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Merge branch 'master' of https://github.com/lammps/lammps into lammps-master

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This commit is contained in:
Jacob Gissinger
2021-06-07 22:48:51 -04:00
parent 26fe17a379 d74d7cfd5f
commit b124de3484
4175 changed files with 127478 additions and 48418 deletions
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2
.gitattributes vendored
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@ -1,3 +1,5 @@
.gitattributes export-ignore
.gitignore export-ignore
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore

16
.github/CODEOWNERS vendored
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@ -13,29 +13,37 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/COMPRESS/* @akohlmey
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/USER-BROWNIAN/* @samueljmcameron
src/USER-CGDNA/* @ohenrich
src/USER-CGSDK/* @akohlmey
src/USER-COLVARS/* @giacomofiorin
src/USER-FEP/* @agiliopadua
src/USER-HDNNP/* @singraber
src/USER-INTEL/* @wmbrownintel
src/USER-MANIFOLD/* @Pakketeretet2
src/USER-MDI/* @taylor-a-barnes
src/USER-MEAMC/* @martok
src/USER-MESONT/* @iafoss
src/USER-MOFFF/* @hheenen
src/USER-MOLFILE/* @akohlmey
src/USER-NETCDF/* @pastewka
src/USER-PACE/* @yury-lysogorskiy
src/USER-PLUMED/* @gtribello
src/USER-PHONON/* @lingtikong
src/USER-PTM/* @pmla
src/USER-OMP/* @akohlmey
src/USER-QMMM/* @akohlmey
src/USER-REAXC/* @hasanmetin
src/USER-REACTION/* @jrgissing
src/USER-SCAFACOS/* @rhalver
src/USER-TALLY/* @akohlmey
src/USER-UEF/* @danicholson
@ -47,7 +55,6 @@ src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/USER-REACTION/fix_bond_react.* @jrgissing
src/USER-MISC/*_grem.* @dstelter92
src/USER-MISC/compute_stress_mop*.* @RomainVermorel
@ -122,6 +129,8 @@ tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/code_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/offline/* @rbberger
# tests
unittest/* @akohlmey @rbberger
@ -130,7 +139,7 @@ unittest/* @akohlmey @rbberger
cmake/* @junghans @rbberger
cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @junghans @rbberger @akohlmey
cmake/presets/*.cmake @akohlmey
# python
python/* @rbberger
@ -142,6 +151,7 @@ fortran/* @akohlmey
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
examples/plugin/* @akohlmey
# for releases
src/version.h @sjplimp

4
.github/codeql/cpp.yml vendored Normal file
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@ -0,0 +1,4 @@
paths:
- src
- lib
- tools

5
.github/codeql/python.yml vendored Normal file
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@ -0,0 +1,5 @@
paths:
- python/lammps
queries:
- uses: security-and-quality

8
.github/workflows/codeql-analysis.yml vendored
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@ -31,16 +31,18 @@ jobs:
uses: github/codeql-action/init@v1
with:
languages: ${{ matrix.language }}
config-file: ./.github/codeql/${{ matrix.language }}.yml
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
if: ${{ matrix.language == 'cpp' }}
run: mkdir build
- name: Building LAMMPS via CMake
if: ${{ matrix.language == 'cpp' }}
shell: bash
working-directory: ${{github.workspace}}/build
working-directory: build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
cmake -C ../cmake/presets/most.cmake ../cmake
cmake --build . --parallel 2
- name: Perform CodeQL Analysis

32
.github/workflows/unittest-macos.yml vendored
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@ -10,6 +10,8 @@ jobs:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
@ -17,20 +19,36 @@ jobs:
with:
fetch-depth: 2
- name: Install ccache
run: brew install ccache
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
run: mkdir build
- name: Set up ccache
uses: actions/cache@v2
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}
restore-keys: macos-ccache-
- name: Building LAMMPS via CMake
shell: bash
working-directory: ${{github.workspace}}/build
working-directory: build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
-C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
$GITHUB_WORKSPACE/cmake \
-DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
ccache -z
cmake -C ../cmake/presets/clang.cmake \
-C ../cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D ENABLE_TESTING=on \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on \
../cmake
cmake --build . --parallel 2
ccache -s
- name: Run Tests
working-directory: ${{github.workspace}}/build
working-directory: build
shell: bash
run: ctest -V

14
.lgtm.yml Normal file
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@ -0,0 +1,14 @@
extraction:
cpp:
configure:
command:
- "mkdir build"
- "cd build"
- "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
index:
build_command:
- "cd build"
- "ninja"
python:
python_setup:
version: 3

20
README
View File

@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
under the terms of the GNU Public License (GPL) version 2.
The primary author of the code is Steve Plimpton, who can be emailed
at sjplimp@sandia.gov. The LAMMPS WWW Site at lammps.sandia.gov has
at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has
more information about the code and its uses.
The LAMMPS distribution includes the following files and directories:
@ -37,14 +37,14 @@ tools pre- and post-processing tools
Point your browser at any of these files to get started:
https://lammps.sandia.gov/doc/Manual.html LAMMPS manual
https://lammps.sandia.gov/doc/Intro.html hi-level introduction
https://lammps.sandia.gov/doc/Build.html how to build LAMMPS
https://lammps.sandia.gov/doc/Run_head.html how to run LAMMPS
https://lammps.sandia.gov/doc/Commands_all.html Table of available commands
https://lammps.sandia.gov/doc/Library.html LAMMPS library interfaces
https://lammps.sandia.gov/doc/Modify.html how to modify and extend LAMMPS
https://lammps.sandia.gov/doc/Developer.html LAMMPS developer info
https://docs.lammps.org/Manual.html LAMMPS manual
https://docs.lammps.org/Intro.html hi-level introduction
https://docs.lammps.org/Build.html how to build LAMMPS
https://docs.lammps.org/Run_head.html how to run LAMMPS
https://docs.lammps.org/Commands_all.html Table of available commands
https://docs.lammps.org/Library.html LAMMPS library interfaces
https://docs.lammps.org/Modify.html how to modify and extend LAMMPS
https://docs.lammps.org/Developer.html LAMMPS developer info
You can also create these doc pages locally:

35
SECURITY.md Normal file
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@ -0,0 +1,35 @@
# Security Policy
LAMMPS is designed as a user-level application to conduct computer
simulations for research using classical mechanics. As such LAMMPS
depends to some degrees on users providing correctly formatted input and
LAMMPS needs to read and write files based on uncontrolled user input.
As a parallel application for use in high-performance computing
environments, performance critical steps are also done without checking
data.
LAMMPS also is interfaced to a number of external libraries, including
libraries with experimental research software, that are not validated
and tested by the LAMMPS developers, so it is easy to import bad
behavior from calling functions in one of those libraries.
Thus is is quite easy to crash LAMMPS through malicious input and do all
kinds of filesystem manipulations. And because of that LAMMPS should
**NEVER** be compiled or **run** as superuser, either from a "root" or
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
# Version Updates
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.

2
bench/POTENTIALS/README
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@ -1,7 +1,7 @@
These are input scripts used to run benchmark tests for many of the
interatomic potentials in LAMMPS. The results of running these
scripts on different machines are shown on the Potentials section of
the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
Examples are shown below of how to run these scripts. Log files for
running them on 1 and 4 processors of a Linux box are included in the

4
bench/README
View File

@ -2,7 +2,7 @@ LAMMPS benchmark problems
This directory contains 5 benchmark problems which are discussed in
the Benchmark section of the LAMMPS documentation, and on the
Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
This directory also has several sub-directories:
@ -11,7 +11,7 @@ KEPLER benchmark scripts for GPU cluster with Kepler GPUs
POTENTIALS benchmarks scripts for various potentials in LAMMPS
The results for all of these benchmarks are displayed and discussed on
the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
The remainder of this file refers to the 5 problems in the top-level
of this directory and how to run them on CPUs, either in serial or

76
cmake/CMakeLists.txt
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@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10)
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
########################################
project(lammps CXX)
@ -72,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
@ -86,6 +91,11 @@ set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# export all symbols when building a .dll file on windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
endif()
########################################################################
# User input options #
########################################################################
@ -104,11 +114,23 @@ endif()
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
# allow enabling clang-tidy for C++ files
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
add_library(lammps ${ALL_SOURCES})
# tell CMake to export all symbols to a .dll on Windows with MinGW cross-compilers
if(BUILD_SHARED_LIBS AND (CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
set_target_properties(lammps PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
add_executable(lmp ${MAIN_SOURCES})
target_link_libraries(lmp PRIVATE lammps)
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
@ -121,10 +143,10 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC
USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@ -151,12 +173,13 @@ if(NOT CMAKE_CROSSCOMPILING)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
set(MPI_CXX_SKIP_MPICXX TRUE)
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
include(MPI4WIN)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else()
@ -190,7 +213,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
# posix_memalign is not available on Windows
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
else()
set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
@ -232,8 +255,9 @@ if(BUILD_OMP)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
@ -296,7 +320,7 @@ find_program(GZIP_EXECUTABLE gzip)
find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
if(WITH_GZIP)
if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP)
else()
message(FATAL_ERROR "gzip executable not found")
@ -307,7 +331,7 @@ find_program(FFMPEG_EXECUTABLE ffmpeg)
find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
if(WITH_FFMPEG)
if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG)
else()
message(FATAL_ERROR "ffmpeg executable not found")
@ -324,8 +348,8 @@ else()
set(CUDA_REQUEST_PIC)
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -422,7 +446,7 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
if(PKG_LIB STREQUAL mesont)
if(PKG_LIB STREQUAL "mesont")
enable_language(Fortran)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
@ -434,9 +458,9 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
if(PKG_LIB STREQUAL "awpmd")
target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
elseif(PKG_LIB STREQUAL h5md)
elseif(PKG_LIB STREQUAL "h5md")
target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
else()
target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
@ -449,7 +473,7 @@ if(PKG_USER-AWPMD)
endif()
if(PKG_USER-ATC)
if(LAMMPS_SIZES STREQUAL BIGBIG)
if(LAMMPS_SIZES STREQUAL "BIGBIG")
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif()
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
@ -493,7 +517,7 @@ endif()
# and the MPI library - if use - has to be linked right before those
# and after everything else that is compiled locally
######################################################################
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
endif()
@ -542,8 +566,8 @@ add_dependencies(lammps gitversion)
# Actually add executable and lib to build
############################################
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index)
if(${_index} GREATER -1)
list(FIND LANGUAGES "Fortran" _index)
if(_index GREATER -1)
target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
@ -621,7 +645,7 @@ if(BUILD_SHARED_LIBS)
else()
find_package(Python COMPONENTS Interpreter)
endif()
if (Python_EXECUTABLE)
if(Python_EXECUTABLE)
add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
@ -654,7 +678,7 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
else()
find_package(Python COMPONENTS Interpreter)
endif()
if (Python_EXECUTABLE)
if(Python_EXECUTABLE)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
endif()
@ -699,15 +723,15 @@ if(OPTIONS)
message(" Options: ${OPTIONS}")
endif()
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index)
if(${_index} GREATER -1)
list(FIND LANGUAGES "Fortran" _index)
if(_index GREATER -1)
message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
Type: ${CMAKE_Fortran_COMPILER_ID}
Version: ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
endif()
list (FIND LANGUAGES "C" _index)
if(${_index} GREATER -1)
list(FIND LANGUAGES "C" _index)
if(_index GREATER -1)
message(STATUS "C compiler: ${CMAKE_C_COMPILER}
Type: ${CMAKE_C_COMPILER_ID}
Version: ${CMAKE_C_COMPILER_VERSION}
@ -772,7 +796,7 @@ if(PKG_KSPACE)
endif()
if(PKG_KOKKOS)
if(Kokkos_ENABLE_CUDA)
if (${FFT} STREQUAL "KISS")
if(FFT STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()
message(STATUS "Kokkos FFT: cuFFT")

10
cmake/Modules/CodingStandard.cmake
View File

@ -15,6 +15,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
@ -25,6 +30,11 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .

61
cmake/Modules/FindN2P2.cmake Normal file
View File

@ -0,0 +1,61 @@
include(FindPackageHandleStandardArgs)
# Check if N2P2_DIR is set manually.
if (DEFINED ENV{N2P2_DIR})
set(N2P2_DIR "${N2P2_DIR}")
# If not, try if directory "lib/hdnnp/n2p2" exists.
else()
get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/hdnnp/n2p2" REALPATH)
if (EXISTS ${_fullpath})
set(N2P2_DIR "${_fullpath}")
endif()
endif()
# Set path to include directory.
find_path(N2P2_INCLUDE_DIR InterfaceLammps.h HINTS "${N2P2_DIR}/include")
# Two libraries need to be linked: libnnp and libnnpif.
find_library(N2P2_LIBNNP NAMES nnp HINTS "${N2P2_DIR}/lib")
find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib")
# Users could compile n2p2 with extra flags which are then also required for
# pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2
# writes a file with cmake commands, e.g.
#
# target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS)
#
# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake.
find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib")
find_package_handle_standard_args(N2P2 DEFAULT_MSG
N2P2_DIR
N2P2_INCLUDE_DIR
N2P2_LIBNNP
N2P2_LIBNNPIF
N2P2_CMAKE_EXTRA)
if(N2P2_FOUND)
if (NOT TARGET N2P2::N2P2)
# n2p2 core library "libnnp"
add_library(N2P2::LIBNNP UNKNOWN IMPORTED)
set_target_properties(N2P2::LIBNNP PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
IMPORTED_LOCATION ${N2P2_LIBNNP})
# n2p2 interface library "libnnpif"
add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED)
set_target_properties(N2P2::LIBNNPIF PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
IMPORTED_LOCATION ${N2P2_LIBNNPIF})
# Put libnnp, libnnpif and include directory together.
add_library(N2P2::N2P2 INTERFACE IMPORTED)
set_property(TARGET N2P2::N2P2 PROPERTY
INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP)
set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA})
endif()
endif()
mark_as_advanced(
N2P2_DIR
N2P2_INCLUDE_DIR
N2P2_LIBNNP
N2P2_LIBNNPIF
N2P2_CMAKE_EXTRA
)

2
cmake/Modules/GTest.cmake
View File

@ -1,6 +1,6 @@
message(STATUS "Downloading and building Google Test library")
if(CMAKE_BUILD_TYPE STREQUAL Debug)
if(CMAKE_BUILD_TYPE STREQUAL "Debug")
set(GTEST_LIB_POSTFIX d)
else()
set(GTEST_LIB_POSTFIX)

