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Merge branch 'develop' into granular-triangles

This commit is contained in:
Steve Plimpton 2025-01-15 15:19:25 -07:00
parent ff40a235dd ffa4765b15
commit 62ce5757ae
1272 changed files with 140426 additions and 42526 deletions
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3
.github/CODEOWNERS vendored
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@ -101,7 +101,8 @@ src/group.* @sjplimp
src/improper.* @sjplimp
src/info.* @akohlmey
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/lmptype.h @sjplimp
src/label_map.* @jrgissing @akohlmey
src/library.* @sjplimp @akohlmey
src/main.cpp @sjplimp
src/min_*.* @sjplimp

108
.github/release_steps.md vendored Normal file
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@ -0,0 +1,108 @@
# LAMMPS Release Steps
The following notes chronicle the current steps for preparing and publishing LAMMPS releases. For
definitions of LAMMPS versions and releases mean, please refer to [the corresponding section in the
LAMMPS manual](https://docs.lammps.org/Manual_version.html).
## LAMMPS Feature Release
A LAMMPS feature release is currently prepared after about 500 to 750 commits to the 'develop'
branch or after a period of four weeks up to two months. This is not a fixed rule, though, since
external circumstances can cause delays in preparing a release, or pull requests that are desired to
be merged for the release are not yet completed.
### Preparing a 'next\_release' branch
Create a 'next\_release' branch off 'develop' and make the following changes:
- set the LAMMPS\_VERSION define to the planned release date in src/version.h in the format
"D Mmm YYYY" or "DD Mmm YYYY"
- remove the LAMMPS\_UPDATE define in src/version.h
- update the release date in doc/lammps.1
- update all TBD arguments for ..versionadded::, ..versionchanged:: ..deprecated:: to the
planned release date in the format "DMmmYYYY" or "DDMmmYYYY"
- check release notes for merged new features and check if ..versionadded:: or ..versionchanged::
are missing and need to be added
Submit this pull request, rebase if needed. This is the last pull request merged for the release
and should not contain any other changes. (Exceptions: this document, last minute trivial(!) changes).
This PR shall not be merged before **all** pending tests have completed and cleared. If needed, a
bugfix pull request should be created and merged to clear all tests.
### Create release on GitHub
When all pending pull requests for the release are merged and have cleared testing, the
'next\_release' branch is merged into 'develop'.
Check out 'develop' locally, pull the latest changes, merge them into 'release', apply a suitable
release tag (for historical reasons the tag starts with "patch_" followed by the date, and finally
push everything back to GitHub. Example:
```
git checkout develop
git pull
git checkout release
git pull
git merge --ff-only develop
git tag -s -m "LAMMPS feature release 19 November 2024" patch_19Nov2024
git push git@github.com:lammps/lammps.git --tags develop release
```
Go to https://github.com/lammps/lammps/releases and create a new (draft) release page or check the
existing draft for any necessary changes from pull requests that were merged but are not listed.
Then select the applied tag for the release in the "Choose a tag" dropdown list. Go to the bottom of
the list and select the "Set as pre-release" checkbox. The "Set as the latest release" button is
reserved for stable releases and updates to them.
If everything is in order, you can click on the "Publish release" button. Otherwise, click on "Save
draft" and finish pending tasks until you can return to edit the release page and publish it.
### Update download website, prepare pre-compiled packages, update packages to GitHub
Publishing the release on GitHub will trigger the Temple Jenkins cluster to update
the https://docs.lammps.org/ website with the documentation for the new feature release
and it will create a tarball for download (which contains the translated manual).
Build a fully static LAMMPS installation using a musl-libc cross-compiler, install into a
lammps-static folder, and create a tarball called lammps-linux-x86_64-19Nov2024.tar.gz (or using a
corresponding date with a future release) from the lammps-static folder and upload it to GitHub
with:
```
gh release upload patch_19Nov2024 ~/Downloads/lammps-linux-x86_64-19Nov2024.tar.gz
```
## LAMMPS Stable Release
A LAMMPS stable release is prepared about once per year in the months July, August, or September.
One (or two, if needed) feature releases before the stable release shall contain only bug fixes
or minor feature updates in optional packages. Also substantial changes to the core of the code
shall be applied rather toward the beginning of a development cycle between two stable releases
than toward the end. The intention is to stablilize significant change to the core and have
outside users and developers try them out during the development cycle; the sooner the changes
are included, the better chances for spotting peripheral bugs and issues.
### Prerequesites
Before making a stable release all remaining backported bugfixes shall be released as a (final)
stable update release (see below).
A LAMMPS stable release process starts like a feature release (see above), only that this feature
release is called a "Stable Release Candidate" and no assets are uploaded to GitHub.
### Synchronize 'maintenance' branch with 'release'
The state of the 'release' branch is then transferred to the 'maintenance' branch (which will
have diverged significantly from 'release' due to the selectively backported bug fixes).
### Fast-forward merge of 'maintenance' into 'stable' and apply tag
At this point it should be possible to do a fast-forward merge of 'maintenance' to 'stable'
and then apply the stable\_DMmmYYYY tag.
### Push branches and tags
## LAMMPS Stable Update Release

