Merge pull request #45 from lammps/master (76e67415) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -453,7 +453,7 @@ if(PKG_VORONOI)
		set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})

		ExternalProject_Add(voro_build
		URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
		URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
		URL_MD5 2338b824c3b7b25590e18e8df5d68af9
		CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
		)

cmake/Modules/StyleHeaderUtils.cmake

+2 −0

Original line number	Diff line number	Diff line
		@@ -50,6 +50,7 @@ function(CreateStyleHeader path filename)
		list(REMOVE_AT ARGV 0 1)
		set(header_list)
		foreach(FNAME ${ARGV})
		set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
		get_filename_component(FNAME ${FNAME} NAME)
		list(APPEND header_list ${FNAME})
		endforeach()
		@@ -61,6 +62,7 @@ function(CreateStyleHeader path filename)
		message(STATUS "Generating ${filename}...")
		file(WRITE "${path}/${filename}.tmp" "${temp}" )
		execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
		set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
		endfunction(CreateStyleHeader)

		function(GenerateStyleHeader path property style)

doc/src/Build_basics.txt

+12 −0

Original line number	Diff line number	Diff line
		@@ -116,6 +116,18 @@ enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel
		compilers it is -qopenmp. If you are using a different compiler,
		please refer to its documentation.

		[OpenMP Compiler compatibility info]: :link(default-none-issues)

		Some compilers do not fully support the 'default(none)' directive
		and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
		semantics, which are incompatible with the OpenMP 3.1 directives used
		in LAMMPS (for maximal compatibility with compiler versions in use).
		In those case, all 'default(none)' directives (which aid in detecting
		incorrect and unwanted sharing) can be replaced with 'default(shared)'
		while dropping all 'shared()' directives. The script
		'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
		this conversion.

		:line

		Choice of compiler and compile/link options :h4,link(compile)

doc/src/Build_extras.txt

+3 −1

Original line number	Diff line number	Diff line
		@@ -932,7 +932,9 @@ LINKFLAGS: -fopenmp # for GNU Compilers
		LINKFLAGS: -qopenmp # for Intel compilers on Linux :pre

		For other platforms and compilers, please consult the documentation
		about OpenMP support for your compiler.
		about OpenMP support for your compiler. Please see the note about
		how to address compatibility "issues with the 'default(none)'
		directive"_Build_basics.html#default-none-issues of some compilers.

		:line

doc/src/compute_ptm_atom.txt

+8 −8

Original line number	Diff line number	Diff line
		@@ -38,20 +38,20 @@ ico (icosahedral) = 4
		sc (simple cubic) = 5
		dcub (diamond cubic) = 6
		dhex (diamond hexagonal) = 7
		other = 8 :ul
		graphene = 8 :ul

		The value of the PTM structure will be 0 for atoms not in the specified
		The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified
		compute group. The choice of structures to search for can be specified using the "structures"
		argument, which is a hyphen-separated list of structure keywords.
		Two convenient pre-set options are provided:

		default: fcc-hcp-bcc-ico
		all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
		all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene :ul

		The 'default' setting detects the same structures as the Common Neighbor Analysis method.
		The 'all' setting searches for all structure types. A small performance penalty is
		incurred for the diamond structures, so it is not recommended to use this option if
		it is known that the simulation does not contain diamond structures.
		The 'all' setting searches for all structure types. A performance penalty is
		incurred for the diamond and graphene structures, so it is not recommended to use this option if
		it is known that the simulation does not contain these structures.


		PTM identifies structures using two steps. First, a graph isomorphism test is used
		@@ -93,9 +93,9 @@ interatomic distance
		qw
		qx
		qy
		qw :ul
		qz :ul

		The type is a number from 0 to 8. The rmsd is a positive real number.
		The type is a number from -1 to 8. The rmsd is a positive real number.
		The interatomic distance is computed from the scale factor in the RMSD equation.
		The (qw,qx,qy,qz) parameters represent the orientation of the local structure
		in quaternion form. The reference coordinates for each template (from which the

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