3
cmake/Modules/GenerateOpenCLHeader.cmake Normal file
View File

@ -0,0 +1,3 @@
# utility script to call WriteOpenCLHeader function
include(${SOURCE_DIR}/Modules/OpenCLUtils.cmake)
WriteOpenCLHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

2
cmake/Modules/LAMMPSUtils.cmake
View File

@ -106,7 +106,7 @@ function(FetchPotentials pkgfolder potfolder)
endfunction(FetchPotentials)
# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
file(STRINGS /etc/os-release distro REGEX "^NAME=")
string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")

4
cmake/Modules/OpenCLLoader.cmake
View File

@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

20
cmake/Modules/OpenCLUtils.cmake
View File

@ -1,10 +1,8 @@
function(GenerateOpenCLHeader varname outfile files)
message("Creating ${outfile}...")
function(WriteOpenCLHeader varname outfile files)
file(WRITE ${outfile} "const char * ${varname} = \n")
math(EXPR ARG_END "${ARGC}-1")
separate_arguments(files)
foreach(IDX RANGE 2 ${ARG_END})
list(GET ARGV ${IDX} filename)
foreach(filename ${files})
file(READ ${filename} content)
string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
@ -15,4 +13,16 @@ function(GenerateOpenCLHeader varname outfile files)
endforeach()
file(APPEND ${outfile} ";\n")
endfunction(WriteOpenCLHeader)
function(GenerateOpenCLHeader varname outfile files)
list(REMOVE_AT ARGV 0 1)
add_custom_command(OUTPUT ${outfile}
COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
-D VARNAME=${varname}
-D HEADER_FILE=${outfile}
-D SOURCE_FILES="${ARGV}"
-P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateOpenCLHeader.cmake
DEPENDS ${ARGV}
COMMENT "Generating ${outfile}...")
endfunction(GenerateOpenCLHeader)

13
cmake/Modules/Packages/GPU.cmake
View File

@ -48,7 +48,7 @@ if(GPU_API STREQUAL "CUDA")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if (GPU_LIB_OLD_CUBIN_HEADERS)
if(GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n"
"Please run\n"
@ -145,9 +145,16 @@ if(GPU_API STREQUAL "CUDA")
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
elseif(GPU_API STREQUAL "OPENCL")
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
# the static OpenCL loader doesn't seem to work on macOS. use the system provided
# version by default instead (for as long as it will be available)
if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
set(_opencl_static_default OFF)
else()
set(_opencl_static_default ON)
endif()
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
mark_as_advanced(USE_STATIC_OPENCL_LOADER)
if (USE_STATIC_OPENCL_LOADER)
if(USE_STATIC_OPENCL_LOADER)
include(OpenCLLoader)
else()
find_package(OpenCL REQUIRED)

8
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -37,8 +37,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
ExternalProject_Add(kokkos_build
@ -58,7 +58,7 @@ if(DOWNLOAD_KOKKOS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.3.01 REQUIRED CONFIG)
find_package(Kokkos 3.4.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()
@ -99,7 +99,7 @@ if(PKG_KSPACE)
${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
if(Kokkos_ENABLE_CUDA)
if(NOT ${FFT} STREQUAL "KISS")
if(NOT (FFT STREQUAL "KISS"))
target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
target_link_libraries(lammps PRIVATE cufft)
endif()

2
cmake/Modules/Packages/MESSAGE.cmake
View File

@ -1,4 +1,4 @@
if(LAMMPS_SIZES STREQUAL BIGBIG)
if(LAMMPS_SIZES STREQUAL "BIGBIG")
message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
endif()
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)

124
cmake/Modules/Packages/USER-HDNNP.cmake Normal file
View File

@ -0,0 +1,124 @@
find_package(N2P2 QUIET)
if(N2P2_FOUND)
set(DOWNLOAD_N2P2_DEFAULT OFF)
else()
set(DOWNLOAD_N2P2_DEFAULT ON)
endif()
option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT})
if(DOWNLOAD_N2P2)
set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball")
set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
mark_as_advanced(N2P2_URL)
mark_as_advanced(N2P2_MD5)
# adjust settings from detected compiler to compiler platform in n2p2 library
# set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang"))
set(N2P2_COMP llvm)
set(N2P2_CXX_STD "-std=c++11")
elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(N2P2_COMP intel)
set(N2P2_CXX_STD "-std=c++11")
elseif(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
set(N2P2_COMP gnu)
set(N2P2_CXX_STD "-std=gnu++11")
elseif(CMAKE_CXX_COMPILER_ID STREQUAL "PGI")
set(N2P2_COMP gnu)
set(N2P2_CXX_STD "--c++11")
else() # default
set(N2P2_COMP "")
endif()
# pass on archive creator command. prefer compiler specific version, if set.
# important when using cross compiler.
if(CMAKE_CXX_COMPILER_AR)
set(N2P2_AR ${CMAKE_CXX_COMPILER_AR})
else()
set(N2P2_AR ${CMAKE_AR})
endif()
# adjust compilation of n2p2 library to whether MPI is requested in LAMMPS or not
# need special care for compiling for MPICH2 with Linux-to-Windows cross compiler.
if(NOT BUILD_MPI)
set(N2P2_PROJECT_OPTIONS "-DN2P2_NO_MPI")
else()
# get path to MPI include directory when cross-compiling to windows
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1")
set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
endif()
endif()
# override compiler (optimization) flags in n2p2 library to flags used for LAMMPS
# specifically -march=native can result in problems when compiling on HPC clusters or with a cross compiler
# this convoluted way gets correct quoting/escaping when configuring the external project
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}")
set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG="
"PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
"PROJECT_AR=${N2P2_AR}")
# echo final flag for debugging
message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}")
# download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
include(ExternalProject)
ExternalProject_Add(n2p2_build
URL ${N2P2_URL}
URL_MD5 ${N2P2_MD5}
UPDATE_COMMAND ""
CONFIGURE_COMMAND ""
PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
BUILD_COMMAND make -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
BUILD_ALWAYS YES
INSTALL_COMMAND ""
BUILD_IN_SOURCE 1
LOG_BUILD ON
SOURCE_SUBDIR src/
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libnnp.a <SOURCE_DIR>/lib/libnnpif.a
)
# create imported target LAMMPS::N2P2 from two libraries nnp and nnpif
ExternalProject_get_property(n2p2_build SOURCE_DIR)
# n2p2 core library "libnnp"
add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED)
set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnp.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
# n2p2 interface library "libnnpif"
add_library(LAMMPS::N2P2::LIBNNPIF UNKNOWN IMPORTED)
set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnpif.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
# nnpif library has MPI calls if MPI is enabled, so we must link with MPI libs
if(BUILD_MPI)
set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
INTERFACE_LINK_LIBRARIES MPI::MPI_CXX)
if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
add_dependencies(LAMMPS::N2P2::LIBNNPIF MPI::MPI_CXX)
endif()
endif()
# final step to define imported target
add_library(LAMMPS::N2P2 INTERFACE IMPORTED)
set_property(TARGET LAMMPS::N2P2 PROPERTY
INTERFACE_LINK_LIBRARIES LAMMPS::N2P2::LIBNNPIF LAMMPS::N2P2::LIBNNP)
target_link_libraries(lammps PRIVATE LAMMPS::N2P2)
add_dependencies(LAMMPS::N2P2 n2p2_build)
# work around issues with older CMake versions
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
file(MAKE_DIRECTORY "${SOURCE_DIR}/lib")
else()
find_package(N2P2)
if(NOT N2P2_FOUND)
message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it")
endif()
target_link_libraries(lammps PRIVATE N2P2::N2P2)
include(${N2P2_CMAKE_EXTRAS})
endif()

8
cmake/Modules/Packages/USER-INTEL.cmake
View File

@ -79,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL")
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
include(CheckCXXCompilerFlag)
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
foreach(_FLAG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
string(REGEX REPLACE "[ =\"]" "" _FLAGX ${_FLAG})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
if(COMPILER_SUPPORTS${_FLAGX})
separate_arguments(_FLAG UNIX_COMMAND "${_FLAG}")
target_compile_options(lammps PRIVATE ${_FLAG})
endif()
endforeach()

118
cmake/Modules/Packages/USER-MDI.cmake Normal file
View File

@ -0,0 +1,118 @@
find_package(mdi QUIET)
if(${mdi_FOUND})
set(DOWNLOAD_MDI_DEFAULT OFF)
else()
set(DOWNLOAD_MDI_DEFAULT ON)
endif()
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)
# only ON/OFF are allowed for "mpi" flag when building MDI library
# so translate boolean value of BUILD_MPI
# always disable MPI when cross-compiling to Windows.
if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
set(MDI_USE_MPI ON)
else()
set(MDI_USE_MPI OFF)
endif()
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()
find_package(Python QUIET COMPONENTS Development)
if(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# download/ build MDI library
# always build static library with -fpic
# support cross-compilation and ninja-build
include(ExternalProject)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-Dlanguage=C
-Dlibtype=STATIC
-Dmpi=${MDI_USE_MPI}
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
)
set(MDI_DEP_LIBS "")
# if compiling with python plugins we need
# to add python libraries as dependency.
if(MDI_USE_PYTHON_PLUGINS)
if(CMAKE_VERSION VERSION_LESS 3.12)
list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
else()
list(APPEND MDI_DEP_LIBS Python::Python)
endif()
endif()
# need to add support for dlopen/dlsym, except when compiling for Windows.
if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")
endif()
if(MDI_DEP_LIBS)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LINK_INTERFACE_LIBRARIES "${MDI_DEP_LIBS}")
endif()
target_link_libraries(lammps PRIVATE LAMMPS::MDI)
target_link_libraries(lmp PRIVATE LAMMPS::MDI)
else()
find_package(mdi)
if(NOT mdi_FOUND)
message(FATAL_ERROR "MDI library not found. Help CMake to find it "
"by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
"to download and compile it")
endif()
# Link the lammps library against MDI
target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
# Link the lammps executable against MDI
target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
endif()
target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

3
cmake/Modules/Packages/USER-PACE.cmake
View File

@ -14,13 +14,12 @@ execute_process(
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE pace)

2
cmake/Modules/PreventInSourceBuilds.cmake
View File

@ -9,7 +9,7 @@ function(prevent_in_source_builds)
get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
# disallow in-source builds
if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
if(("${srcdir}" STREQUAL "${bindir}") OR ("${srcdir2}" STREQUAL "${bindir}") OR ("${srcdir3}" STREQUAL "${bindir}"))
message(FATAL_ERROR "\
CMake must not to be run in the source directory. \

16
cmake/Modules/Testing.cmake
View File

@ -19,11 +19,11 @@ if(ENABLE_TESTING)
# we need to build and link a LOT of tester executables, so it is worth checking if
# a faster linker is available. requires GNU or Clang compiler, newer CMake.
# also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
include(CheckCXXCompilerFlag)
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@ -58,7 +58,7 @@ if(ENABLE_TESTING)
endif()
# Compiler specific features for testing
if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
mark_as_advanced(ENABLE_COVERAGE)
if(ENABLE_COVERAGE)
@ -83,7 +83,7 @@ mark_as_advanced(ENABLE_IWYU)
if(ENABLE_IWYU)
# enforce these settings
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
if(NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
endif()
# detect the "native" header folder so we can include them first
@ -91,7 +91,7 @@ if(ENABLE_IWYU)
string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
find_program(IWYU_EXE NAMES include-what-you-use iwyu)
find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
if (IWYU_EXE AND IWYU_TOOL)
if(IWYU_EXE AND IWYU_TOOL)
add_custom_target(
iwyu
${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp

2
cmake/Modules/Tools.cmake
View File

@ -45,7 +45,7 @@ if(BUILD_LAMMPS_SHELL)
target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
# workaround for broken readline pkg-config file on FreeBSD
if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD)
if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
target_include_directories(lammps-shell PRIVATE /usr/local/include)
endif()
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)

18
cmake/Modules/YAML.cmake
View File

@ -6,15 +6,27 @@ set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of li
mark_as_advanced(YAML_URL)
mark_as_advanced(YAML_MD5)
# support cross-compilation to windows
if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
set(YAML_CROSS_HOST --host=i686-mingw64)
elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
set(YAML_CROSS_HOST --host=x86_64-mingw64)
else()
message(FATAL_ERROR "Unsupported cross-compilation "
" for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
" on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
endif()
endif()
ExternalProject_Add(libyaml
URL ${YAML_URL}
URL_MD5 ${YAML_MD5}
SOURCE_DIR "${CMAKE_BINARY_DIR}/yaml-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/yaml-build"
CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
CXX=${CMAKE_CXX_COMPILER}
CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared
CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
TEST_COMMAND "")

2
cmake/pkgconfig/liblammps.pc.in
View File

@ -24,7 +24,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
URL: https://www.lammps.org
Version: @PROJECT_VERSION@
Requires:
Libs: -L${libdir} -llammps@LAMMPS_MACHINE@

14
cmake/presets/all_off.cmake
View File

@ -5,13 +5,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

14
cmake/presets/all_on.cmake
View File

@ -7,13 +7,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
USER-VTK USER-YAFF)
USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-YAFF)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)

10
cmake/presets/clang.cmake
View File

@ -4,10 +4,18 @@ set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

8
cmake/presets/download.cmake
View File

@ -1,7 +1,7 @@
# preset that turns on packages with automatic downloads of sources of potentials
# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
# Preset that turns on packages with automatic downloads of sources or potentials.
# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@ -9,9 +9,11 @@ endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)
set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)

12
cmake/presets/intel.cmake
View File

@ -3,10 +3,20 @@
set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

6
cmake/presets/mingw-cross.cmake
View File

@ -1,9 +1,9 @@
set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF

6
cmake/presets/most.cmake
View File

@ -5,9 +5,9 @@
set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
foreach(PKG ${ALL_PACKAGES})

6
cmake/presets/nolib.cmake
View File

@ -3,9 +3,9 @@
set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
PYTHON VORONOI
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
USER-SMD USER-VTK)
USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE
USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
USER-SCAFACOS USER-SMD USER-VTK)
foreach(PKG ${PACKAGES_WITH_LIB})
set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