1
.github/workflows/coverity.yml vendored
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@ -67,7 +67,6 @@ jobs:
-D PKG_MANIFOLD=on \
-D PKG_MDI=on \
-D PKG_MGPT=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_MOLFILE=on \
-D PKG_NETCDF=on \

14
.github/workflows/kokkos-regression.yaml vendored
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@ -2,7 +2,7 @@
name: "Kokkos OpenMP Regression Test"
on:
pull_request:
push:
branches:
- develop
@ -17,9 +17,9 @@ jobs:
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 4
max-parallel: 6
matrix:
idx: [ 'pair', 'fix', 'compute', 'misc' ]
idx: [ 'pair-0', 'pair-1', 'fix-0', 'fix-1', 'compute', 'misc' ]
steps:
- name: Checkout repository
@ -83,6 +83,7 @@ jobs:
-D PKG_REAXFF=on \
-D PKG_REPLICA=on \
-D PKG_SRD=on \
-D PKG_SPH=on \
-D PKG_VORONOI=on \
-G Ninja
cmake --build build
@ -93,9 +94,10 @@ jobs:
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/get_kokkos_input.py \
--examples-top-level=examples \
--filter-out="balance;fire;gcmc;granregion;mdi;mliap;neb;pace;prd;pour;python;snap"
--examples-top-level=examples --batch-size=50 \
--filter-out="balance;fire;gcmc;granregion;hyper;mc;mdi;mliap;neb;pace;prd;pour;python;rigid;snap;streitz;shear;ttm"
export OMP_PROC_BIND=false
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_kokkos_openmp.yaml \
@ -103,7 +105,7 @@ jobs:
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log \
--quick-max=100 --verbose
--quick-max=100
tar -cvf kokkos-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml

53
.github/workflows/lammps-gui-flatpak.yml vendored Normal file
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@ -0,0 +1,53 @@
# GitHub action to build LAMMPS-GUI as a flatpak bundle
name: "Build LAMMPS-GUI as flatpak bundle"
on:
push:
branches:
- develop
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: LAMMPS-GUI flatpak build
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
- name: Install extra packages
run: |
sudo apt-get update
sudo apt-get install -y ccache \
libeigen3-dev \
libcurl4-openssl-dev \
mold \
ninja-build \
python3-dev \
flatpak \
flatpak-builder
- name: Set up access to flatpak repo
run: flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
- name: Build flatpak
run: |
mkdir flatpack-state
sed -i -e 's/branch:.*/branch: develop/' tools/lammps-gui/org.lammps.lammps-gui.yml
flatpak-builder --force-clean --verbose --repo=flatpak-repo \
--install-deps-from=flathub --state-dir=flatpak-state \
--user --ccache --default-branch=${{ github.ref_name }} \
flatpak-build tools/lammps-gui/org.lammps.lammps-gui.yml
flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo \
--verbose flatpak-repo LAMMPS-Linux-x86_64-GUI.flatpak \
org.lammps.lammps-gui ${{ github.ref_name }}
flatpak install -y -v --user LAMMPS-Linux-x86_64-GUI.flatpak

