Merge branch 'master' into sdpd to resolve merge conflicts (e0955f64) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+31 −3

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		@@ -171,8 +171,9 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
		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-SDPD USER-SMD
		USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
		USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
		USER-SDPD 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})
		@@ -193,6 +194,8 @@ if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
		enable_language(C)
		endif()

		include_directories(${LAMMPS_SOURCE_DIR})

		# do MPI detection after language activation, if MPI for these language is required
		find_package(MPI QUIET)
		option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
		@@ -526,6 +529,32 @@ if(PKG_USER-SCAFACOS)
		include_directories(${SCAFACOS_INCLUDE_DIRS})
		endif()

		if(PKG_USER-PLUMED)
		find_package(GSL REQUIRED)
		option(DOWNLOAD_PLUMED "Download Plumed (instead of using the system's one)" OFF)
		if(DOWNLOAD_PLUMED)
		include(ExternalProject)
		ExternalProject_Add(plumed_build
		URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
		URL_MD5 b1be7c48971627febc11c61b70767fc5
		BUILD_IN_SOURCE 1
		CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
		$<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic> )
		ExternalProject_get_property(plumed_build INSTALL_DIR)
		set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
		list(APPEND LAMMPS_DEPS plumed_build)
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
		${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
		set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
		else()
		find_package(PkgConfig REQUIRED)
		pkg_check_modules(PLUMED plumed REQUIRED)
		include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
		endif()
		include_directories(${PLUMED_INCLUDE_DIRS})
		endif()

		if(PKG_USER-MOLFILE)
		add_library(molfile INTERFACE)
		target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
		@@ -1180,7 +1209,6 @@ set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)

		GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})

		include_directories(${LAMMPS_SOURCE_DIR})
		include_directories(${LAMMPS_STYLE_HEADERS_DIR})

		######################################

cmake/pkgconfig/liblammps.pc.in

+22 −2

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		# pkg-config file for lammps
		# https://people.freedesktop.org/~dbn/pkg-config-guide.html
		# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
		# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,

		# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH
		# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig

		# Use this on commandline with:
		# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp

		# Use this in a Makefile:
		# myapp: myapp.cpp
		# $(CC) `pkg-config --cflags --libs lammps` -o $@ $<

		# Use this in autotools:
		# configure.ac:
		# PKG_CHECK_MODULES([LAMMPS], [lammps])
		# Makefile.am:
		# myapp_CFLAGS = $(LAMMPS_CFLAGS)
		# myapp_LDADD = $(LAMMPS_LIBS)

		# Use this in CMake:
		# CMakeLists.txt:
		# find_package(PkgConfig)
		# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
		# target_link_libraries(<lib> PkgConfig::LAMMPS)

		prefix=@CMAKE_INSTALL_PREFIX@
		libdir=@CMAKE_INSTALL_FULL_LIBDIR@
		includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@

doc/src/Build_extras.txt

+57 −0

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		@@ -41,6 +41,7 @@ This is the list of packages that may require additional steps.
		"USER-ATC"_#user-atc,
		"USER-AWPMD"_#user-awpmd,
		"USER-COLVARS"_#user-colvars,
		"USER-PLUMED" _#user-plumed,
		"USER-H5MD"_#user-h5md,
		"USER-INTEL"_#user-intel,
		"USER-MOLFILE"_#user-molfile,
		@@ -712,6 +713,62 @@ a corresponding Makefile.lammps.machine file.

		:line

		USER-PLUMED package :h4,link(user-plumed)

		[CMake build]:

		[Traditional make]:

		Before building LAMMPS with this package, you must first build
		PLUMED. We recommending building PLUMED separately to LAMMPS using
		the instructions that can be found at http://plumed.github.io/doc-master/user-doc/html/_installation.html.
		Before compiling LAMMPS you can then install the fix plumed command
		and compile LAMMPS in the usual manner:

		make yes-user-plumed
		make machine :pre

		Once this compilation completes you should be able to run LAMMPS in the usual
		way. When running LAMMPS with an input script that contains a fix
		plumed command LAMMPS will try to call the PLUMED runtime library. PLUMED
		must therefore be available in your path if LAMMPS is compiled in this way.

		On some machines it is not possible to call runtime libraries in the way described
		above. When compiling on these machines it is thus better to statically link
		PLUMED when compiling LAMMPS. To do this you must either download a PLUMED
		tarball from http://www.plumed.org/get-it or clone it using
		git clone https://github.com/plumed/plumed2.git. If you download the tarball
		unpack it in the /lib/plumed directory. Similarly if you clone
		it clone it to the /lib/plumed directory as if there is a version of PLUMED within
		this directory LAMMPS will always try to statically link the version of PLUMED
		that this directory contains instead of dynamically linking the library.

		Once you have downloaded PLUMED into /lib/plumed you must again build the code
		here by following the instructions that can be found at
		http://plumed.github.io/doc-master/user-doc/html/_installation.html.

		You can statically link PLUMED manually and if you want to access the full
		range of PLUMED functionalities this is what you should do. If you only want the
		basic range of functionalities, however, (i.e. no user contributed modules) then
		you can download and compile PLUMED in one step from the lammps/src dir, using a
		command like like those below:

		make lib-plumed # print help message
		make lib-plumed args="-b" # download and build the latest stable version of PLUMED

		These commands will simply invoke the lib/plumed/Install.py script with
		args specified. Furthermore, once the script has completed you should
		have a compiled version of PLUMED. With this built you can install/un-install
		PLUMED and build LAMMPS in the usual manner:

		make yes-user-plumed
		make machine :pre

		make no-user-plumed
		make machine :pre

		:line

		USER-H5MD package :h4,link(user-h5md)

		To build with this package you must have the HDF5 software package

doc/src/PDF/colvars-refman-lammps.pdf

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doc/src/Packages_details.txt

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		@@ -1201,6 +1201,34 @@ examples/USER/colvars :ul

		:line

		USER-PLUMED package :link(USER-PLUMED),h4

		[Contents:]

		The fix plumed command allows you to use the plugin for molecular
		dynamics PLUMED to analyse and bias your LAMMPS trajectory on the fly.
		In practise PLUMED is called from within the lammps input script by using
		the "fix plumed _fix_plumed.html command.

		[Authors:] The PLUMED library is written and maintained by
		Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and
		Gareth Tribello.

		[Install:]

		This package has "specific installation
		instructions"_Build_extras.html#gpu on the "Build
		extras"_Build_extras.html doc page.

		[Supporting info:]

		src/USER-PLUMED/README
		lib/plumed/README
		"fix plumed "_fix_plumed.html
		examples/USER/plumed :ul

		:line

		USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4

		[Contents:]

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