14
cmake/presets/oneapi.cmake
View File

@ -1,12 +1,22 @@
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes)
set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpx" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

16
doc/Makefile
View File

@ -10,7 +10,6 @@ endif
BUILDDIR = ${CURDIR}
RSTDIR = $(BUILDDIR)/src
VENV = $(BUILDDIR)/docenv
TXT2RST = $(VENV)/bin/txt2rst
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
@ -59,7 +58,7 @@ SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiproc
# we only want to use explicitly listed files.
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check xmlgen
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen
# ------------------------------------------
@ -68,7 +67,6 @@ help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html create HTML pages in html dir"
@echo " pdf create Manual.pdf in this dir"
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
@echo " epub create ePUB format manual for e-book readers"
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@echo " (requires ebook-convert tool from calibre)"
@ -185,13 +183,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@rm -rf latex/PDF/.[sg]*
@echo "Build finished. Manual.pdf is in this directory."
fetch:
@rm -rf html_www Manual_www.pdf
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
@tar xzf lammps-doc.tar.gz
@rm -f lammps-doc.tar.gz
anchor_check : $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ;\
@ -213,6 +204,9 @@ package_check : $(VENV)
deactivate ;\
)
char_check :
@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
xmlgen : doxygen/xml/index.xml
doxygen/Doxyfile: doxygen/Doxyfile.in
@ -238,7 +232,7 @@ $(VENV):
$(MATHJAX):
@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
$(TXT2RST) $(ANCHORCHECK): $(VENV)
$(ANCHORCHECK): $(VENV)
@( \
. $(VENV)/bin/activate; \
(cd utils/converters;\

13
doc/README
View File

@ -25,16 +25,11 @@ github-development-workflow.md notes on the LAMMPS development workflow
include-file-conventions.md notes on LAMMPS' include file conventions
documentation_conventions.md notes on writing documentation for LAMMPS
If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
If you downloaded a LAMMPS tarball from www.lammps.org, then the html
folder and the PDF manual should be included. If you downloaded LAMMPS
from GitHub then you either need to download them or build them.
from GitHub then you either need to build them.
(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type "make fetch". This should create a html_www directory
and Manual_www.pdf file. These will always represent the latest published
patch/development version of LAMMPS.
(b) You can build the HTML and PDF files yourself, by typing "make html"
You can build the HTML and PDF files yourself, by typing "make html"
or by "make pdf", respectively. This requires various tools and files.
Some of them have to be installed (more on that below). For the rest the
build process will attempt to download and install into a python virtual
@ -78,4 +73,4 @@ the tool 'ebook-convert' from the 'calibre' e-book management software
----------------
More details this can be found in the manual itself. The online
version is at: https://lammps.sandia.gov/doc/Manual_build.html
version is at: https://docs.lammps.org/Build_manual.html

4
doc/lammps.1
View File

@ -1,4 +1,4 @@
.TH LAMMPS "8 April 2021" "2021-04-08"
.TH LAMMPS "27 May 2021" "2021-05-27"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator.
@ -34,7 +34,7 @@ semiconductors) and coarse-grained or mesoscopic systems. It can be used to
model atoms or, more generically, as a parallel particle simulator at the
atomic, meso, or continuum scale.
See https://lammps.sandia.gov/ for more information and documentation.
See https://www.lammps.org/ for more information and documentation.
.SH EXECUTABLE NAME
The

6
doc/src/Bibliography.rst
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@ -1129,6 +1129,9 @@ Bibliography
**(Sutmann)**
Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems.
In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014.
**(Swinburne)**
Swinburne and Marinica, Physical Review Letters, 120, 1 (2018)
@ -1285,9 +1288,6 @@ Bibliography
**(Wennberg)**
Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013).
**(Who)**
Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012).
**(Wicaksono1)**
Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016).

50
doc/src/Build_development.rst
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@ -28,6 +28,28 @@ variable VERBOSE set to 1:
----------
.. _clang-tidy:
Enable static code analysis with clang-tidy
-------------------------------------------
The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
static code analysis tool to diagnose (and potentially fix) typical
programming errors or coding style violations. It has a modular framework
of tests that can be adjusted to help identifying problems before they
become bugs and also assist in modernizing large code bases (like LAMMPS).
It can be enabled for all C++ code with the following CMake flag
.. code-block:: bash
-D ENABLE_CLANG_TIDY=value # value = no (default) or yes
With this flag enabled all source files will be processed twice, first to
be compiled and then to be analyzed. Please note that the analysis can be
significantly more time consuming than the compilation itself.
----------
.. _iwyu_processing:
Report missing and unneeded '#include' statements
@ -447,12 +469,24 @@ The following options are available.
.. code-block:: bash
make check-whitespace # generate coverage report in HTML format
make fix-whitespace # generate coverage report in XML format
make check-permissions # delete folder with HTML format coverage report
make fix-permissions # delete all collected coverage data and HTML output
make check-whitespace # search for files with whitespace issues
make fix-whitespace # correct whitespace issues in files
make check-homepage # search for files with old LAMMPS homepage URLs
make fix-homepage # correct LAMMPS homepage URLs in files
make check-permissions # search for files with permissions issues
make fix-permissions # correct permissions issues in files
For the code in the ``unittest`` tree we are using the `clang-format`
tool (Clang version 8.0 or later is required). If available, the source
code files in the ``unittest`` tree can be updated to conform to the
formatting settings using ``make format-tests``.
For the code in the ``unittest`` and ``src`` trees we are transitioning
to use the `clang-format` tool to assist with having a consistent source
code style. The `clang-format` command bundled with Clang version 8.0
or later is required. The configuration is in files ``.clang-format``
in the respective folders. Since the modifications from `clang-format`
can be significant and - especially for "legacy style code" - also is
not always improving readability, a large number of files currently have
a ``// clang-format off`` at the top, which will disable the processing.
Over time, files will be refactored and updated to that `clang-format`
may be applied to them (at least in part).
If `clang-format` is available, the source code files in the ``unittest``
tree can be updated to conform to the formatting settings using
``make format-tests`` and the files in ``src`` with ``make format-src``.

98
doc/src/Build_extras.rst
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@ -48,7 +48,9 @@ This is the list of packages that may require additional steps.
* :ref:`USER-AWPMD <user-awpmd>`
* :ref:`USER-COLVARS <user-colvars>`
* :ref:`USER-H5MD <user-h5md>`
* :ref:`USER-HDNNP <user-hdnnp>`
* :ref:`USER-INTEL <user-intel>`
* :ref:`USER-MDI <user-mdi>`
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
@ -455,6 +457,9 @@ They must be specified in uppercase.
* - ZEN2
- HOST
- AMD Zen2 class CPU (AVX 2)
* - ZEN3
- HOST
- AMD Zen3 class CPU (AVX 2)
* - ARMV80
- HOST
- ARMv8.0 Compatible CPU
@ -467,6 +472,9 @@ They must be specified in uppercase.
* - ARMV8_THUNDERX2
- HOST
- ARMv8 Cavium ThunderX2 CPU
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - WSM
- HOST
- Intel Westmere CPU (SSE 4.2)
@ -539,6 +547,9 @@ They must be specified in uppercase.
* - AMPERE80
- GPU
- NVIDIA Ampere generation CC 8.0 GPU
* - AMPERE86
- GPU
- NVIDIA Ampere generation CC 8.6 GPU
* - VEGA900
- GPU
- AMD GPU MI25 GFX900
@ -547,12 +558,12 @@ They must be specified in uppercase.
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- GPU
- AMD GPU GFX908
- AMD GPU MI100 GFX908
* - INTEL_GEN
- GPU
- Intel GPUs Gen9+
This list was last updated for version 3.3 of the Kokkos library.
This list was last updated for version 3.4.1 of the Kokkos library.
.. tabs::
@ -1463,6 +1474,60 @@ the HDF5 library.
----------
.. _user-hdnnp:
USER-HDNNP package
---------------------------------
To build with the USER-HDNNP package it is required to download and build the
external `n2p2 <https://github.com/CompPhysVienna/n2p2>`__ library ``v2.1.4``
(or higher). The LAMMPS build process offers an automatic download and
compilation of *n2p2* or allows you to choose the installation directory of
*n2p2* manually. Please see the boxes below for the CMake and traditional build
system for detailed information.
In case of a manual installation of *n2p2* you only need to build the *n2p2* core
library ``libnnp`` and interface library ``libnnpif``. When using GCC it should
suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more
details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
<https://compphysvienna.github.io/n2p2/topics/build.html>`__.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_N2P2=value # download n2p2 for build, value = no (default) or yes
-D N2P2_DIR=path # n2p2 base directory (only needed if a custom location)
If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
built inside the CMake build directory. If the *n2p2* library is already
on your system (in a location CMake cannot find it), set the ``N2P2_DIR``
to path where *n2p2* is located. If *n2p2* is located directly in
``lib/hdnnp/n2p2`` it will be automatically found by CMake.
.. tab:: Traditional make
You can download and build the *n2p2* library manually if you prefer;
follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-hdnnp # print help message
$ make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-...
$ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
$ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
respectively. When LAMMPS is built in ``src`` it will use these links.
----------
.. _user-intel:
USER-INTEL package
@ -1533,6 +1598,35 @@ TBB and MKL.
----------
.. _user-mdi:
USER-MDI package
-----------------------------
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes
.. tab:: Traditional make
Before building LAMMPS, you must build the MDI Library in
``lib/mdi``\ . You can do this by executing a command like one
of the following from the ``lib/mdi`` directory:
.. code-block:: bash
$ python Install.py -m gcc # build using gcc compiler
$ python Install.py -m icc # build using icc compiler
The build should produce two files: ``lib/mdi/includelink/mdi.h``
and ``lib/mdi/liblink/libmdi.so``\ .
----------
.. _user-mesont:
USER-MESONT package

31
doc/src/Build_manual.rst
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@ -28,29 +28,18 @@ If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
the html folder and the PDF files should be included.
If you downloaded LAMMPS from the public git repository, then the HTML
and PDF files are not included. Instead you need to create them, in one
of two ways:
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
site. Just type ``make fetch``. This should download a ``html_www``
directory and a ``Manual_www.pdf`` file. Note that if new LAMMPS features
have been added more recently than the date of your LAMMPS version, the
fetched documentation will include those changes (but your source code
will not, unless you update your local repository).
b. You can build the HTML or PDF files yourself, by typing ``make html``
or ``make pdf`` in the ``doc`` folder. This requires various tools
and files. Some of them have to be installed (see below). For the
rest the build process will attempt to download and install them into
a python virtual environment and local folders.
and PDF files are not included. You can build the HTML or PDF files yourself,
by typing ``make html`` or ``make pdf`` in the ``doc`` folder. This requires
various tools and files. Some of them have to be installed (see below). For
the rest the build process will attempt to download and install them into
a python virtual environment and local folders.
A current version of the manual (latest patch release, aka unstable
branch) is is available online at:
`https://lammps.sandia.gov/doc/Manual.html
<https://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual
corresponding to the ongoing development (aka master branch) is
available online at: `https://docs.lammps.org/
<https://docs.lammps.org/>`_
`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
A version of the manual corresponding to the ongoing development (aka master branch)
is available online at: `https://docs.lammps.org/latest/
<https://docs.lammps.org/latest/>`_
Build using GNU make
--------------------
@ -257,4 +246,4 @@ the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org

18
doc/src/Build_package.rst
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@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
These links take you to the extra instructions for those select
packages:
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PACE <user-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-HDNNP <user-hdnnp>` | :ref:`USER-INTEL <user-intel>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-MOLFILE <user-molfile>` | :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PACE <user-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
| :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | |
+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
The mechanism for including packages is simple but different for CMake
versus make.

1
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@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
* :doc:`mdi/engine <mdi_engine>`
* :doc:`message <message>`
* :doc:`minimize <minimize>`
* :doc:`min_modify <min_modify>`

4
doc/src/Commands_fix.rst
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@ -39,6 +39,9 @@ OPT.
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
* :doc:`brownian <fix_brownian>`
* :doc:`brownian/asphere <fix_brownian>`
* :doc:`brownian/sphere <fix_brownian>`
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`
@ -98,6 +101,7 @@ OPT.
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`mdi/engine <fix_mdi_engine>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`momentum (k) <fix_momentum>`
* :doc:`momentum/chunk <fix_momentum>`

6
doc/src/Commands_pair.rst
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@ -87,6 +87,8 @@ OPT.
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (gio) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/ext <pair_dpd_ext>`
* :doc:`dpd/ext/tstat <pair_dpd_ext>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (go) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -116,6 +118,7 @@ OPT.
* :doc:`gw/zbl <pair_gw>`
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
@ -169,7 +172,7 @@ OPT.
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (o) <pair_lj_smooth>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`lj96/cut (go) <pair_lj96>`
@ -224,6 +227,7 @@ OPT.
* :doc:`polymorphic <pair_polymorphic>`
* :doc:`python <pair_python>`
* :doc:`quip <pair_quip>`
* :doc:`rann <pair_rann>`
* :doc:`reax/c (ko) <pair_reaxc>`
* :doc:`rebo (io) <pair_airebo>`
* :doc:`resquared (go) <pair_resquared>`

20
doc/src/Developer_utils.rst
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@ -9,8 +9,8 @@ reading or writing to files with error checking or translation of
strings into specific types of numbers with checking for validity. This
reduces redundant implementations and encourages consistent behavior.
I/O with status check
^^^^^^^^^^^^^^^^^^^^^
I/O with status check and similar functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The the first two functions are wrappers around the corresponding C
library calls ``fgets()`` or ``fread()``. They will check if there
@ -19,6 +19,14 @@ In that case, the functions will stop with an error message, indicating
the name of the problematic file, if possible unless the *error* argument
is a NULL pointer.
The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
but it will read in a whole line (i.e. until the end of line or end
of file), but store only as many characters as will fit into the buffer
including a final newline character and the terminating NULL byte.
If the line in the file is longer it will thus be truncated in the buffer.
This function is used by :cpp:func:`read_lines_from_file` to read individual
lines but make certain they follow the size constraints.
The :cpp:func:`read_lines_from_file` function will read the requested
number of lines of a maximum length into a buffer and will return 0
if successful or 1 if not. It also guarantees that all lines are
@ -33,6 +41,9 @@ NULL character.
.. doxygenfunction:: sfread
:project: progguide
.. doxygenfunction:: fgets_trunc
:project: progguide
.. doxygenfunction:: read_lines_from_file
:project: progguide
@ -174,7 +185,10 @@ Argument processing
Convenience functions
^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: logmesg
.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
:project: progguide
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
:project: progguide
.. doxygenfunction:: getsyserror

6
doc/src/Errors_bugs.rst
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@ -5,8 +5,8 @@ If you are confident that you have found a bug in LAMMPS, please follow
the steps outlined below:
* Check the `New features and bug fixes
<https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
<https://lammps.sandia.gov>`_ or the
<https://www.lammps.org/bug.html>`_ section of the `LAMMPS WWW site
<https://www.lammps.org>`_ or the
`GitHub Releases page <https://github.com/lammps/lammps/releases>`_ to
see if the bug has already been addressed in a patch release.
* Check that your issue can be reproduced with the latest development
@ -17,7 +17,7 @@ the steps outlined below:
if your issue has already been reported and if it is still open.
* Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
to see if there is already a fix for your bug pending.
* Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
* Check the `mailing list archives <https://www.lammps.org/mail.html>`_
to see if the issue has been discussed before.
If none of these steps yields any useful information, please file a new

2
doc/src/Errors_common.rst
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@ -39,7 +39,7 @@ figure out your physics or numerical mistakes, like choosing too big a
timestep, specifying erroneous force field coefficients, or putting 2
atoms on top of each other! If you run into errors that LAMMPS
does not catch that you think it should flag, please send an email to
the `developers <https://lammps.sandia.gov/authors.html>`_.
the `developers <https://www.lammps.org/authors.html>`_.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by

2
doc/src/Errors_messages.rst
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@ -3871,7 +3871,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Fix orient/fcc found self twice*
The neighbor lists used by fix orient/fcc are messed up. If this
error occurs, it is likely a bug, so send an email to the
`developers <https://lammps.sandia.gov/authors.html>`_.
`developers <https://www.lammps.org/authors.html>`_.
*Fix peri neigh does not exist*
Somehow a fix that the pair style defines has been deleted.

