Merge pull request #28 from lammps/master (b16a83cd) · Commits · 郑智淋 / lammps

.github/CODEOWNERS

+1 −0

Original line number	Diff line number	Diff line
		@@ -30,6 +30,7 @@ src/USER-MOFFF/* @hheenen
		src/USER-MOLFILE/* @akohlmey
		src/USER-NETCDF/* @pastewka
		src/USER-PHONON/* @lingtikong
		src/USER-PTM/* @pmla
		src/USER-OMP/* @akohlmey
		src/USER-QMMM/* @akohlmey
		src/USER-REAXC/* @hasanmetin

cmake/CMakeLists.txt

+29 −24

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUT


		# To avoid conflicts with the conventional Makefile build system, we build everything here
		file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp)
		file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
		file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
		list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})

		@@ -164,12 +164,13 @@ set(LAMMPS_DEPS)
		set(LAMMPS_API_DEFINES)

		set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
		KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
		SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
		USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
		USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
		USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS
		USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
		KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
		SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
		USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
		USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
		USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
		USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ
		USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
		set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
		set(OTHER_PACKAGES CORESHELL QEQ)
		foreach(PKG ${DEFAULT_PACKAGES})
		@@ -348,7 +349,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
		find_package(BLAS)
		if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
		enable_language(Fortran)
		file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
		file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
		add_library(linalg STATIC ${LAPACK_SOURCES})
		set(LAPACK_LIBRARIES linalg)
		else()
		@@ -550,8 +551,9 @@ if(PKG_USER-SMD)
		set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
		list(APPEND LAMMPS_DEPS Eigen3_build)
		else()
		find_package(Eigen3)
		if(NOT Eigen3_FOUND)
		find_package(Eigen3 NO_MODULE)
		mark_as_advanced(Eigen3_DIR)
		if(NOT EIGEN3_FOUND)
		message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
		endif()
		endif()
		@@ -603,8 +605,9 @@ endif()

		if(PKG_MESSAGE)
		option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
		file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/*.F
		${LAMMPS_LIB_SOURCE_DIR}/message/cslib/.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/.cpp)
		file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
		${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
		${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)

		if(BUILD_SHARED_LIBS)
		add_library(cslib SHARED ${cslib_SOURCES})
		@@ -720,8 +723,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
		foreach(PKG ${DEFAULT_PACKAGES})
		set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})

		file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
		file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
		file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
		file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)

		# check for package files in src directory due to old make system
		DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
		@@ -739,8 +742,8 @@ endforeach()
		foreach(PKG ${ACCEL_PACKAGES})
		set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})

		file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
		file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
		file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
		file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)

		# check for package files in src directory due to old make system
		DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
		@@ -754,8 +757,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
		if(PKG_${SIMPLE_LIB})
		string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
		string(TOLOWER "${PKG_LIB}" PKG_LIB)
		file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
		${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/.cpp)
		file(GLOB_RECURSE ${PKG_LIB}_SOURCES
		${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
		${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
		${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
		add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
		list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
		if(PKG_LIB STREQUAL awpmd)
		@@ -1039,7 +1044,7 @@ if(PKG_GPU)
		set(GPU_PREC_SETTING "SINGLE_SINGLE")
		endif()

		file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
		file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
		file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)

		if(GPU_API STREQUAL "CUDA")
		@@ -1052,15 +1057,15 @@ if(PKG_GPU)

		set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")

		file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/.cu)
		file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.].cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.].cu)
		list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)

		cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)

		if(CUDPP_OPT)
		cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
		file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
		file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
		file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
		file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
		endif()

		cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
		@@ -1109,7 +1114,7 @@ if(PKG_GPU)
		include(OpenCLUtils)
		set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)

		file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
		file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
		list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)

		foreach(GPU_KERNEL ${GPU_LIB_CU})
		@@ -1236,7 +1241,7 @@ if(BUILD_DOC)

		set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)

		file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt)
		file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
		file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
		list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})

cmake/Modules/StyleHeaderUtils.cmake

+3 −3

Original line number	Diff line number	Diff line
		@@ -94,14 +94,14 @@ function(RegisterStyles search_path)
		FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
		FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body
		FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force
		FindStyleHeaders(${search_path} COMMAND_CLASS "" COMMAND ) # command ) # input
		FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input
		FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify
		FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
		FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
		FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
		FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
		FindStyleHeaders(${search_path} INTEGRATE_CLASS "" INTEGRATE ) # integrate ) # update
		FindStyleHeaders(${search_path} KSPACE_CLASS "" KSPACE ) # kspace ) # force
		FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
		FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
		FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update
		FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
		FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor

doc/src/Build_basics.txt

+4 −0

Original line number	Diff line number	Diff line
		@@ -292,6 +292,10 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
		you can browse them locally on your system. Type "make" from the
		lammps/doc dir to see other options.

		NOTE: You can also download a tarball of the documention for the
		current LAMMPS version (HTML and PDF files), from the website
		"download page"_http://lammps.sandia.gov/download.html.

		:line

		Install LAMMPS after a build :h4,link(install)

doc/src/Build_package.txt

+2 −2

Original line number	Diff line number	Diff line
		@@ -42,7 +42,7 @@ packages:
		"KOKKOS"_Build_extras.html#kokkos,
		"LATTE"_Build_extras.html#latte,
		"MEAM"_Build_extras.html#meam,
		"MESSAGE"_#Build_extras.html#message,
		"MESSAGE"_Build_extras.html#message,
		"MSCG"_Build_extras.html#mscg,
		"OPT"_Build_extras.html#opt,
		"POEMS"_Build_extras.html#poems,
		@@ -59,7 +59,7 @@ packages:
		"USER-OMP"_Build_extras.html#user-omp,
		"USER-QMMM"_Build_extras.html#user-qmmm,
		"USER-QUIP"_Build_extras.html#user-quip,
		"USER-SCAFACOS"_#Build_extras.html#user-scafacos,
		"USER-SCAFACOS"_Build_extras.html#user-scafacos,
		"USER-SMD"_Build_extras.html#user-smd,
		"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)

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