Merge pull request #18 from lammps/master (f94cdf85) · Commits · 郑智淋 / lammps

.github/CODEOWNERS

+11 −0

Original line number	Diff line number	Diff line
		@@ -43,3 +43,14 @@ src/USER-MISC/_grem. @dstelter92

		# tools
		tools/msi2lmp/* @akohlmey

		# cmake
		cmake/* @junghans @rbberger

		# python
		python/* @rbberger

		# docs
		doc/utils// @rbberger
		doc/Makefile @rbberger
		doc/README @rbberger

cmake/CMakeLists.txt

+76 −41

Original line number	Diff line number	Diff line
		@@ -49,6 +49,11 @@ if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
		set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
		endif()

		option(ENABLE_COVERAGE "Enable code coverage" OFF)
		if(ENABLE_COVERAGE)
		set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
		endif()

		########################################################################
		# User input options #
		########################################################################
		@@ -147,23 +152,12 @@ pkg_depends(CORESHELL KSPACE)
		######################################################
		if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
		enable_language(Fortran)
		list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
		endif()

		if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
		enable_language(C)
		endif()

		if(PKG_MSCG)
		if (CMAKE_VERSION VERSION_LESS "3.1")
		message(FATAL_ERROR "For the MSCG package you need at least cmake-3.1")
		endif()
		# starting with CMake 3.1 this is all you have to do to enforce C++11
		set(CMAKE_CXX_STANDARD 11) # C++11...
		set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
		set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
		endif()

		find_package(OpenMP QUIET)
		option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
		if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
		@@ -207,7 +201,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
		find_package(LAPACK)
		if(NOT LAPACK_FOUND)
		enable_language(Fortran)
		file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
		file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
		add_library(linalg STATIC ${LAPACK_SOURCES})
		set(LAPACK_LIBRARIES linalg)
		endif()
		@@ -302,8 +296,8 @@ if(PKG_LATTE)
		message(STATUS "LATTE not found - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(latte_build
		URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz
		URL_MD5 cb86f1d2473ce00aa61ff6a023154b03
		URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
		URL_MD5 bed76e7e76c545c36dd848a8f1fd35eb
		SOURCE_SUBDIR cmake
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
		)
		@@ -340,13 +334,10 @@ if(PKG_USER-SMD)
		ExternalProject_Add(Eigen3_build
		URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
		URL_MD5 1a47e78efe365a97de0c022d127607c3
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DEIGEN_TEST_NOQT=ON
		-DCMAKE_DISABLE_FIND_PACKAGE_LAPACK=ON -DCMAKE_DISABLE_FIND_PACKAGE_Cholmod=ON -DCMAKE_DISABLE_FIND_PACKAGE_Umfpack=ON -DCMAKE_DISABLE_FIND_PACKAGE_SuperLU=ON
		-DCMAKE_DISABLE_FIND_PACKAGE_PASTIX=ON -DCMAKE_DISABLE_FIND_PACKAGE_SPQR=ON -DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON -DCMAKE_DISABLE_FIND_PACKAGE_CUDA=ON
		-DCMAKE_DISABLE_FIND_PACKAGE_FFTW=ON -DCMAKE_DISABLE_FIND_PACKAGE_MPFR=ON -DCMAKE_DISABLE_FIND_PACKAGE_OpenGL=ON
		CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
		)
		ExternalProject_get_property(Eigen3_build INSTALL_DIR)
		set(EIGEN3_INCLUDE_DIR ${INSTALL_DIR}/include/eigen3)
		ExternalProject_get_property(Eigen3_build SOURCE_DIR)
		set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
		list(APPEND LAMMPS_DEPS Eigen3_build)
		else()
		find_package(Eigen3)
		@@ -402,26 +393,36 @@ endif()