8
doc/src/Examples.rst
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@ -18,7 +18,7 @@ files and image files.
If you uncomment the :doc:`dump <dump>` command in the input script, a
text dump file will be produced, which can be animated by various
`visualization programs <https://lammps.sandia.gov/viz.html>`_.
`visualization programs <https://www.lammps.org/viz.html>`_.
If you uncomment the :doc:`dump image <dump>` command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the
:doc:`dump image <dump_image>` doc page.
Animations of many of the examples can be viewed on the Movies section
of the `LAMMPS web site <https://lammps.sandia.gov/movies.html>`_.
of the `LAMMPS web site <https://www.lammps.org/movies.html>`_.
There are two kinds of sub-directories in the examples folder. Lower
case named directories contain one or a few simple, quick-to-run
@ -108,6 +108,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| msst | MSST shock dynamics |
+-------------+------------------------------------------------------------------+
| multi | multi neighboring for systems with large interaction disparities |
+-------------+------------------------------------------------------------------+
| nb3b | use of non-bonded 3-body harmonic pair style |
+-------------+------------------------------------------------------------------+
| neb | nudged elastic band (NEB) calculation for barrier finding |
@ -164,7 +166,7 @@ Here is how you can run and visualize one of the sample problems:
Running the simulation produces the files *dump.indent* and
*log.lammps*\ . You can visualize the dump file of snapshots with a
variety of third-party tools highlighted on the
`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
`Visualization <https://www.lammps.org/viz.html>`_ page of the LAMMPS
web site.
If you uncomment the :doc:`dump image <dump_image>` line(s) in the input

3
doc/src/Howto.rst
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@ -3,7 +3,7 @@ Howto discussions
These doc pages describe how to perform various tasks with LAMMPS,
both for users and developers. The
`glossary <https://lammps.sandia.gov/glossary.html>`_ website page also lists MD
`glossary <https://www.lammps.org/glossary.html>`_ website page also lists MD
terminology with links to corresponding LAMMPS manual pages. The
example input scripts included in the examples directory of the LAMMPS
distribution and highlighted on the :doc:`Examples <Examples>` doc page
@ -23,6 +23,7 @@ General howto
Howto_library
Howto_couple
Howto_client_server
Howto_mdi
Settings howto
==============

2
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@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts
have to be modified to include the Drude dipoles and how to handle
them.
Example input scripts available: examples/USER/drude
----------
**Overview of Drude induced dipoles**

132
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@ -0,0 +1,132 @@
Using LAMMPS with the MDI library for code coupling
===================================================
.. note::
This Howto doc page will eventually replace the
:doc:`Howto client/server <Howto_client_server>` doc page.
Client/server coupling of two codes is where one code is the "client"
and sends request messages (data) to a "server" code. The server
responds to each request with a reply message. This enables the two
codes to work in tandem to perform a simulation. LAMMPS can act as
either a client or server code; it does this by using the `MolSSI
Driver Interface (MDI) library
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
developed by the `Molecular Sciences Software Institute (MolSSI)
<https://molssi.org>`_.
Alternate methods for code coupling with LAMMPS are described on the
:doc:`Howto couple <Howto_couple>` doc page.
Some advantages of client/server coupling are that the two codes can run
as stand-alone executables; they need not be linked together. Thus
neither code needs to have a library interface. This also makes it easy
to run the two codes on different numbers of processors. If a message
protocol (format and content) is defined for a particular kind of
simulation, then in principle any code which implements the client-side
protocol can be used in tandem with any code which implements the
server-side protocol. Neither code needs to know what specific other
code it is working with.
In MDI nomenclature, a client code is the "driver", and a server code is
an "engine". One driver code can communicate with one or more instances
of one or more engine codes. Driver and engine codes can be written in
any language: C, C++, Fortran, Python, etc.
In addition to allowing driver and engine(s) running to run as
stand-alone executables, MDI also enables a server code to be a
"plugin" to the client code. In this scenario, server code(s) are
compiled as shared libraries, and one (or more) instances of the
server are instantiated by the driver code. If the driver code runs
in parallel, it can split its MPI communicator into multiple
sub-communicators, and launch each plugin engine instance on a
sub-communicator. Driver processors in that sub-communicator exchange
messages with that engine instance, and can also send MPI messages to
other processors in the driver. The driver code can also destroy
engine instances and re-instantiate them.
The way that a driver communicates with an engine is by making
MDI_Send() and MDI_Recv() calls, which are conceptually similar to
MPI_Send() and MPI_Recv() calls. Each send or receive has a string
which identifies the command name, and optionally some data, which can
be a single value or vector of values of any data type. Inside the
MDI library, data is exchanged between the driver and engine via MPI
calls or sockets. This a run-time choice by the user.
-------------
As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a
suite of quantum DFT codes), can work together via the MDI library to
perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
simulation and sends a message each timestep to ``pw.x`` asking it to
compute quantum forces on the current configuration of atoms. Here is
how the 2 codes are launched to communicate by MPI:
.. code-block:: bash
% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
-in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16
processors.
Here is how the 2 codes are launched to communicate by sockets:
.. code-block:: bash
% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
% mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
These commands could be issued in different windows on a desktop
machine. Or in the same window, if the first command is ended with
"&" so as to run in the background. If "localhost" is replaced by an
IP address, ``pw.x`` could be run on another machine on the same network, or
even on another machine across the country.
After both codes initialize themselves to model the same system, this is
what occurs each timestep:
* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
* LAMMPS receives the forces and time integrates to complete a single timestep
-------------
Examples scripts for using LAMMPS as an MDI engine are in the
examples/mdi directory. See the README file in that directory for
instructions on how to run the examples.
.. note::
Work is underway to add commands that allow LAMMPS to be used as an
MDI driver, e.g. for the AIMD example discussed above. Example
scripts for this usage mode will be added the same directory when
available.
If LAMMPS is used as a stand-alone engine it should set up the system
it will be modeling in its input script, then invoke the
:doc:`mdi/engine <mdi_engine>` command. This will put LAMMPS into
"engine mode" where it waits for messages and data from the driver.
When the driver sends an "EXIT" command, LAMMPS will exit engine mode
and the input script will continue.
If LAMMPS is used as a plugin engine it operates the same way, except
that the driver will pass LAMMPS an input script to initialize itself.
Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the
input script will continue. After finishing execution of the input
script, the instance of LAMMPS will be destroyed.
LAMMPS supports the full set of MD-appropriate engine commands defined
by the MDI library. See the :doc:`mdi/engine <mdi_engine>` doc page for
a list of these.
If those commands are not sufficient for a user-developed driver to use
LAMMPS as an engine, then new commands can be easily added. See these
two files which implement the definition of MDI commands and the logic
for responding to them:
* src/MDI/mdi_engine.cpp
* src/MDI/fix_mdi_engine.cpp

2
doc/src/Howto_wsl.rst
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@ -201,7 +201,7 @@ build configuration and any binaries generated during compilation.
There are countless ways to compile LAMMPS. It is beyond the scope of this
tutorial. If you want to find out more about what can be enabled, please
consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_.
consult the extensive `documentation <https://docs.lammps.org/Build_cmake.html>`_.
To compile a minimal version of LAMMPS, we're going to use a preset.
Presets are a way to specify a collection of CMake options using a file.

2
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@ -78,7 +78,7 @@ this is as follows.
$ git checkout tagID
Stable versions and what tagID to use for a particular stable version
are discussed on `this page <https://lammps.sandia.gov/bug.html#version>`_.
are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
Note that this command will print some warnings, because in order to get
back to the latest revision and to be able to update with ``git pull``
again, you will need to do ``git checkout unstable`` (or

2
doc/src/Install_patch.rst
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@ -10,7 +10,7 @@ If you prefer to download a tarball, as described on the
:doc:`tarball download <Install_tarball>` page, you can stay current by
downloading "patch files" when new patch releases are made. A link to
a patch file is posted on the
`bug fixes and new feature page <https://lammps.sandia.gov/bug.html>`_
`bug fixes and new feature page <https://www.lammps.org/bug.html>`_
of the LAMMPS website, along
with a list of changed files and details about what is in the new patch
release. This page explains how to apply the patch file to your local

8
doc/src/Install_tarball.rst
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@ -4,10 +4,10 @@ Download source and documentation as a tarball
You can download a current LAMMPS tarball from the `download page <download_>`_
of the `LAMMPS website <lws_>`_.
.. _download: https://lammps.sandia.gov/download.html
.. _bug: https://lammps.sandia.gov/bug.html
.. _older: https://lammps.sandia.gov/tars
.. _lws: https://lammps.sandia.gov
.. _download: https://www.lammps.org/download.html
.. _bug: https://www.lammps.org/bug.html
.. _older: https://www.lammps.org/tars
.. _lws: https://www.lammps.org
You have two choices of tarballs, either the most recent stable
release or the most current patch release. Stable releases occur a

6
doc/src/Intro_authors.rst
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@ -11,14 +11,14 @@ University:
* Richard Berger, richard.berger at temple.edu
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
and Ray Shan, now at Materials Design.
----------
The `Authors page <https://lammps.sandia.gov/authors.html>`_ of the
The `Authors page <https://www.lammps.org/authors.html>`_ of the
`LAMMPS website <lws_>`_ has a comprehensive list of all the individuals
who have contributed code for a new feature or command or tool to
LAMMPS.
@ -46,7 +46,7 @@ general-purpose as it is without their expertise and efforts.
----------
As discussed on the `History page <https://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
As discussed on the `History page <https://www.lammps.org/history.html>`_ of the website, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:

4
doc/src/Intro_citing.rst
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@ -38,8 +38,8 @@ In addition there are DOIs for individual stable releases. Currently there are:
Home page
^^^^^^^^^
The LAMMPS website at `https://lammps.sandia.gov/
<https://lammps.sandia.gov>`_ is the canonical location for information
The LAMMPS website at `https://www.lammps.org/
<https://www.lammps.org>`_ is the canonical location for information
about LAMMPS and its features.
Citing contributions

4
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@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
linear bead-spring polymer chains. The moltemplate program is a true
molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` doc page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
LAMMPS. The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
@ -67,7 +67,7 @@ Here are suggestions on how to perform these tasks:
them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
movies from them. For high-quality, interactive visualization there are
many excellent and free tools available. See the
`Visualization Tools <https://lammps.sandia.gov/viz.html>`_ page of the
`Visualization Tools <https://www.lammps.org/viz.html>`_ page of the
LAMMPS website for
visualization packages that can process LAMMPS output data.
* **Plotting:** See the next bullet about Pizza.py as well as the

30
doc/src/Intro_opensource.rst
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@ -2,18 +2,20 @@ LAMMPS open-source license
--------------------------
LAMMPS is a freely-available open-source code, distributed under the
terms of the `GNU Public License <gnu_>`_, which means you can use or
modify the code however you wish.
terms of the `GNU Public License Version 2 <gpl_>`_, which means you can
use or modify the code however you wish for your own purposes, but have
to adhere to certain rules when redistributing it or software derived
from it or that includes parts of it.
LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the `GNU Public License <gnu_>`_ (GPL). This
is often referred to as open-source distribution - see
`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_. The legal
text of the GPL is in the LICENSE file included in the LAMMPS
charge, under the terms of the `GNU Public License Version 2 <gpl_>`_
(GPLv2). This is often referred to as open-source distribution - see
`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_. The
legal text of the GPL is in the LICENSE file included in the LAMMPS
distribution.
.. _gnu: http://www.gnu.org/copyleft/gpl.html
.. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE
.. _gnuorg: http://www.gnu.org
@ -24,14 +26,14 @@ Here is a summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.
(2) If you distribute a modified version of LAMMPS, it must remain
open-source, meaning you distribute it under the terms of the GPL.
You should clearly annotate such a code as a derivative version of
LAMMPS.
(2) If you **distribute** a modified version of LAMMPS, it must remain
open-source, meaning you distribute **all** of it under the terms of
the GPL. You should clearly annotate such a code as a derivative version
of LAMMPS.
(3) If you release any code that includes LAMMPS source code, then it
must also be open-sourced, meaning you distribute it under the terms
of the GPL.
(3) If you release any code that includes or uses LAMMPS source code,
then it must also be open-sourced, meaning you distribute it under
the terms of the GPL.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should

4
doc/src/Intro_overview.rst
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@ -16,10 +16,10 @@ shared-memory boxes and distributed-memory clusters and
supercomputers.
.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
LAMMPS is written in C++. Earlier versions were written in F77 and
F90. See the `History page <https://lammps.sandia.gov/history.html>`_ of
F90. See the `History page <https://www.lammps.org/history.html>`_ of
the website for details. All versions can be downloaded from the
`LAMMPS website <lws_>`_.

