Merge branch 'master' into user-cgdna (c6f637f7) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+6 −10

Original line number	Diff line number	Diff line
		@@ -322,13 +322,14 @@ endif()
		include(Packages/KSPACE)
		include(Packages/PYTHON)
		include(Packages/VORONOI)
		include(Packages/USER-SCAFACOS)
		include(Packages/USER-PLUMED)
		include(Packages/USER-COLVARS)
		include(Packages/USER-MOLFILE)
		include(Packages/USER-NETCDF)
		include(Packages/USER-SMD)
		include(Packages/USER-QUIP)
		include(Packages/USER-PLUMED)
		include(Packages/USER-QMMM)
		include(Packages/USER-QUIP)
		include(Packages/USER-SCAFACOS)
		include(Packages/USER-SMD)
		include(Packages/USER-VTK)
		include(Packages/KIM)
		include(Packages/LATTE)
		@@ -418,8 +419,7 @@ endforeach()
		##############################################
		# add lib sources of (simple) enabled packages
		############################################
		foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
		USER-QMMM)
		foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-QMMM)
		if(PKG_${SIMPLE_LIB})
		string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
		string(TOLOWER "${PKG_LIB}" PKG_LIB)
		@@ -433,10 +433,6 @@ foreach(SIMPLE_LIB 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 ${HDF5_INCLUDE_DIRS})
		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()

cmake/Modules/Packages/USER-COLVARS.cmake

0 → 100644

+42 −0

Original line number	Diff line number	Diff line
		if(PKG_USER-COLVARS)

		set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)

		file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)

		# Build Lepton by default
		set(COLVARS_LEPTON_DEFAULT ON)
		# but not if C++11 is disabled per user request
		if(DEFINED DISABLE_CXX11_REQUIREMENT)
		if(DISABLE_CXX11_REQUIREMENT)
		set(COLVARS_LEPTON_DEFAULT OFF)
		endif()
		endif()

		option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})

		# Verify that the user's choice is consistent
		if(DEFINED DISABLE_CXX11_REQUIREMENT)
		if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
		message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
		endif()
		endif()

		if(COLVARS_LEPTON)
		set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
		file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
		add_library(lepton STATIC ${LEPTON_SOURCES})
		target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
		endif()

		add_library(colvars STATIC ${COLVARS_SOURCES})
		target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
		list(APPEND LAMMPS_LINK_LIBS colvars)

		if(COLVARS_LEPTON)
		list(APPEND LAMMPS_LINK_LIBS lepton)
		target_compile_options(colvars PRIVATE -DLEPTON)
		target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
		endif()

		endif()

doc/src/Tools.txt

+10 −0

Original line number	Diff line number	Diff line
		@@ -87,6 +87,7 @@ Miscellaneous tools :h3
		"emacs"_#emacs,
		"i-pi"_#ipi,
		"kate"_#kate,
		"singularity"_#singularity_tool,
		"vim"_#vim :tb(c=5,ea=c,a=l)

		:line
		@@ -542,6 +543,15 @@ Ivanov, at University of Iceland (ali5 at hi.is).

		:line

		singularity tool :h4,link(singularity_tool)

		The singularity sub-directory contains container definitions files
		that can be used to build container images for building and testing
		LAMMPS on specific OS variants using the "Singularity"_https://sylabs.io
		container software. Contributions for additional variants are welcome.

		:line

		vim tool :h4,link(vim)

		The files in the tools/vim directory are add-ons to the VIM editor

doc/src/compute_gyration_shape.txt

+3 −0

Original line number	Diff line number	Diff line
		@@ -84,3 +84,6 @@ package"_Build_package.html doc page for more info.
		:link(Theodorou)
		[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).

		:link(Mattice)
		[(Mattice)] Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.

doc/utils/sphinx-config/false_positives.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -1582,6 +1582,7 @@ Materias
		mathbf
		matlab
		matplotlib
		Mattice
		Mattox
		Mattson
		maxangle

Admin message