		if(PKG_MSCG)
		find_package(GSL REQUIRED)
		set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
		set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
		set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)
		if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})
		if(NOT EXISTS ${MSCG_TARBALL})
		message(STATUS "Downloading ${MSCG_TARBALL}")
		file(DOWNLOAD
		https://github.com/uchicago-voth/MSCG-release/archive/master.zip
		${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
		endif()
		message(STATUS "Unpacking ${MSCG_TARBALL}")
		execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}
		WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
		endif()
		file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
		add_library(mscg STATIC ${MSCG_SOURCES})
		list(APPEND LAMMPS_LINK_LIBS mscg)
		target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
		target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
		target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
		option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
		if(DOWNLOAD_MSCG)
		include(ExternalProject)
		if(NOT LAPACK_FOUND)
		set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
		endif()
		ExternalProject_Add(mscg_build
		URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
		URL_MD5 8c45e269ee13f60b303edd7823866a91
		SOURCE_SUBDIR src/CMake
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}
		BUILD_COMMAND make mscg INSTALL_COMMAND ""
		)
		ExternalProject_get_property(mscg_build BINARY_DIR)
		set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
		ExternalProject_get_property(mscg_build SOURCE_DIR)
		set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
		list(APPEND LAMMPS_DEPS mscg_build)
		if(NOT LAPACK_FOUND)
		file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
		add_dependencies(mscg_build linalg)
		endif()
		else()
		find_package(MSCG)
		if(NOT MSCG_FOUND)
		message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
		endif()
		endif()
		list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
		include_directories(${MSCG_INCLUDE_DIRS})
		endif()

		if(PKG_COMPRESS)
		@@ -800,6 +801,11 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
		# Actually add executable and lib to build
		############################################
		add_library(lammps ${LIB_SOURCES})
		get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
		list (FIND LANGUAGES "Fortran" _index)
		if (${_index} GREATER -1)
		list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
		endif()
		list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)
		target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
		if(LAMMPS_DEPS)
		@@ -822,9 +828,38 @@ if(ENABLE_TESTING)
		add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
		endif()

		##################################
		###############################################################################
		# Testing
		#
		# Requires latest gcovr (for GCC 8.1 support):#
		# pip install git+https://github.com/gcovr/gcovr.git
		###############################################################################
		if(ENABLE_COVERAGE)
		find_program(GCOVR_BINARY gcovr)
		find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)

		if(GCOVR_FOUND)
		get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)

		add_custom_target(
		gen_coverage_xml
		COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
		COMMENT "Generating XML Coverage Report..."
		)

		add_custom_target(
		gen_coverage_html
		COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
		COMMENT "Generating HTML Coverage Report..."
		)
		endif()
		endif()

		###############################################################################
		# Print package summary
		##################################
		###############################################################################
		foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
		if(PKG_${PKG})
		message(STATUS "Building package: ${PKG}")

cmake/Modules/FindMSCG.cmake

0 → 100644

+22 −0

Original line number	Diff line number	Diff line
		# - Find mscg
		# Find the native MSCG headers and libraries.
		#
		# MSCG_INCLUDE_DIRS - where to find mscg.h, etc.
		# MSCG_LIBRARIES - List of libraries when using mscg.
		# MSCG_FOUND - True if mscg found.
		#

		find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg)

		find_library(MSCG_LIBRARY NAMES mscg)

		set(MSCG_LIBRARIES ${MSCG_LIBRARY})
		set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})

		include(FindPackageHandleStandardArgs)
		# handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE
		# if all listed variables are TRUE

		find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR)

		mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY )

cmake/README.md

+1628 −10

File changed.

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doc/Makefile

+8 −1

Original line number	Diff line number	Diff line
		@@ -9,6 +9,7 @@ TXT2RST = $(VENV)/bin/txt2rst
		ANCHORCHECK = $(VENV)/bin/doc_anchor_check

		PYTHON = $(shell which python3)
		VIRTUALENV = virtualenv
		HAS_PYTHON3 = NO
		HAS_VIRTUALENV = NO

		@@ -16,7 +17,13 @@ ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
		HAS_PYTHON3 = YES
		endif

		ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
		VIRTUALENV = virtualenv-3
		HAS_VIRTUALENV = YES
		endif

		ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
		VIRTUALENV = virtualenv
		HAS_VIRTUALENV = YES
		endif

		@@ -158,7 +165,7 @@ $(VENV):
		@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
		@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
		@( \
		virtualenv -p $(PYTHON) $(VENV); \
		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
		. $(VENV)/bin/activate; \
		pip install Sphinx; \
		pip install sphinxcontrib-images; \

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