40
doc/src/Intro_website.rst
View File

@ -5,31 +5,31 @@ The `LAMMPS website <lws_>`_ has a variety of additional info about
LAMMPS, beyond what is in this manual. Some other useful resources
available online are listed below.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
* `Brief intro and recently added significant features <lws_>`_
* `List of features <https://lammps.sandia.gov/doc/Intro_features.html>`_
* `List of non-features <https://lammps.sandia.gov/doc/Intro_nonfeatures.html>`_
* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_
* `List of features <https://docs.lammps.org/Intro_features.html>`_
* `List of non-features <https://docs.lammps.org/Intro_nonfeatures.html>`_
* `Recent bug fixes and new features <https://www.lammps.org/bug.html>`_
* `Download info <https://lammps.sandia.gov/download.html>`_
* `Download info <https://www.lammps.org/download.html>`_
* `GitHub site <https://github.com/lammps/lammps>`_
* `SourceForge site <https://sourceforge.net/projects/lammps>`_
* `LAMMPS open-source license <https://lammps.sandia.gov/doc/Intro_opensource.html>`_
* `LAMMPS open-source license <https://docs.lammps.org/Intro_opensource.html>`_
* `Glossary of terms relevant to LAMMPS <https://lammps.sandia.gov/glossary.html>`_
* `LAMMPS highlights with images <https://lammps.sandia.gov/pictures.html>`_
* `LAMMPS highlights with movies <https://lammps.sandia.gov/movies.html>`_
* `Mail list <https://lammps.sandia.gov/mail.html>`_
* `Workshops <https://lammps.sandia.gov/workshops.html>`_
* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_
* `Glossary of terms relevant to LAMMPS <https://www.lammps.org/glossary.html>`_
* `LAMMPS highlights with images <https://www.lammps.org/pictures.html>`_
* `LAMMPS highlights with movies <https://www.lammps.org/movies.html>`_
* `Mail list <https://www.lammps.org/mail.html>`_
* `Workshops <https://www.lammps.org/workshops.html>`_
* `Tutorials <https://www.lammps.org/tutorials.html>`_
* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_
* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_
* `Viz tools usable with LAMMPS <https://lammps.sandia.gov/viz.html>`_
* `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
* `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
* `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
* `Benchmark performance <https://lammps.sandia.gov/bench.html>`_
* `Publications that have cited LAMMPS <https://lammps.sandia.gov/papers.html>`_
* `Authors of LAMMPS <https://lammps.sandia.gov/authors.html>`_
* `History of LAMMPS development <https://lammps.sandia.gov/history.html>`_
* `Funding for LAMMPS <https://lammps.sandia.gov/funding.html>`_
* `Benchmark performance <https://www.lammps.org/bench.html>`_
* `Publications that have cited LAMMPS <https://www.lammps.org/papers.html>`_
* `Authors of LAMMPS <https://www.lammps.org/authors.html>`_
* `History of LAMMPS development <https://www.lammps.org/history.html>`_
* `Funding for LAMMPS <https://www.lammps.org/funding.html>`_

12
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@ -15,6 +15,8 @@ This section documents the following functions:
- :cpp:func:`lammps_config_package_count`
- :cpp:func:`lammps_config_package_name`
- :cpp:func:`lammps_config_accelerator`
- :cpp:func:`lammps_has_gpu_device`
- :cpp:func:`lammps_gpu_device_info`
- :cpp:func:`lammps_has_style`
- :cpp:func:`lammps_style_count`
- :cpp:func:`lammps_style_name`
@ -132,6 +134,16 @@ approach.
-----------------------
.. doxygenfunction:: lammps_has_gpu_device
:project: progguide
-----------------------
.. doxygenfunction:: lammps_get_gpu_device_info
:project: progguide
-----------------------
.. doxygenfunction:: lammps_has_style
:project: progguide

36
doc/src/Manual.rst
View File

@ -1,6 +1,6 @@
######################################
LAMMPS version |version| Documentation
######################################
########################################
LAMMPS Documentation (|version| version)
########################################
LAMMPS stands for **L**\ arge-scale **A**\ tomic/**M**\ olecular
**M**\ assively **P**\ arallel **S**\ imulator.
@ -11,11 +11,12 @@ computers. It was developed originally at Sandia National
Laboratories, a US Department of Energy facility. The majority of
funding for LAMMPS has come from the US Department of Energy (DOE).
LAMMPS is an open-source code, distributed freely under the terms of
the GNU Public License (GPL).
the GNU Public License Version 2 (GPLv2).
The `LAMMPS website <lws_>`_ has a variety of information about the
code. It includes links to an on-line version of this manual, a
`mailing list <https://lammps.sandia.gov/mail.html>`_ where users can
`mailing list <https://www.lammps.org/mail.html>`_ and
`online forum <https://www.lammps.org/forum.html>`_ where users can
post questions, and a `GitHub site <https://github.com/lammps/lammps>`_
where all LAMMPS development is coordinated.
@ -30,11 +31,13 @@ please :ref:`see this note <webbrowser>`.
-----------
The manual is organized in two parts:
The manual is organized in three parts:
1) the :ref:`User Guide <user_documentation>` for how to install
and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>`
and use LAMMPS, 2) the :ref:`Programmer Guide <programmer_documentation>`
for how to write programs using the LAMMPS library from different
programming languages and how to modify and extend LAMMPS.
programming languages and how to modify and extend LAMMPS, and 3) the
:ref:`Command Reference <command_reference>` which includes detailed
descriptions of all commands included in the LAMMPS code.
.. only:: html
@ -42,7 +45,7 @@ programming languages and how to modify and extend LAMMPS.
:doc:`this page <Commands_all>` since it gives quick access
the documentation for all LAMMPS commands.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
----------
@ -89,10 +92,15 @@ Programmer Guide
Modify
Developer
*****************
Command Reference
*****************
.. _command_reference:
.. toctree::
:caption: Index
:name: index
:hidden:
:name: reference
:maxdepth: 1
:caption: Command Reference
commands_list
fixes
@ -118,10 +126,10 @@ Indices and tables
.. admonition:: Web Browser Compatibility
The HTML version of the manual makes use of advanced features present
int "modern" web browsers. This can lead to incompatibilities with older
in "modern" web browsers. This can lead to incompatibilities with older
web browsers (released more than 4 years ago) and specific vendor browsers
(e.g. Internet Explorer on Windows; Microsoft Edge works well though)
where parts of the pages are not rendered as expected (e.g. the layout is
broken or mathematical expressions not typeset). In that case we
recommend to install/use a different/newer web browser or use
the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_.
the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.

2
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@ -5,7 +5,7 @@ The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it in the next *patch* release, which are
typically made every couple of weeks. Info on patch releases are on
`this website page <https://lammps.sandia.gov/bug.html>`_. Every few
`this website page <https://www.lammps.org/bug.html>`_. Every few
months, the latest patch release is subjected to more thorough testing
and labeled as a *stable* version.

85
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@ -2,7 +2,7 @@ Submitting new features for inclusion in LAMMPS
===============================================
We encourage users to submit new features or modifications for LAMMPS to
`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
`the core developers <https://www.lammps.org/authors.html>`_ so they
can be added to the LAMMPS distribution. The preferred way to manage and
coordinate this is via the LAMMPS project on `GitHub
<https://github.com/lammps/lammps>`_. Please see the :doc:`GitHub
@ -10,14 +10,14 @@ Tutorial <Howto_github>` for a demonstration on how to do that. An
alternative is to contact the LAMMPS developers or the indicated
developer of a package or feature directly and send in your contribution
via e-mail, but that can add a significant delay on getting your
contribution included, depending on how busy the developer is you
contact, how complex a task it would be to integrate that code, and how
contribution included, depending on how busy the respective developer
is, how complex a task it would be to integrate that code, and how
many - if any - changes are required before the code can be included.
For any larger modifications or programming project, you are encouraged
to contact the LAMMPS developers ahead of time, in order to discuss
implementation strategies and coding guidelines, that will make it
easier to integrate your contribution and result in less work for
to contact the LAMMPS developers ahead of time in order to discuss
implementation strategies and coding guidelines. That will make it
easier to integrate your contribution and results in less work for
everybody involved. You are also encouraged to search through the list
of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
and submit a new issue for a planned feature, so you would not duplicate
@ -31,21 +31,22 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
you are working on. Only discussions related to LAMMPS development are
tolerated, so this is **NOT** for people that look for help with compiling,
installing, or using LAMMPS. Please contact the `lammps-users mailing
list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead.
list <https://www.lammps.org/mail.html>`_ for those purposes instead.
How quickly your contribution will be integrated depends largely on how
much effort it will cause to integrate and test it, how much it requires
changes to the core codebase, and of how much interest it is to the
larger LAMMPS community. Please see below for a checklist of typical
requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub
Tutorial <Howto_github>` page for instructions on
how to submit your changes or new files through a GitHub pull
request. If you prefer to submit patches or full files, you should first
make certain, that your code works correctly with the latest patch-level
version of LAMMPS and contains all bug fixes from it. Then create a
gzipped tar file of all changed or added files or a corresponding patch
file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
use gzip compression, as this works well on all platforms.
much effort it will cause to integrate and test it, how many and what
kind of changes it requires to the core codebase, and of how much
interest it is to the larger LAMMPS community. Please see below for a
checklist of typical requirements. Once you have prepared everything,
see the :doc:`LAMMPS GitHub Tutorial <Howto_github>` page for
instructions on how to submit your changes or new files through a GitHub
pull request. If you prefer to submit patches or full files, you should
first make certain, that your code works correctly with the latest
patch-level version of LAMMPS and contains all bug fixes from it. Then
create a gzipped tar file of all changed or added files or a
corresponding patch file using 'diff -u' or 'diff -c' and compress it
with gzip. Please only use gzip compression, as this works well and is
available on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`. Else we will add them as a
@ -57,13 +58,16 @@ added to the LAMMPS distribution. All the standard and user packages
are listed and described on the :doc:`Packages details <Packages_details>` doc page.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
used as a license for the rest of LAMMPS. See the :doc:`LAMMPS license
<Intro_opensource>` doc page for details.
them open-source, i.e. we can release them under the terms of the GPL
(version 2), used as a license for the rest of LAMMPS. And as part of
a LGPL (version 2.1) distribution that we make available to developers
on request only and with files that are authorized for that kind of
distribution removed (e.g. interface to FFTW). See the
:doc:`LAMMPS license <Intro_opensource>` doc page for details.
With user packages and files, all we are really providing (aside from
the fame and fortune that accompanies having your name in the source
code and on the `Authors page <https://lammps.sandia.gov/authors.html>`_
code and on the `Authors page <https://www.lammps.org/authors.html>`_
of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
work to the LAMMPS user community, and a mechanism for others to
easily try out your new feature. This may help you find bugs or make
@ -77,13 +81,13 @@ unusual event).
If you prefer to actively develop and support your add-on
feature yourself, then you may wish to make it available for download
from your own website, as a user package that LAMMPS users can add to
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
their copy of LAMMPS. See the `Offsite LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page of the LAMMPS web
site for examples of groups that do this. We are happy to advertise
your package and web site from that page. Simply email the
`developers <https://lammps.sandia.gov/authors.html>`_ with info about
`developers <https://www.lammps.org/authors.html>`_ with info about
your package and we will post it there.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
The previous sections of this doc page describe how to add new "style"
files of various kinds to LAMMPS. Packages are simply collections of
@ -92,7 +96,7 @@ LAMMPS input script. If designed correctly, these additions typically
do not require changes to the main core of LAMMPS; they are simply
add-on files. If you think your new feature requires non-trivial
changes in core LAMMPS files, you should `communicate with the
developers <https://lammps.sandia.gov/authors.html>`_, since we may or
developers <https://www.lammps.org/authors.html>`_, since we may or
may not want to include those changes for some reason. An example of a
trivial change is making a parent-class method "virtual" when you derive
a new child class from it.
@ -112,7 +116,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
your contribution(s) to be added to main LAMMPS code or one of its
standard packages, it needs to be written in a style compatible with
other LAMMPS source files. This means: 2-character indentation per
level, **no tabs**\ , no lines over 80 characters. I/O is done via
level, **no tabs**\ , no lines over 100 characters. I/O is done via
the C-style stdio library (mixing of stdio and iostreams is generally
discouraged), class header files should not import any system headers
outside of <cstdio>, STL containers should be avoided in headers,
@ -131,6 +135,31 @@ packages in the src directory for examples. If you are uncertain, please ask.
LAMMPS source files, including the use of the error class for error
and warning messages.
* To simplify reformatting contributed code in a way that is compatible
with the LAMMPS formatting styles, you can use clang-format (version 8
or later). The LAMMPS distribution includes a suitable ``.clang-format``
file which will be applied if you run ``clang-format -i some_file.cpp``
on your files inside the LAMMPS src tree. Please only reformat files
that you have contributed. For header files containing a
``SomeStyle(keyword, ClassName)`` macros it is required to have this
macro embedded with a pair of ``// clang-format off``, ``// clang-format on``
commends and the line must be terminated with a semi-colon (;).
Example:
.. code-block:: c++
#ifdef COMMAND_CLASS
// clang-format off
CommandStyle(run,Run);
// clang-format on
#else
#ifndef LMP_RUN_H
[...]
You may also use ``// clang-format on/off`` throughout your file
to protect sections of the file from being reformatted.
* If you want your contribution to be added as a user-contributed
feature, and it's a single file (actually a \*.cpp and \*.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line

