing LAMMPS commands
add_executable(test_simple_commands test_simple_commands.cpp) add_executable(test_simple_commands test_simple_commands.cpp)

1
unittest/cplusplus/CMakeLists.txt
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@ -1,3 +1,4 @@
# -*- CMake -*- file for testing the direct calls to individual C++ classes
add_executable(test_lammps_class test_lammps_class.cpp) add_executable(test_lammps_class test_lammps_class.cpp)
target_link_libraries(test_lammps_class PRIVATE lammps GTest::GMockMain) target_link_libraries(test_lammps_class PRIVATE lammps GTest::GMockMain)

2
unittest/force-styles/CMakeLists.libyaml
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@ -1,6 +1,6 @@
# Custom minimal -*- CMake -*- file for libyaml # Custom minimal -*- CMake -*- file for libyaml
cmake_minimum_required(VERSION 3.10) cmake_minimum_required(VERSION 3.16)
project(libyaml VERSION 0.2.5 project(libyaml VERSION 0.2.5
DESCRIPTION "LibYAML a YAML parser and emitter library" DESCRIPTION "LibYAML a YAML parser and emitter library"
LANGUAGES C LANGUAGES C

36
unittest/force-styles/CMakeLists.txt
View File

@ -1,3 +1,4 @@
# -*- CMake -*- file for tests of classes computing or modifying forces
find_package(YAML) find_package(YAML)
if(NOT YAML_FOUND) if(NOT YAML_FOUND)
@ -19,16 +20,7 @@ function(extract_tags out yaml_file)
set(${out} "${TAGS}" PARENT_SCOPE) set(${out} "${TAGS}" PARENT_SCOPE)
endfunction() endfunction()
if(CMAKE_VERSION VERSION_LESS 3.12) find_package(Python COMPONENTS Interpreter)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE) if(Python_EXECUTABLE)
add_custom_target(check-tests add_custom_target(check-tests
${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check_tests.py ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check_tests.py
@ -53,10 +45,8 @@ target_link_libraries(style_tests PUBLIC GTest::GMock Yaml::Yaml lammps)
# propagate sanitizer options to test tools # propagate sanitizer options to test tools
if(ENABLE_SANITIZER AND (NOT (ENABLE_SANITIZER STREQUAL "none"))) if(ENABLE_SANITIZER AND (NOT (ENABLE_SANITIZER STREQUAL "none")))
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) target_compile_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_compile_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER}) target_link_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER})
target_link_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER})
endif()
endif() endif()
# unit test for error stats class # unit test for error stats class
@ -97,7 +87,7 @@ else()
endif() endif()
# tests for molecular systems and related pair styles # tests for molecular systems and related pair styles
file(GLOB MOL_PAIR_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/mol-pair-*.yaml) file(GLOB MOL_PAIR_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/mol-pair-*.yaml)
# cannot test MSM with single precision data # cannot test MSM with single precision data
if(FFT_SINGLE) if(FFT_SINGLE)
list(FILTER MOL_PAIR_TESTS EXCLUDE REGEX "msm") list(FILTER MOL_PAIR_TESTS EXCLUDE REGEX "msm")
@ -115,7 +105,7 @@ foreach(TEST ${MOL_PAIR_TESTS})
endforeach() endforeach()
# tests for metal-like atomic systems and related pair styles # tests for metal-like atomic systems and related pair styles
file(GLOB ATOMIC_PAIR_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/atomic-pair-*.yaml) file(GLOB ATOMIC_PAIR_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/atomic-pair-*.yaml)
foreach(TEST ${ATOMIC_PAIR_TESTS}) foreach(TEST ${ATOMIC_PAIR_TESTS})
string(REGEX REPLACE "^.*atomic-pair-(.*)\.yaml" "AtomicPairStyle:\\1" TNAME ${TEST}) string(REGEX REPLACE "^.*atomic-pair-(.*)\.yaml" "AtomicPairStyle:\\1" TNAME ${TEST})
extract_tags(TEST_TAGS ${TEST}) extract_tags(TEST_TAGS ${TEST})
@ -129,7 +119,7 @@ foreach(TEST ${ATOMIC_PAIR_TESTS})
endforeach() endforeach()
# tests for Si-like manybody systems and related pair styles # tests for Si-like manybody systems and related pair styles
file(GLOB MANYBODY_PAIR_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/manybody-pair-*.yaml) file(GLOB MANYBODY_PAIR_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/manybody-pair-*.yaml)
foreach(TEST ${MANYBODY_PAIR_TESTS}) foreach(TEST ${MANYBODY_PAIR_TESTS})
string(REGEX REPLACE "^.*manybody-pair-(.*)\.yaml" "ManybodyPairStyle:\\1" TNAME ${TEST}) string(REGEX REPLACE "^.*manybody-pair-(.*)\.yaml" "ManybodyPairStyle:\\1" TNAME ${TEST})
extract_tags(TEST_TAGS ${TEST}) extract_tags(TEST_TAGS ${TEST})
