Merge branch 'master' into reax_dup (f10c9889) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+25 −16

Original line number	Diff line number	Diff line
		@@ -104,7 +104,7 @@ set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
		USER-ATC USER-AWPMD 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-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
		USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
		USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
		set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
		foreach(PKG ${DEFAULT_PACKAGES})
		@@ -170,13 +170,6 @@ if(ENABLE_KSPACE)
		endif()
		endif()

		if(ENABLE_MISC)
		option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
		if(LAMMPS_XDR)
		add_definitions(-DLAMMPS_XDR) # for liblammps
		endif()
		endif()

		if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
		find_package(LAPACK)
		if(NOT LAPACK_FOUND)
		@@ -198,14 +191,13 @@ if(ENABLE_PYTHON)
		add_definitions(-DLMP_PYTHON)
		include_directories(${PYTHON_INCLUDE_DIR})
		list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
		if(BUILD_SHARED_LIBS)
		if(NOT PYTHON_INSTDIR)
		execute_process(COMMAND ${PYTHON_EXECUTABLE}
		-c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
		OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
		endif()
		install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
		if(NOT BUILD_SHARED_LIBS)
		message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
		endif()
		endif()

		@@ -401,6 +393,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
		target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
		elseif(PKG_LIB STREQUAL h5md)
		target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
		elseif(PKG_LIB STREQUAL colvars)
		target_compile_options(colvars PRIVATE -DLEPTON)
		target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
		target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
		else()
		target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
		endif()
		@@ -480,6 +476,8 @@ if(ENABLE_KOKKOS)
		${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
		${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
		${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
		${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
		${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
		${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
		${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
		set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
		@@ -487,6 +485,17 @@ if(ENABLE_KOKKOS)
		# detects styles which have KOKKOS version
		RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)

		# register kokkos-only styles
		RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
		RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)

		if(ENABLE_USER-DPD)
		get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
		list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
		RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
		set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
		endif()

		get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)

		list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})

cmake/Modules/StyleHeaderUtils.cmake

+22 −0

Original line number	Diff line number	Diff line
		@@ -11,6 +11,12 @@ function(FindStyleHeaders path style_class file_pattern headers)
		set_property(GLOBAL PROPERTY ${headers} "${hlist}")
		endfunction(FindStyleHeaders)

		function(AddStyleHeader path headers)
		get_property(hlist GLOBAL PROPERTY ${headers})
		list(APPEND hlist ${path})
		set_property(GLOBAL PROPERTY ${headers} "${hlist}")
		endfunction(AddStyleHeader)

		function(FindStyleHeadersExt path style_class extension headers sources)
		get_property(hlist GLOBAL PROPERTY ${headers})
		get_property(slist GLOBAL PROPERTY ${sources})
		@@ -62,6 +68,22 @@ function(GenerateStyleHeader path property style)
		CreateStyleHeader("${path}" "style_${style}.h" ${files})
		endfunction(GenerateStyleHeader)

		function(RegisterNBinStyles search_path)
		FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
		endfunction(RegisterNBinStyles)

		function(RegisterNPairStyles search_path)
		FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor
		endfunction(RegisterNPairStyles)

		function(RegisterNBinStyle path)
		AddStyleHeader(${path} NBIN)
		endfunction(RegisterNBinStyle)

		function(RegisterNPairStyle path)
		AddStyleHeader(${path} NPAIR)
		endfunction(RegisterNPairStyle)

		function(RegisterStyles search_path)
		FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
		FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid

doc/Makefile

+4 −3

Original line number	Diff line number	Diff line
		@@ -20,6 +20,7 @@ ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
		HAS_VIRTUALENV = YES
		endif

		SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
		SOURCES=$(wildcard src/*.txt)
		OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)

		@@ -55,7 +56,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
		@(\
		. $(VENV)/bin/activate ;\
		cp -r src/* $(RSTDIR)/ ;\
		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
		echo "############################################" ;\
		doc_anchor_check src/*.txt ;\
		echo "############################################" ;\
		@@ -91,7 +92,7 @@ epub: $(OBJECTS)
		@(\
		. $(VENV)/bin/activate ;\
		cp -r src/* $(RSTDIR)/ ;\
		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
		deactivate ;\
		)
		@mv epub/LAMMPS.epub .
		@@ -159,7 +160,7 @@ $(VENV):
		@( \
		virtualenv -p $(PYTHON) $(VENV); \
		. $(VENV)/bin/activate; \
		pip install Sphinx==1.5.6; \
		pip install Sphinx; \
		pip install sphinxcontrib-images; \
		deactivate;\
		)

doc/src/Eqs/angle_class2_p6.jpg

0 → 100644

+13.5 KiB

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doc/src/Eqs/angle_cosine_buck6d.jpg

0 → 100644

+5.25 KiB

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