168
doc/src/Packages_details.rst
View File

@ -69,6 +69,7 @@ page gives those details.
* :ref:`USER-ATC <PKG-USER-ATC>`
* :ref:`USER-AWPMD <PKG-USER-AWPMD>`
* :ref:`USER-BOCS <PKG-USER-BOCS>`
* :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
* :ref:`USER-CGDNA <PKG-USER-CGDNA>`
* :ref:`USER-CGSDK <PKG-USER-CGSDK>`
* :ref:`USER-COLVARS <PKG-USER-COLVARS>`
@ -78,9 +79,11 @@ page gives those details.
* :ref:`USER-EFF <PKG-USER-EFF>`
* :ref:`USER-FEP <PKG-USER-FEP>`
* :ref:`USER-H5MD <PKG-USER-H5MD>`
* :ref:`USER-HDNNP <PKG-USER-HDNNP>`
* :ref:`USER-INTEL <PKG-USER-INTEL>`
* :ref:`USER-LB <PKG-USER-LB>`
* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
* :ref:`USER-MDI <PKG-USER-MDI>`
* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
* :ref:`USER-MESODPD <PKG-USER-MESODPD>`
* :ref:`USER-MESONT <PKG-USER-MESONT>`
@ -97,6 +100,7 @@ page gives those details.
* :ref:`USER-QMMM <PKG-USER-QMMM>`
* :ref:`USER-QTB <PKG-USER-QTB>`
* :ref:`USER-QUIP <PKG-USER-QUIP>`
* :ref:`USER-RANN <PKG-USER-RANN>`
* :ref:`USER-REACTION <PKG-USER-REACTION>`
* :ref:`USER-REAXC <PKG-USER-REAXC>`
* :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`
@ -131,8 +135,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
* examples/ASPHERE
* examples/ellipse
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#tri
* https://www.lammps.org/movies.html#line
* https://www.lammps.org/movies.html#tri
----------
@ -328,7 +332,7 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
* :doc:`package gpu <package>`
* :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)
for styles followed by (g)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -354,11 +358,11 @@ potentials.
* examples/granregion
* examples/pour
* bench/in.chute
* https://lammps.sandia.gov/pictures.html#jamming
* https://lammps.sandia.gov/movies.html#hopper
* https://lammps.sandia.gov/movies.html#dem
* https://lammps.sandia.gov/movies.html#brazil
* https://lammps.sandia.gov/movies.html#granregion
* https://www.lammps.org/pictures.html#jamming
* https://www.lammps.org/movies.html#hopper
* https://www.lammps.org/movies.html#dem
* https://www.lammps.org/movies.html#brazil
* https://www.lammps.org/movies.html#granregion
----------
@ -445,7 +449,7 @@ time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`
:ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
You must have a C++14 compatible compiler to use this package.
KOKKOS makes extensive use of advanced C++ features, which can
expose compiler bugs, especially when compiling for maximum
performance at high optimization levels. Please see the file
@ -477,7 +481,7 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (k)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -601,7 +605,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
* :doc:`fix tfmc <fix_tfmc>`
* :doc:`fix widom <fix_widom>`
* :doc:`pair_style dsmc <pair_dsmc>`
* https://lammps.sandia.gov/movies.html#gcmc
* https://www.lammps.org/movies.html#gcmc
----------
@ -658,8 +662,8 @@ listing, "ls src/MISC", to see the list of commands.
* :doc:`fix viscosity <fix_viscosity>`
* examples/KAPPA
* examples/VISCOSITY
* https://lammps.sandia.gov/pictures.html#ttm
* https://lammps.sandia.gov/movies.html#evaporation
* https://www.lammps.org/pictures.html#ttm
* https://www.lammps.org/movies.html#evaporation
----------
@ -814,7 +818,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
* :doc:`OPT package <Speed_opt>`
* :doc:`Section 2.6 -sf opt <Run_options>`
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -845,7 +849,7 @@ Foster (UTSA).
* :doc:`compute damage/atom <compute_damage_atom>`
* :doc:`compute plasticity/atom <compute_plasticity_atom>`
* examples/peri
* https://lammps.sandia.gov/movies.html#peri
* https://www.lammps.org/movies.html#peri
----------
@ -1006,8 +1010,8 @@ Also several computes which calculate properties of rigid bodies.
* examples/ASPHERE
* examples/rigid
* bench/in.rhodo
* https://lammps.sandia.gov/movies.html#box
* https://lammps.sandia.gov/movies.html#star
* https://www.lammps.org/movies.html#box
* https://www.lammps.org/movies.html#star
----------
@ -1108,9 +1112,9 @@ colloidal particles.
* :doc:`fix wall/srd <fix_wall_srd>`
* examples/srd
* examples/ASPHERE
* https://lammps.sandia.gov/movies.html#tri
* https://lammps.sandia.gov/movies.html#line
* https://lammps.sandia.gov/movies.html#poly
* https://www.lammps.org/movies.html#tri
* https://www.lammps.org/movies.html#line
* https://www.lammps.org/movies.html#poly
----------
@ -1202,7 +1206,7 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do
* src/USER-ATC/README
* :doc:`fix atc <fix_atc>`
* examples/USER/atc
* https://lammps.sandia.gov/pictures.html#atc
* https://www.lammps.org/pictures.html#atc
----------
@ -1266,6 +1270,26 @@ Example inputs are in the examples/USER/bocs folder.
----------
.. _PKG-USER-BROWNIAN:
USER-BROWNIAN package
---------------------
**Contents:**
This package provides :doc:`fix brownian, fix brownian/sphere, and
fix brownian/asphere <fix_brownian>` as well as
:doc:`fix propel/self <fix_propel_self>` which allow to do Brownian
Dynamics time integration of point, spherical and aspherical particles
and also support self-propelled particles.
**Authors:** Sam Cameron (University of Bristol),
Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
Example inputs are in the examples/USER/brownian folder.
----------
.. _PKG-USER-CGDNA:
USER-CGDNA package
@ -1315,7 +1339,7 @@ acids.
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/USER/cgsdk
* https://lammps.sandia.gov/pictures.html#cg
* https://www.lammps.org/pictures.html#cg
----------
@ -1552,7 +1576,7 @@ tools/eff; see its README file.
* examples/USER/eff
* tools/eff/README
* tools/eff
* https://lammps.sandia.gov/movies.html#eff
* https://www.lammps.org/movies.html#eff
----------
@ -1617,6 +1641,39 @@ This package has :ref:`specific installation instructions <user-h5md>` on the :d
----------
.. _PKG-USER-HDNNP:
USER-HDNNP package
------------------
**Contents:**
A :doc:`pair_style hdnnp <pair_hdnnp>` command which allows to use
high-dimensional neural network potentials (HDNNPs), a form of machine learning
potentials. HDNNPs must be carefully trained prior to their application in a
molecular dynamics simulation.
.. _n2p2: https://github.com/CompPhysVienna/n2p2
To use this package you must have the `n2p2 <n2p2_>`_ library installed and
compiled on your system.
**Author:** Andreas Singraber
**Install:**
This package has :ref:`specific installation instructions <user-hdnnp>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-HDNNP: filenames -> commands
* src/USER-HDNNP/README
* lib/hdnnp/README
* :doc:`pair_style hdnnp <pair_hdnnp>`
* examples/USER/hdnnp
----------
.. _PKG-USER-INTEL:
USER-INTEL package
@ -1661,7 +1718,7 @@ This package has :ref:`specific installation instructions <user-intel>` on the :
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
* src/USER-INTEL/TEST
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -1766,7 +1823,29 @@ Waltham, MA, USA)
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
* examples/USER/manifold
* https://lammps.sandia.gov/movies.html#manifold
* https://www.lammps.org/movies.html#manifold
----------
.. _PKG-USER-MDI:
USER-MDI package
----------------
**Contents:**
A LAMMPS command and fix to allow client-server coupling of LAMMPS to
other atomic or molecular simulation codes via the `MolSSI Driver Interface
(MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
**Supporting info:**
* src/USER-MDI/README
* :doc:`mdi/engine <mdi_engine>`
* :doc:`fix mdi/engine <fix_mdi_engine>`
* examples/USER/mdi
----------
@ -1822,10 +1901,10 @@ algorithm.
* :doc:`pair_style tdpd <pair_mesodpd>`
* :doc:`fix mvv/dpd <fix_mvv_dpd>`
* examples/USER/mesodpd
* https://lammps.sandia.gov/movies.html#mesodpd
* https://www.lammps.org/movies.html#mesodpd
* examples/USER/meso
* http://lammps.sandia.gov/movies.html#mesodpd
* http://www.lammps.org/movies.html#mesodpd
----------
@ -2041,7 +2120,7 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
:doc:`kspace <Commands_kspace>`) for styles followed by (o)
* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
----------
@ -2199,6 +2278,31 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d
----------
.. _PKG-USER-RANN:
USER-RANN package
-----------------
**Contents:**
A pair style for using rapid atomistic neural network (RANN) potentials.
These neural network potentials work by first generating a series of symmetry
functions from the neighbor list and then using these values as the input layer
of a neural network.
**Authors:**
This package was written by Christopher Barrett
with contributions by Doyl Dickel, Mississippi State University.
**Supporting info:**
* src/USER-RANN: filenames -> commands
* :doc:`pair_style rann <pair_rann>`
* examples/USER/rann
----------
.. _PKG-USER-REACTION:
USER-REACTION package
@ -2224,8 +2328,8 @@ molecules, and chiral-sensitive reactions.
* src/USER-REACTION/README
* :doc:`fix bond/react <fix_bond_react>`
* examples/USER/reaction
* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
* reacter.org
----------
@ -2352,7 +2456,7 @@ This package has :ref:`specific installation instructions <user-smd>` on the :do
* src/USER-SMD/README
* doc/PDF/SMD_LAMMPS_userguide.pdf
* examples/USER/smd
* https://lammps.sandia.gov/movies.html#smd
* https://www.lammps.org/movies.html#smd
----------
@ -2409,7 +2513,7 @@ Dynamics, Ernst Mach Institute, Germany).
* src/USER-SPH/README
* doc/PDF/SPH_LAMMPS_userguide.pdf
* examples/USER/sph
* https://lammps.sandia.gov/movies.html#sph
* https://www.lammps.org/movies.html#sph
----------

6
doc/src/Packages_standard.rst
View File

@ -39,13 +39,13 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`DIPOLE <PKG-DIPOLE>` | point dipole particles | :doc:`pair_style lj/.../dipole <pair_dipole>` | dipole | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | int |
| :ref:`GPU <PKG-GPU>` | GPU-enabled styles | :doc:`Section gpu <Speed_gpu>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | int |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`GRANULAR <PKG-GRANULAR>` | granular systems | :doc:`Howto granular <Howto_granular>` | pour | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KIM <PKG-KIM>` | OpenKIM wrapper | :doc:`pair_style kim <pair_kim>` | kim | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`KOKKOS <PKG-KOKKOS>` | Kokkos-enabled styles | :doc:`Speed kokkos <Speed_kokkos>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`KSPACE <PKG-KSPACE>` | long-range Coulombic solvers | :doc:`kspace_style <kspace_style>` | peptide | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
@ -67,7 +67,7 @@ package:
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`MSCG <PKG-MSCG>` | multi-scale coarse-graining wrapper | :doc:`fix mscg <fix_mscg>` | mscg | ext |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`OPT <PKG-OPT>` | optimized pair styles | :doc:`Speed opt <Speed_opt>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
| :ref:`PERI <PKG-PERI>` | Peridynamics models | :doc:`pair_style peri <pair_peri>` | peri | no |
+----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+

12
doc/src/Packages_user.rst
View File

@ -39,6 +39,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
@ -57,12 +59,16 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`USER-HDNNP <PKG-USER-HDNNP>` | High-dimensional neural network potentials | :doc:`pair_style hdnnp <pair_hdnnp>` | USER/hdnnp | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MDI <PKG-USER-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
@ -79,7 +85,7 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
@ -95,6 +101,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-RANN <PKG-USER-RANN>` | rapid atomistic neural network (RANN) potentials | :doc:`pair rann <pair_rann>` | USER/rann | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |

8
doc/src/Python_install.rst
View File

@ -377,14 +377,6 @@ make MPI calls directly from Python in your script, if you desire.
We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
(aka mpi4py) and you will find installation instruction for it below.
.. note::
Older LAMMPS versions were also tested with `PyPar <https://github.com/daleroberts/pypar>`_
but we can no longer test it, since it does not work with the Python
(3.x) versions on our test servers. Since there have been no updates
to PyPar visible in its repository since November 2016 we have to assume
it is no longer maintained.
Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
follows:

19
doc/src/Run_options.rst
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@ -10,6 +10,7 @@ letter abbreviation can be used:
* :ref:`-i or -in <file>`
* :ref:`-k or -kokkos <run-kokkos>`
* :ref:`-l or -log <log>`
* :ref:`-mdi <mdi>`
* :ref:`-m or -mpicolor <mpicolor>`
* :ref:`-c or -cite <cite>`
* :ref:`-nc or -nocite <nocite>`
@ -196,9 +197,23 @@ Option -plog will override the name of the partition log files file.N.
----------
.. _mdi:
**-mdi 'multiple flags'**
This flag is only recognized and used when LAMMPS has support for the MolSSI
Driver Interface (MDI) included as part of the :ref:`USER-MDI <PKG-USER-MDI>`
package. This flag is specific to the MDI library and controls how LAMMPS
interacts with MDI. There are usually multiple flags that have to follow it
and those have to be placed in quotation marks. For more information about
how to launch LAMMPS in MDI client/server mode please refer to the
:doc:`MDI Howto <Howto_mdi>`.
----------
.. _mpicolor:
**-mpicolor** color
**-mpicolor color**
If used, this must be the first command-line argument after the LAMMPS
executable name. It is only used when LAMMPS is launched by an mpirun
@ -223,7 +238,7 @@ links with from the lib/message directory. See the
.. _cite:
**-cite style or file name**
**-cite style** or **file name**
Select how and where to output a reminder about citing contributions
to the LAMMPS code that were used during the run. Available styles are

2
doc/src/Speed.rst
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@ -12,7 +12,7 @@ accelerator packages provided with LAMMPS that contain code optimized
for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi co-processors.
The `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS
The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
web site gives performance results for the various accelerator
packages discussed on the :doc:`Speed packages <Speed_packages>` doc
page, for several of the standard LAMMPS benchmark problems, as a

8
doc/src/Speed_bench.rst
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@ -1,7 +1,7 @@
Benchmarks
==========
Current LAMMPS performance is discussed on the `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of the `LAMMPS website <lws_>`_
Current LAMMPS performance is discussed on the `Benchmarks page <https://www.lammps.org/bench.html>`_ of the `LAMMPS website <lws_>`_
where timings and parallel efficiency are listed. The page has
several sections, which are briefly described below:
@ -43,11 +43,11 @@ to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the
table of results on the
`Potentials <https://lammps.sandia.gov/bench.html#potentials>`_ section of
`Potentials <https://www.lammps.org/bench.html#potentials>`_ section of
the Benchmarks web page. So you can also run those test problems on
your machine.
The `billion-atom <https://lammps.sandia.gov/bench.html#billion>`_ section
The `billion-atom <https://www.lammps.org/bench.html#billion>`_ section
of the Benchmarks web page has performance data for very large
benchmark runs of simple Lennard-Jones (LJ) models, which use the
bench/in.lj input script.
@ -73,4 +73,4 @@ estimate parallel performance for multi-node runs using the same logic
as for all-MPI mode, except that now you will typically need many more
atoms/node to achieve good scalability.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org

2
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@ -152,7 +152,7 @@ in OpenCL mode on CPUs (which uses vectorization and multithreading) is
usually resulting in inferior performance compared to using LAMMPS' native
threading and vectorization support in the USER-OMP and USER-INTEL packages.
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the GPU package on various
hardware, including the Titan HPC platform at ORNL.