@ -146,7 +136,7 @@ endforeach()
add_executable(test_bond_style test_bond_style.cpp) add_executable(test_bond_style test_bond_style.cpp)
target_link_libraries(test_bond_style PRIVATE lammps style_tests) target_link_libraries(test_bond_style PRIVATE lammps style_tests)
file(GLOB BOND_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/bond-*.yaml) file(GLOB BOND_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/bond-*.yaml)
foreach(TEST ${BOND_TESTS}) foreach(TEST ${BOND_TESTS})
string(REGEX REPLACE "^.*bond-(.*)\.yaml" "BondStyle:\\1" TNAME ${TEST}) string(REGEX REPLACE "^.*bond-(.*)\.yaml" "BondStyle:\\1" TNAME ${TEST})
extract_tags(TEST_TAGS ${TEST}) extract_tags(TEST_TAGS ${TEST})
@ -163,7 +153,7 @@ endforeach()
add_executable(test_angle_style test_angle_style.cpp) add_executable(test_angle_style test_angle_style.cpp)
target_link_libraries(test_angle_style PRIVATE lammps style_tests) target_link_libraries(test_angle_style PRIVATE lammps style_tests)
file(GLOB ANGLE_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/angle-*.yaml) file(GLOB ANGLE_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/angle-*.yaml)
foreach(TEST ${ANGLE_TESTS}) foreach(TEST ${ANGLE_TESTS})
string(REGEX REPLACE "^.*angle-(.*)\.yaml" "AngleStyle:\\1" TNAME ${TEST}) string(REGEX REPLACE "^.*angle-(.*)\.yaml" "AngleStyle:\\1" TNAME ${TEST})
extract_tags(TEST_TAGS ${TEST}) extract_tags(TEST_TAGS ${TEST})
@ -177,7 +167,7 @@ foreach(TEST ${ANGLE_TESTS})
endforeach() endforeach()
# kspace style tester, currently uses the pair style tool # kspace style tester, currently uses the pair style tool
file(GLOB KSPACE_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/kspace-*.yaml) file(GLOB KSPACE_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/kspace-*.yaml)
# cannot test MSM with single precision data # cannot test MSM with single precision data
if(FFT_SINGLE) if(FFT_SINGLE)
list(FILTER KSPACE_TESTS EXCLUDE REGEX "msm") list(FILTER KSPACE_TESTS EXCLUDE REGEX "msm")
@ -205,7 +195,7 @@ endif()
target_link_libraries(test_fix_timestep PRIVATE lammps style_tests) target_link_libraries(test_fix_timestep PRIVATE lammps style_tests)
# tests for timestep related fixes (time integration, thermostat, force manipulation, constraints/restraints) # tests for timestep related fixes (time integration, thermostat, force manipulation, constraints/restraints)
file(GLOB FIX_TIMESTEP_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/fix-timestep-*.yaml) file(GLOB FIX_TIMESTEP_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/fix-timestep-*.yaml)
foreach(TEST ${FIX_TIMESTEP_TESTS}) foreach(TEST ${FIX_TIMESTEP_TESTS})
string(REGEX REPLACE "^.*fix-timestep-(.*)\.yaml" "FixTimestep:\\1" TNAME ${TEST}) string(REGEX REPLACE "^.*fix-timestep-(.*)\.yaml" "FixTimestep:\\1" TNAME ${TEST})
extract_tags(TEST_TAGS ${TEST}) extract_tags(TEST_TAGS ${TEST})
@ -226,7 +216,7 @@ endforeach()
add_executable(test_dihedral_style test_dihedral_style.cpp) add_executable(test_dihedral_style test_dihedral_style.cpp)
target_link_libraries(test_dihedral_style PRIVATE lammps style_tests) target_link_libraries(test_dihedral_style PRIVATE lammps style_tests)
file(GLOB DIHEDRAL_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/dihedral-*.yaml) file(GLOB DIHEDRAL_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/dihedral-*.yaml)
foreach(TEST ${DIHEDRAL_TESTS}) foreach(TEST ${DIHEDRAL_TESTS})
string(REGEX REPLACE "^.*dihedral-(.*)\.yaml" "DihedralStyle:\\1" TNAME ${TEST}) string(REGEX REPLACE "^.*dihedral-(.*)\.yaml" "DihedralStyle:\\1" TNAME ${TEST})
extract_tags(TEST_TAGS ${TEST}) extract_tags(TEST_TAGS ${TEST})
@ -243,7 +233,7 @@ endforeach()
add_executable(test_improper_style test_improper_style.cpp) add_executable(test_improper_style test_improper_style.cpp)
target_link_libraries(test_improper_style PRIVATE lammps style_tests) target_link_libraries(test_improper_style PRIVATE lammps style_tests)
file(GLOB IMPROPER_TESTS LIST_DIRECTORIES false ${CONFIGURE_DEPENDS} ${TEST_INPUT_FOLDER}/improper-*.yaml) file(GLOB IMPROPER_TESTS LIST_DIRECTORIES false CONFIGURE_DEPENDS ${TEST_INPUT_FOLDER}/improper-*.yaml)
foreach(TEST ${IMPROPER_TESTS}) foreach(TEST ${IMPROPER_TESTS})
string(REGEX REPLACE "^.*improper-(.*)\.yaml" "ImproperStyle:\\1" TNAME ${TEST}) string(REGEX REPLACE "^.*improper-(.*)\.yaml" "ImproperStyle:\\1" TNAME ${TEST})
extract_tags(TEST_TAGS ${TEST}) extract_tags(TEST_TAGS ${TEST})

