Merge branch 'master' into kk_snap (3d374aa8) · Commits · 郑智淋 / lammps

cmake/CMakeLists.txt

+5 −5

Original line number	Diff line number	Diff line
		@@ -171,7 +171,7 @@ set(LAMMPS_DEPS)
		set(LAMMPS_API_DEFINES)

		set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
		KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
		KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
		SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
		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
		@@ -191,11 +191,11 @@ endforeach()
		######################################################
		# packages with special compiler needs or external libs
		######################################################
		if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
		if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
		enable_language(Fortran)
		endif()

		if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
		if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
		enable_language(C)
		endif()

		@@ -826,7 +826,7 @@ endforeach()
		##############################################
		# add lib sources of (simple) enabled packages
		############################################
		foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
		foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
		USER-QMMM)
		if(PKG_${SIMPLE_LIB})
		string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
		@@ -1325,7 +1325,7 @@ if(BUILD_LIB)
		configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
		configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
		else()
		list(APPEND LMP_SOURCES ${LIB_SOURCES})
		endif()

cmake/README.md

+19 −2

Original line number	Diff line number	Diff line
		@@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases.
		* [Build directory vs. Source Directory](#build-directory-vs-source-directory)
		* [Defining and using presets](#defining-and-using-presets)
		* [Reference](#reference)
		* [Common CMAKE Configuration Options](#common-cmake-configuration-options)
		* [Common CMake Configuration Options](#common-cmake-configuration-options)
		* [LAMMPS Configuration Options](#lammps-configuration-options)
		* [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
		* [Default Packages](#default-packages)
		@@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake

		# Reference

		## Common CMAKE Configuration Options
		## Common CMake Configuration Options


		<table>
		@@ -208,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
		</dl>
		</td>
		</tr>
		<tr>
		<td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
		<td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
		<td>
		<dl>
		<dt><code>off</code> (default)</dt>
		<dt><code>on</code></dt>
		</dl>
		</td>
		</tr>
		</tbody>
		</table>

		@@ -1729,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
		value of `FC` environment variable at first `cmake` run
		</td>
		</tr>
		<tr>
		<td><code>CXX_COMPILER_LAUNCHER</code></td>
		<td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
		<td>
		(empty)
		</td>
		</tr>
		</tbody>
		</table>

doc/Makefile

+1 −0

Original line number	Diff line number	Diff line
		@@ -48,6 +48,7 @@ help:
		@echo " clean-all reset the entire build environment"
		@echo " txt2html build txt2html tool"
		@echo " anchor_check scan for duplicate anchor labels"
		@echo " spelling spell-check the manual"

		# ------------------------------------------

doc/github-development-workflow.md

+5 −4

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
		tools, but do not set policies, so it is up to the developers to come to
		an agreement as to how to define and interpret policies. This document
		is likely to change as our experiences and needs change and we try to
		adapt accordingly. Last change 2018-11-15.
		adapt accordingly. Last change 2018-12-19.

		## Table of Contents

		@@ -129,16 +129,17 @@ Here are some items to check:
		* stdlib.h -> cstdlib
		* string.h -> cstring
		* time.h -> ctime
		Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
		* Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
		* Code should follow the C++-98 standard. C++-11 is only accepted
		in individual special purpose packages
		* indentation is two spaces per level
		* there should be no tabs and no trailing whitespace
		* indentation is 2 spaces per level
		* there should be NO tabs and no trailing whitespace
		* header files, especially of new styles, should not include any
		other headers, except the header with the base class or cstdio.
		Forward declarations should be used instead when possible.
		* iostreams should be avoided. LAMMPS uses stdio from the C-library.
		* use of STL in headers and class definitions should be avoided.
		* there MUST NOT be any "using namespace XXX;" statements in headers.
		* static class members should be avoided at all cost.
		* anything storing atom IDs should be using `tagint` and not `int`.
		This can be flagged by the compiler only for pointers and only when

doc/src/Build_extras.txt

+0 −40

Original line number	Diff line number	Diff line
		@@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
		"OPT"_#opt,
		"POEMS"_#poems,
		"PYTHON"_#python,
		"REAX"_#reax,
		"VORONOI"_#voronoi,
		"USER-ATC"_#user-atc,
		"USER-AWPMD"_#user-awpmd,
		@@ -536,45 +535,6 @@ build fails.

		:line

		REAX package :h4,link(reax)

		NOTE: the use of the REAX package and its "pair_style
		reax"_pair_reax.html command is discouraged, as it is no longer
		maintained. Please use the USER-REAXC package and its "pair_style
		reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
		enabled variant (pair_style reax/c/kk), which has a more robust memory
		management. See the "pair_style reax/c"_pair_reaxc.html doc page for
		details.

		[CMake build]:

		No additional settings are needed besides "-D PKG_REAX=yes".

		[Traditional make]:

		Before building LAMMPS, you must build the REAX library in lib/reax.
		You can do this manually if you prefer; follow the instructions in
		lib/reax/README. You can also do it in one step from the lammps/src
		dir, using a command like these, which simply invoke the
		lib/reax/Install.py script with the specified args:

		make lib-reax # print help message
		make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
		make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
		make lib-reax args="-m ifort" # build with Intel ifort compiler :pre

		The build should produce two files: lib/reax/libreax.a and
		lib/reax/Makefile.lammps. The latter is copied from an existing
		Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
		Fortran (REAX library). Typically the two compilers used for LAMMPS
		and the REAX library need to be consistent (e.g. both Intel or both
		GNU compilers). If necessary, you can edit/create a new
		lib/reax/Makefile.machine file for your system, which should define an
		EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
		file.

		:line

		VORONOI package :h4,link(voronoi)

		To build with this package, you must download and build the "Voro++

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