2
doc/src/Speed_kokkos.rst
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@ -406,7 +406,7 @@ Generally speaking, the following rules of thumb apply:
package also can increase the vector length of vector instructions
by switching to single or mixed precision mode.
See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
LAMMPS web site for performance of the KOKKOS package on different
hardware.

2
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@ -145,7 +145,7 @@ sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those directories.
As mentioned above, the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS web site gives
As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.

104
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@ -6,15 +6,15 @@ molecular dynamics computations. Additional pre- and post-processing
steps are often necessary to setup and analyze a simulation. A list
of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
* `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_
* `Pre/Post processing <https://www.lammps.org/prepost.html>`_
* `Offsite LAMMPS packages & tools <https://www.lammps.org/offsite.html>`_
* `Pizza.py toolkit <pizza_>`_
The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at
Sandia which provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations.
.. _lws: https://lammps.sandia.gov
.. _lws: https://www.lammps.org
.. _pizza: https://pizza.sandia.gov
.. _python: https://www.python.org
@ -94,6 +94,7 @@ Miscellaneous tools
* :ref:`kate <kate>`
* :ref:`LAMMPS shell <lammps_shell>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
* :ref:`Offline build tool <offline>`
* :ref:`singularity <singularity_tool>`
* :ref:`SWIG interface <swig>`
* :ref:`vim <vim>`
@ -756,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information.
----------
.. _offline:
Scripts for building LAMMPS when offline
----------------------------------------
In some situations it might be necessary to build LAMMPS on a system
without direct internet access. The scripts in ``tools/offline`` folder
allow you to pre-load external dependencies for both the documentation
build and for building LAMMPS with CMake.
It does so by
#. downloading necessary ``pip`` packages,
#. cloning ``git`` repositories
#. downloading tarballs
to a designated cache folder.
As of April 2021, all of these downloads make up around 600MB. By
default, the offline scripts will download everything into the
``$HOME/.cache/lammps`` folder, but this can be changed by setting the
``LAMMPS_CACHING_DIR`` environment variable.
Once the caches have been initialized, they can be used for building the
LAMMPS documentation or compiling LAMMPS using CMake on an offline
system.
The ``use_caches.sh`` script must be sourced into the current shell
to initialize the offline build environment. Note that it must use
the same ``LAMMPS_CACHING_DIR``. This script does the following:
#. Set up environment variables that modify the behavior of both,
``pip`` and ``git``
#. Start a simple local HTTP server using Python to host files for CMake
Afterwards, it will print out instruction on how to modify the CMake
command line to make sure it uses the local HTTP server.
To undo the environment changes and shutdown the local HTTP server,
run the ``deactivate_caches`` command.
Examples
^^^^^^^^
For all of the examples below, you first need to create the cache, which
requires an internet connection.
.. code-block:: bash
./tools/offline/init_caches.sh
Afterwards, you can disconnect or copy the contents of the
``LAMMPS_CACHING_DIR`` folder to an offline system.
Documentation Build
^^^^^^^^^^^^^^^^^^^
The documentation build will create a new virtual environment that
typically first installs dependencies from ``pip``. With the offline
environment loaded, these installations will instead grab the necessary
packages from your local cache.
.. code-block:: bash
# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
# export LAMMPS_CACHING_DIR=path/to/folder
source tools/offline/use_caches.sh
cd doc/
make html
deactivate_caches
CMake Build
^^^^^^^^^^^
When compiling certain packages with external dependencies, the CMake
build system will download necessary files or sources from the web. For
more flexibility the CMake configuration allows users to specify the URL
of each of these dependencies. What the ``init_caches.sh`` script does
is create a CMake "preset" file, which sets the URLs for all of the known
dependencies and redirects the download to the local cache.
.. code-block:: bash
# if LAMMPS_CACHING_DIR is different from default, make sure to set it first
# export LAMMPS_CACHING_DIR=path/to/folder
source tools/offline/use_caches.sh
mkdir build
cd build
cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
make -j 8
deactivate_caches
----------
.. _phonon:
phonon tool

1
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@ -69,7 +69,6 @@ parenthesized comments):
HAM (keyword is the first text on line)
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
(blank line)
N 181 FP 0 0 (N, FP parameters)
1 0.0 200.5 2.5 (index, angle, energy, derivative)
2 1.0 198.0 2.5
...

2
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@ -80,7 +80,7 @@ LAMMPS commands require a map, even for atomic systems, and will
generate an error if one does not exist. The *map* keyword thus
allows you to force the creation of a map. The *yes* value will
create either an *array* or *hash* style map, as explained in the next
paragraph. The *array* and *hash* values create an atom-style or
paragraph. The *array* and *hash* values create an array-style or
hash-style map respectively.
For an *array*\ -style map, each processor stores a lookup table of

58
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@ -11,13 +11,17 @@ Syntax
comm_modify keyword value ...
* zero or more keyword/value pairs may be appended
* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel*
.. parsed-literal::
*mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
*mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances
*cutoff* value = Rcut (distance units) = communicate atoms from this far away
*cutoff/multi* type value
*cutoff/multi* collection value
collection = atom collection or collection range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style
*cutoff/multi/old* type value
type = atom type or type range (supports asterisk notation)
value = Rcut (distance units) = communicate atoms for selected types from this far away
*group* value = group-ID = only communicate atoms in the group
@ -28,9 +32,9 @@ Examples
.. code-block:: LAMMPS
comm_modify mode multi
comm_modify mode multi reduce/multi
comm_modify mode multi group solvent
comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
comm_modify vel yes
comm_modify mode single cutoff 5.0 vel yes
comm_modify cutoff/multi * 0.0
@ -62,12 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor
cutoff across all atom type pairs.
For many systems this is an efficient algorithm, but for systems with
widely varying cutoffs for different type pairs, the *multi* mode can
be faster. In this case, each atom type is assigned its own distance
widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
be faster. In *multi*, each atom is assigned to a collection which should
correspond to a set of atoms with similar interaction cutoffs.
In this case, each atom collection is assigned its own distance
cutoff for communication purposes, and fewer atoms will be
communicated. See the :doc:`neighbor multi <neighbor>` command for a
neighbor list construction option that may also be beneficial for
simulations of this kind.
communicated. in *multi/old*, a similar technique is used but atoms
are grouped by atom type. See the :doc:`neighbor multi <neighbor>` and
:doc:`neighbor multi/old <neighbor>` commands for
neighbor list construction options that may also be beneficial for
simulations of this kind. The *multi* communication mode is only compatible
with the *multi* neighbor style. The *multi/old* communication mode is comparable
with both the *multi* and *multi/old* neighbor styles.
The *cutoff* keyword allows you to extend the ghost cutoff distance
for communication mode *single*\ , which is the distance from the borders
@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the
communication cutoff used.
The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
communication mode *multi* instead. Since in this case the communication
cutoffs are determined per atom type, a type specifier is needed and
cutoff for one or multiple types can be extended. Also ranges of types
using the usual asterisk notation can be given. For granular pair styles,
the default cutoff is set to the sum of the current maximum atomic radii
for each type.
communication mode *multi* instead. Since the communication cutoffs are
determined per atom collections, a collection specifier is needed and
cutoff for one or multiple collections can be extended. Also ranges of
collections using the usual asterisk notation can be given. Collections
are indexed from 1 to N where N is the total number of collections.
Note that the arguments for *cutoff/multi* are parsed right before each
simulation to account for potential changes in the number of
collections. Custom cutoffs are preserved between runs but if
collections are redefined, one may want to re-specify the communication
cutoffs. For granular pair styles,the default cutoff is set to the sum
of the current maximum atomic radii for each collection. The
*cutoff/multi/old* option is similar to *cutoff/multi* except it
operates on atom types as opposed to collections.
The *reduce/multi* option applies to *multi* and sets the communication
cutoff for a particle equal to the maximum interaction distance between particles
in the same collection. This reduces the number of
ghost atoms that need to be communicated. This method is only compatible with the
*multi* neighbor style and requires a half neighbor list and Newton on.
See the :doc:`neighbor multi <neighbor>` command for more information.
These are simulation scenarios in which it may be useful or even
necessary to set a ghost cutoff > neighbor cutoff:
@ -123,7 +147,7 @@ ghost cutoff should be set.
In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
:doc:`pairwise potential <pair_style>` needs to calculate with ghost
atoms beyond the normal pairwise cutoff for some computation it
performs (e.g. locate neighbors of ghost atoms in a multibody pair
performs (e.g. locate neighbors of ghost atoms in a manybody pair
potential). Setting the ghost cutoff appropriately can insure it will
find the needed atoms.

1
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@ -59,6 +59,7 @@ Commands
lattice
log
mass
mdi_engine
message
min_modify
min_spin

2
doc/src/compute_fep.rst
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@ -48,6 +48,8 @@ Examples
compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
compute 1 all fep 300 atom charge 2 v_delta
Example input scripts available: examples/USER/fep
Description
"""""""""""

2
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@ -20,6 +20,8 @@ Examples
compute TDRUDE all temp/drude
Example input scripts available: examples/USER/drude
Description
"""""""""""

4
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@ -182,6 +182,9 @@ accelerated styles exist.
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`balance <fix_balance>` - perform dynamic load-balancing
* :doc:`brownian <fix_brownian>` - overdamped translational brownian motion
* :doc:`brownian/asphere <fix_brownian>` - overdamped translational and rotational brownian motion for ellipsoids
* :doc:`brownian/sphere <fix_brownian>` - overdamped translational and rotational brownian motion for spheres
* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
* :doc:`bond/break <fix_bond_break>` - break bonds on the fly
* :doc:`bond/create <fix_bond_create>` - create bonds on the fly
@ -241,6 +244,7 @@ accelerated styles exist.
* :doc:`lb/viscous <fix_lb_viscous>` -
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
* :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms

3
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@ -56,6 +56,9 @@ Examples
fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt/fep 10 atom diameter 1 v_size
Example input scripts available: examples/USER/fep
Description
"""""""""""

45
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@ -17,7 +17,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command.
* bond/react = style name of this fix command
* the common keyword/values may be appended directly after 'bond/react'
* this applies to all reaction specifications (below)
* common keywords apply to all reaction specifications
* common_keyword = *stabilization* or *reset_mol_ids*
.. parsed-literal::
@ -328,8 +328,8 @@ keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
handedness should be enforced. The fifth optional section begins with
the keyword 'Constraints' and lists additional criteria that must be
satisfied in order for the reaction to occur. Currently, there are
five types of constraints available, as discussed below: 'distance',
'angle', 'dihedral', 'arrhenius', and 'rmsd'.
six types of constraints available, as discussed below: 'distance',
'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'.
A sample map file is given below:
@ -500,6 +500,45 @@ example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
The constraint of type 'custom' has the following syntax:
.. parsed-literal::
custom *varstring*
where 'custom' is the required keyword, and *varstring* is a
variable expression. The expression must be a valid equal-style
variable formula that can be read by the :doc:`variable <variable>` command,
after any special reaction functions are evaluated. If the resulting
expression is zero, the reaction is prevented from occurring;
otherwise, it is permitted to occur. There are two special reaction
functions available, 'rxnsum' and 'rxnave'. These functions operate
over the atoms in a given reaction site, and have one mandatory
argument and one optional argument. The mandatory argument is the
identifier for an atom-style variable. The second, optional argument
is the name of a molecule fragment in the pre-reaction template, and
can be used to operate over a subset of atoms in the reaction site.
The 'rxnsum' function sums the atom-style variable over the reaction
site, while the 'rxnave' returns the average value. For example, a
constraint on the total potential energy of atoms involved in the
reaction can be imposed as follows:
.. code-block:: LAMMPS
compute 1 all pe/atom # in LAMMPS input script
variable my_pe atom c_1 # in LAMMPS input script
.. code-block:: LAMMPS
custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file
The above example prevents the reaction from occurring unless the
total potential energy of the reaction site is above 100. The variable
expression can be interpreted as the probability of the reaction
occurring by using an inequality and the 'random(x,y,z)' function
available as an equal-style variable input, similar to the 'arrhenius'
constraint above.
By default, all constraints must be satisfied for the reaction to
occur. In other words, constraints are evaluated as a series of
logical values using the logical AND operator "&&". More complex logic

