Merge pull request #1592 from akohlmey/collected-small-changes (69a5ff22) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+1 −2

Original line number	Diff line number	Diff line
		@@ -219,8 +219,7 @@ if(BUILD_OMP)
		set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
		endif()


		if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
		if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
		find_package(LAPACK)
		find_package(BLAS)
		if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)

cmake/Modules/Packages/USER-PLUMED.cmake

+19 −7

Original line number	Diff line number	Diff line
		if(PKG_USER-PLUMED)
		find_package(GSL REQUIRED)
		set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
		set(PLUMED_MODE_VALUES static shared runtime)
		set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
		validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
		string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)

		set(PLUMED_LINK_LIBS "")
		if(PLUMED_MODE STREQUAL "STATIC")
		find_package(LAPACK REQUIRED)
		find_package(BLAS REQUIRED)
		find_package(GSL REQUIRED)
		list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
		list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
		find_package(ZLIB QUIET)
		if(ZLIB_FOUND)
		list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
		endif()
		endif()

		find_package(PkgConfig QUIET)
		set(DOWNLOAD_PLUMED_DEFAULT ON)
		if(PKG_CONFIG_FOUND)
		@@ -37,8 +49,8 @@ if(PKG_USER-PLUMED)
		message(STATUS "PLUMED download requested - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(plumed_build
		URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
		URL_MD5 c2a7b519e32197a120cdf47e0f194f81
		URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz
		URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a
		BUILD_IN_SOURCE 1
		CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
		${CONFIGURE_REQUEST_PIC}
		@@ -53,11 +65,11 @@ if(PKG_USER-PLUMED)
		list(APPEND LAMMPS_DEPS plumed_build)
		if(PLUMED_MODE STREQUAL "STATIC")
		add_definitions(-D__PLUMED_WRAPPER_CXX=1)
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
		elseif(PLUMED_MODE STREQUAL "SHARED")
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
		elseif(PLUMED_MODE STREQUAL "RUNTIME")
		add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
		add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
		endif()
		set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
		@@ -70,7 +82,7 @@ if(PKG_USER-PLUMED)
		elseif(PLUMED_MODE STREQUAL "SHARED")
		include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
		elseif(PLUMED_MODE STREQUAL "RUNTIME")
		add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)
		add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
		include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
		endif()
		list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})

doc/include-file-conventions.md

+1 −1

Original line number	Diff line number	Diff line
		@@ -107,7 +107,7 @@ Include files should be included in this order:
		#### pointers.h

		The `pointer.h` header file also includes `cstdio` and `lmptype.h`
		(and through it `stdint.h`, `intttypes.h`, and `climits`).
		(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
		This means any header including `pointers.h` can assume that `FILE`,
		`NULL`, `INT_MAX` are defined.

doc/src/compute_hexorder_atom.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -65,7 +65,7 @@ In an isotropic liquid, local neighborhoods may still exhibit
		weak hexagonal symmetry, but because the orientational correlation
		decays quickly with distance, the value of phi will be different for
		different atoms, and so when {q}6 is averaged over all the atoms
		in the system, \\|<{q}6>\\| << 1.
		in the system, \|<{q}6>\| << 1.

		The value of {qn} is set to zero for atoms not in the
		specified compute group, as well as for atoms that have less than

doc/src/fix_plumed.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -114,5 +114,5 @@ The default options are plumedfile = NULL and outfile = NULL
		:link(PLUMED)
		[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)

		:link(plumeddocs,http://www.plumed.org/documentation)
		:link(plumeddocs,http://www.plumed.org/doc.html)
		:link(plumedhome,http://www.plumed.org/)

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