1
unittest/formats/CMakeLists.txt
View File

@ -1,3 +1,4 @@
# -*- CMake -*- file for tests of file reading or writing classes and functions in LAMMPS
add_executable(test_atom_styles test_atom_styles.cpp) add_executable(test_atom_styles test_atom_styles.cpp)
target_link_libraries(test_atom_styles PRIVATE lammps GTest::GMock) target_link_libraries(test_atom_styles PRIVATE lammps GTest::GMock)

4
unittest/formats/test_file_operations.cpp
View File

@ -612,6 +612,10 @@ TEST_F(FileOperationsTest, read_data_fix)
EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8); EXPECT_EQ(lmp->atom->tag[GETIDX(8)], 8);
EXPECT_EQ(lmp->atom->tag[GETIDX(9)], 9); EXPECT_EQ(lmp->atom->tag[GETIDX(9)], 9);
EXPECT_EQ(lmp->atom->tag[GETIDX(10)], 10); EXPECT_EQ(lmp->atom->tag[GETIDX(10)], 10);
// clean up
delete_file("test_mol_id_merge.data");
delete_file("test_mol_id.data");
} }
int main(int argc, char **argv) int main(int argc, char **argv)

2
unittest/fortran/CMakeLists.txt
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@ -1,3 +1,5 @@
# -*- CMake -*- file for testing the Fortran interface to LAMMPS
include(CheckGeneratorSupport) include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN) if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran support in build tool") message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran support in build tool")

19
unittest/python/CMakeLists.txt
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@ -1,7 +1,8 @@
# Test calling Python from LAMMPS (and importing the LAMMPS module # -*- CMake -*- file for tests calling Python from LAMMPS (and importing
# inside those functions). This can do an "anonymous" import of symbols # the LAMMPS module inside those functions). This can do an "anonymous"
# from the executable, so the shared library is not needed. The # import of symbols from the executable, so the shared library is not
# availability of the PYTHON package is tested for inside the tester. # needed. The availability of the PYTHON package is tested for inside
# the tester.
set(TEST_INPUT_FOLDER ${CMAKE_CURRENT_SOURCE_DIR}) set(TEST_INPUT_FOLDER ${CMAKE_CURRENT_SOURCE_DIR})
@ -11,20 +12,12 @@ if(NOT BUILD_SHARED_LIBS)
return() return()
endif() endif()
if(CMAKE_VERSION VERSION_LESS 3.12) find_package(Python 3.6 COMPONENTS Interpreter Development)
find_package(PythonInterp 3.6) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python COMPONENTS Interpreter Development)
endif()
if(PKG_PYTHON) if(PKG_PYTHON)
add_executable(test_python_package test_python_package.cpp) add_executable(test_python_package test_python_package.cpp)
target_link_libraries(test_python_package PRIVATE lammps GTest::GMock) target_link_libraries(test_python_package PRIVATE lammps GTest::GMock)
target_compile_definitions(test_python_package PRIVATE -DTEST_INPUT_FOLDER=${TEST_INPUT_FOLDER}) target_compile_definitions(test_python_package PRIVATE -DTEST_INPUT_FOLDER=${TEST_INPUT_FOLDER})
# this requires CMake 3.12. don't care to add backward compatibility for this.
if(Python_Development_FOUND) if(Python_Development_FOUND)
target_compile_definitions(test_python_package PRIVATE -DTEST_HAVE_PYTHON_DEVELOPMENT=1) target_compile_definitions(test_python_package PRIVATE -DTEST_HAVE_PYTHON_DEVELOPMENT=1)
target_link_libraries(test_python_package PRIVATE Python::Python) target_link_libraries(test_python_package PRIVATE Python::Python)

11
unittest/tools/CMakeLists.txt
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@ -1,13 +1,8 @@
# -*- CMake -*- file for tests of utily functions and classes in LAMMPS
# we use python 3's subprocess module to run the tools and check the output # we use python 3's subprocess module to run the tools and check the output
if(CMAKE_VERSION VERSION_LESS 3.12) find_package(Python 3.6 COMPONENTS Interpreter)
find_package(PythonInterp 3.5) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python 3.5 COMPONENTS Interpreter)
endif()
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG) get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
if(BUILD_IS_MULTI_CONFIG) if(BUILD_IS_MULTI_CONFIG)
set(LAMMPS_SHELL_EXE_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>) set(LAMMPS_SHELL_EXE_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)

1
unittest/utils/CMakeLists.txt
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@ -1,3 +1,4 @@
# -*- CMake -*- file for tests of utily functions and classes in LAMMPS
add_executable(test_tokenizer test_tokenizer.cpp) add_executable(test_tokenizer test_tokenizer.cpp)
target_link_libraries(test_tokenizer PRIVATE lammps GTest::GMockMain) target_link_libraries(test_tokenizer PRIVATE lammps GTest::GMockMain)