216
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@ -0,0 +1,216 @@
.. index:: fix brownian
.. index:: fix brownian/sphere
.. index:: fix brownian/asphere
fix brownian command
===========================
fix brownian/sphere command
===========================
fix brownian/sphere command
===========================
Syntax
""""""
.. parsed-literal::
fix ID group-ID style_name temp seed keyword args
* ID, group-ID are documented in :doc:`fix <fix>` command
* style_name = *brownian* or *brownian/sphere* or *brownian/asphere*
* temp = temperature
* seed = random number generator seed
* one or more keyword/value pairs may be appended
* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t*
.. parsed-literal::
*rng* value = *uniform* or *gaussian* or *none*
*uniform* = use uniform random number generator
*gaussian* = use gaussian random number generator
*none* = turn off noise
*dipole* value = *mux* and *muy* and *muz* for *brownian/asphere*
*mux*, *muy*, and *muz* = update orientation of dipole having direction (*mux*,*muy*,*muz*) in body frame of rigid body
*gamma_r_eigen* values = *gr1* and *gr2* and *gr3* for *brownian/asphere*
*gr1*, *gr2*, and *gr3* = diagonal entries of body frame rotational friction tensor
*gamma_r* values = *gr* for *brownian/sphere*
*gr* = magnitude of the (isotropic) rotational friction tensor
*gamma_t_eigen* values = *gt1* and *gt2* and *gt3* for *brownian/asphere*
*gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor
*gamma_t* values = *gt* for *brownian* and *brownian/sphere*
*gt* = magnitude of the (isotropic) translational friction tensor
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all brownian 1.0 12908410 gamma_t 1.0
fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian
fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0
fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian
fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0
Description
"""""""""""
Perform Brownian Dynamics time integration to update position, velocity,
dipole orientation (for spheres) and quaternion orientation (for
ellipsoids, with optional dipole update as well) of all particles in the
fix group in each timestep. Brownian Dynamics uses Newton's laws of
motion in the limit that inertial forces are negligible compared to
viscous forces. The stochastic equation of motion for the center of mass
positions is
.. math::
d\mathbf{r} = \mathbf{\gamma}_t^{-1}\mathbf{F}dt+\sqrt{2k_BT}\mathbf{\gamma}_t^{-1/2}d\mathbf{W}_t,
in the lab-frame (i.e. :math:`\mathbf{\gamma}_t` is not diagonal, but
only depends on orientation and so the noise is still additive).
The rotational motion for the spherical and ellipsoidal particles is not
as simple an expression, but is chosen to replicate the Boltzmann
distribution for the case of conservative torques (see :ref:`(Ilie)
<Ilie1>` or :ref:`(Delong) <Delong1>`).
For the style *brownian*, only the positions of the particles are
updated. This is therefore suitable for point particle simulations.
For the style *brownian/sphere*, the positions of the particles are
updated, and a dipole slaved to the spherical orientation is also
updated. This style therefore requires the hybrid atom style
:doc:`atom_style dipole <atom_style>` and :doc:`atom_style sphere
<atom_style>`.
For the style *brownian/asphere*, the center of mass positions and the
quaternions of ellipsoidal particles are updated. This fix style is
suitable for equations of motion where the rotational and translational
friction tensors can be diagonalized in a certain (body) reference frame.
---------
.. note::
This integrator does not by default assume a relationship between the
rotational and translational friction tensors, though such a relationship
should exist in the case of no-slip boundary conditions between the particles and
the surrounding (implicit) solvent. E.g. in the case of spherical particles,
the condition :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly
accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where
:math:`\sigma` is the spherical diameter). A similar (though more complex)
relationship holds for ellipsoids and rod-like particles.
---------
.. note::
Temperature computation using the :doc:`compute temp <compute_temp>`
will not correctly compute temperature of these overdamped dynamics
since we are explicitly neglecting inertial effects.
Furthermore, this time integrator does not add the stochastic terms or
viscous terms to the force and/or torques. Rather, they are just added
in to the equations of motion to update the degrees of freedom.
---------
If the *rng* keyword is used with the *uniform* value, then the noise
is generated from a uniform distribution (see
:ref:`(Dunweg) <Dunweg7>` for why this works). This is the same method
of noise generation as used in :doc:`fix_langevin <fix_langevin>`.
If the *rng* keyword is used with the *gaussian* value, then the noise
is generated from a gaussian distribution. Typically this added
complexity is unnecessary, and one should be fine using the *uniform*
value for reasons argued in :ref:`(Dunweg) <Dunweg7>`.
If the *rng* keyword is used with the *none* value, then the noise
terms are set to zero.
The *gamma_t* keyword sets the (isotropic) translational viscous damping.
Required for (and only compatible with) *brownian* and *brownian/sphere*.
The units of *gamma_t* are mass/time.
The *gamma_r* keyword sets the (isotropic) rotational viscous damping.
Required for (and only compatible with) *brownian/sphere*.
The units of *gamma_r* are mass*length**2/time.
The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of
the rotational and viscous damping tensors (having the same units as
their isotropic counterparts). Required for (and only compatible with)
*brownian/asphere*. For a 2D system, the first two values of *gamma_r_eigen*
must be inf (only rotation in xy plane), and the third value of *gamma_t_eigen*
must be inf (only diffusion in xy plane).
If the *dipole* keyword is used, then the dipole moments of the particles
are updated as described above. Only compatible with *brownian/asphere*
(as *brownian/sphere* updates dipoles automatically).
----------
.. note::
For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and
*gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the
*brownian/sphere* style with *gamma_t* = x and *gamma_r* = y.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`.
No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
The style *brownian/sphere* fix requires that atoms store torque and angular velocity (omega)
as defined by the :doc:`atom_style sphere <atom_style>` command.
The style *brownian/asphere* fix requires that atoms store torque and quaternions
as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
If the *dipole* keyword is used, they must also store a dipole moment
as defined by the :doc:`atom_style dipole <atom_style>` command.
This fix is part of the USER-BROWNIAN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""
:doc:`fix propel/self <fix_propel_self>`,
:doc:`fix langevin <fix_langevin>`, :doc:`fix nve/sphere <fix_nve_sphere>`,
Default
"""""""
The default for *rng* is *uniform*. The default for the rotational and translational friction
tensors are the identity tensor.
----------
.. _Ilie1:
**(Ilie)** Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
.. _Delong1:
**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015)
.. _Dunweg7:
**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).

2
doc/src/fix_drude.rst
View File

@ -22,6 +22,8 @@ Examples
fix 1 all drude 1 1 0 1 0 2 2 2
fix 1 all drude C C N C N D D D
Example input scripts available: examples/USER/drude
Description
"""""""""""

2
doc/src/fix_drude_transform.rst
View File

@ -25,6 +25,8 @@ Examples
fix 3 all drude/transform/direct
fix 1 all drude/transform/inverse
Example input scripts available: examples/USER/drude
Description
"""""""""""

5
doc/src/fix_grem.rst
View File

@ -92,6 +92,11 @@ The :doc:`thermo_modify <thermo_modify>` *press* option is supported
by this fix to add the rescaled kinetic pressure as part of
:doc:`thermodynamic output <thermo_style>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the effective
temperature :math:`T_{eff}`. The scalar value calculated by this
fix is "intensive".
Restrictions
""""""""""""

2
doc/src/fix_langevin_drude.rst
View File

@ -35,6 +35,8 @@ Examples
fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
Example input scripts available: examples/USER/drude
Description
"""""""""""

59
doc/src/fix_mdi_engine.rst Normal file
View File

@ -0,0 +1,59 @@
.. index:: fix mdi/engine
fix mdi/engine command
======================
Syntax
""""""
.. parsed-literal::
fix ID group-ID mdi/engine
* ID, group-ID are documented in :doc:`fix <fix>` command
* mdi/engine = style name of this fix command
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all mdi/engine
Description
"""""""""""
This fix is used along with the :doc:`mdi/engine <mdi_engine>` command
to enable LAMMPS to use the `MDI Library
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ to run as
an MDI engine. The fix provides hooks that enable MDI driver codes to
communicate with LAMMPS at various points within a LAMMPS timestep.
It is not generally necessary to add this fix to a LAMMPS input file,
even when using the :doc:`mdi/engine <mdi_engine>` command. If the
:doc:`mdi/engine <mdi_engine>` command is executed and this fix is not
present, it will automatically be added and applied as a new fix for
all atoms for the duration of the command. Thus it is only necessary
to add this fix to an input file when you want to modify the group-ID
or the ordering of this fix relative to other fixes in the input script.
For more information about running LAMMPS as an MDI engine, see the
:doc:`mdi/engine <mdi_engine>` command and the :doc:`Howto mdi
<Howto_mdi>` doc page.
Restrictions
""""""""""""
This command is part of the USER-MDI package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`mdi/engine <mdi_engine>`
Default
"""""""
none

183
doc/src/fix_propel_self.rst
View File

@ -8,52 +8,121 @@ Syntax
.. parsed-literal::
fix ID group-ID propel/self mode magnitude keyword values ...
fix ID group-ID propel/self mode magnitude keyword values
* ID, group-ID are documented in :doc:`fix <fix>` command
* propel/self = style name of this fix command
* mode = velocity or quat
* magnitude = magnitude of the active force
* one or more keyword/value pairs may be appended to args
* keyword = *types*
* mode = *dipole* or *velocity* or *quat*
* magnitude = magnitude of self-propulsion force
* zero or one keyword/value pairs may be appended
* keyword = *qvector*
.. parsed-literal::
*qvector* value = direction of force in ellipsoid frame
*sx*, *sy*, *sz* = components of *qvector*
*types* values = one or more atom types
Examples
""""""""
.. code-block:: LAMMPS
fix active_group all propel/self velocity 1.0
fix constant_velocity all viscous 1.0
fix active_group all propel/self quat 1.0
fix active all propel/self quat 1.0 types 1 2 4
fix active all propel/self dipole 40.0
fix active all propel/self velocity 10.0
fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0
Description
"""""""""""
Adds a force of a constant magnitude to each atom in the group. The nature in
which the force is added depends on the mode.
Add a force to each atom in the group due to a self-propulsion force. The
force is given by
For *mode* = *velocity*, the active force acts along the velocity vector of
each atom. This can be interpreted as a velocity-dependent friction,
such as proposed by :ref:`(Erdmann) <Erdmann>`.
.. math::
For *mode* = *quat* the force is applied along the axis obtained
by rotating the x-axis along the atom's quaternion. In other words, the
force is along the x-axis in the atom's body frame. This mode requires
all atoms in the group to have a quaternion, so atom_style should
either be ellipsoid or body. In combination with Langevin thermostat
for translation and rotation in the overdamped regime, the quaternion
mode corresponds to the active Brownian particle model introduced by
:ref:`(Henkes) <Henkes>`, :ref:`(Bialke) <Bialke>` and :ref:`(Fily)
<Fily>`.
F_i = f_P e_i
By default, this fix is applied to all atoms in the group. You can
override this behavior by specifying the atom types the fix should work
on through the *types* keyword.
where *i* is the particle the force is being applied to, :math:`f_P`
is the magnitude of the force, and :math:`e_i` is the vector direction
of the force. The specification of :math:`e_i` is based on which of the
three keywords (*dipole* or *velocity* or *quat*) one selects.
For mode *dipole*, :math:`e_i` is just equal to
the dipole vectors of the atoms in the group. Therefore, if the dipoles
are not unit vectors, the :math:`e_i` will not be unit vectors.
.. note::
If another command changes the magnitude of the dipole, this force will
change accordingly (since :math:`|e_i|` will change, which is physically
equivalent to re-scaling :math:`f_P` while keeping :math:`|e_i|` constant),
and no warning will be provided by LAMMPS. This is almost never what you
want, so ensure you are not changing dipole magnitudes with another LAMMPS
fix or pair style. Furthermore, self-propulsion forces (almost) always
set :math:`e_i` to be a unit vector for all times, so it's best to set
all the dipole magnitudes to 1.0 unless you have a good reason not to
(see the :doc:`set <set>` command on how to do this).
For mode *velocity*, :math:`e_i` points in the direction
of the current velocity (a unit-vector). This can be interpreted as a
velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) <Erdmann1>`.
For mode *quat*, :math:`e_i` points in the direction of a unit
vector, oriented in the coordinate frame of the ellipsoidal particles,
which defaults to point along the x-direction. This default behavior
can be changed by via the *quatvec* keyword.
The optional *quatvec* keyword specifies the direction of self-propulsion
via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are
defined within the coordinate frame of the atom's
ellipsoid. For instance, for an ellipsoid with long axis along
its x-direction, if one wanted the self-propulsion force to also
be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal
to zero. This keyword may only be specified for mode *quat*.
.. note::
In using keyword *quatvec*, the three arguments *sx*,
*sy*, and *sz* will be automatically normalized to components
of a unit vector internally to avoid users having to explicitly
do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i`
will always be of unit length.
Along with adding a force contribution, this fix can also
contribute to the virial (pressure) of the system, defined as
:math:`f_P \sum_i <e_i . r_i>/(d V)`, where :math:`r_i` is the
*unwrapped* coordinate of particle i in the case of periodic
boundary conditions. See :ref:`(Winkler) <Winkler1>` for a
discussion of this active pressure contribution.
For modes *dipole* and *quat*, this fix is by default
included in pressure computations.
For mode *velocity*, this fix is by default not included
in pressure computations.
.. note::
In contrast to equilibrium systems, pressure of active systems
in general depends on the geometry of the container.
The active pressure contribution as calculated in this fix
is only valid for certain boundary conditions (spherical
walls, rectangular walls, or periodic boundary conditions).
For other geometries, the pressure must be measured via
explicit calculation of the force per unit area on a wall,
and so one must not calculate it using this fix.
(Use :doc:`fix_modify <fix_modify>` as described below
to turn off the virial contribution of this fix). Again,
see :ref:`(Winkler) <Winkler1>` for discussion of why this
is the case.
Furthermore, when dealing with active systems, the temperature
is no longer well defined. Therefore, one should ensure that
the *virial* flag is used in the
:doc:`compute pressure <compute_pressure>` command (turning
off temperature contributions).
----------
@ -62,40 +131,48 @@ Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to :doc:`binary restart files <restart>`.
This fix is not imposed during minimization.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added forces on atoms to the
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
The default is *virial yes* for keywords *dipole* and *quat*. The
default is *virial no* for keyword *velocity*.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
Restrictions
""""""""""""
In quat mode, this fix makes use of per-atom quaternions to take
into account the fact that the orientation can rotate and hence the
direction of the active force can change. The quat mode
of this fix only works with atom_style ellipsoid.
With keyword *dipole*, this fix only works when the DIPOLE package is enabled.
See the :doc:`Build package <Build_package>` doc page for more info.
This fix is part of the USER-BROWNIAN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""
:doc:`fix setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`
.. _Erdmann:
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
Eur. Phys. J. B 15, 105-113, 2000.
.. _Henkes:
**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
.. _Bialke:
**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
.. _Fily:
**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.
:doc:`fix efield <fix_efield>` , :doc:`fix setforce <fix_setforce>`,
:doc:`fix addforce <fix_addforce>`
Default
"""""""
types
none
----------
.. _Erdmann1:
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
Eur. Phys. J. B 15, 105-113, 2000.
.. _Winkler1:
**(Winkler)** Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).

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