75
cmake/CMakeLists.txt
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@ -3,6 +3,9 @@
# CMake build system
# This file is part of LAMMPS
cmake_minimum_required(VERSION 3.16)
if(CMAKE_VERSION VERSION_LESS 3.20)
message(WARNING "LAMMPS is planning to require at least CMake version 3.20 by Summer 2025. Please upgrade!")
endif()
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
@ -95,24 +98,21 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
#####################################################################
include(CheckIncludeFileCXX)
# set required compiler flags and compiler/CPU arch specific optimizations
# set required compiler flags, apply checks, and compiler/CPU arch specific optimizations
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
# Intel classic compilers version 19 are broken and fail to compile the embedded fmtlib
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 20.0)
message(ERROR "Intel classic compiler version ${CMAKE_CXX_COMPILER_VERSION} is too old")
endif()
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
endif()
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "/QxHost")
endif()
set(CMAKE_TUNE_DEFAULT "/QxHost")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
endif()
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
endif()
endif()
@ -141,19 +141,31 @@ endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma -Xcudafe --diag_suppress=128")
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
endif()
# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
# we *require* C++11 without extensions but prefer C++17.
# Kokkos requires at least C++17 (currently)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
set(CMAKE_CXX_STANDARD 17)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(CMAKE_CXX_STANDARD LESS 17)
message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
# turn off C++17 check in lmptype.h
if(LAMMPS_CXX11)
add_compile_definitions(LAMMPS_CXX11)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
@ -347,6 +359,17 @@ foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
set(DEPRECATED_PACKAGES AWPMD ATC POEMS)
foreach(PKG ${DEPRECATED_PACKAGES})
if(PKG_${PKG})
message(WARNING
"The ${PKG} package will be removed from LAMMPS in Summer 2025 due to lack of "
"maintenance and use of code constructs that conflict with modern C++ compilers "
"and standards. Please contact developers@lammps.org if you have any concerns "
"about this step.")
endif()
endforeach()
######################################################
# packages with special compiler needs or external libs
######################################################
@ -579,6 +602,16 @@ foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE
endif()
endforeach()
# settings for misc packages and styles
if(PKG_MISC)
option(LAMMPS_ASYNC_IMD "Asynchronous IMD processing" OFF)
mark_as_advanced(LAMMPS_ASYNC_IMD)
if(LAMMPS_ASYNC_IMD)
target_compile_definitions(lammps PRIVATE -DLAMMPS_ASYNC_IMD)
message(STATUS "Using IMD in asynchronous mode")
endif()
endif()
# optionally enable building script wrappers using swig
option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
if(WITH_SWIG)
@ -588,13 +621,8 @@ endif()
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
separate_arguments(CMAKE_TUNE_FLAGS)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
target_compile_options(lammps PRIVATE ${_FLAG})
# skip these flags when linking the main executable
if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma"))))
target_compile_options(lmp PRIVATE ${_FLAG})
endif()
endforeach()
target_compile_options(lammps PRIVATE ${CMAKE_TUNE_FLAGS})
target_compile_options(lmp PRIVATE ${CMAKE_TUNE_FLAGS})
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
@ -1083,12 +1111,15 @@ if(BUILD_TOOLS)
message(STATUS "<<< Building Tools >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
message(STATUS "<<< Building LAMMPS-GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)
message(STATUS "Loading LAMMPS library as plugin at run time")
else()
message(STATUS "Linking LAMMPS library at compile time")
endif()
if(BUILD_WHAM)
message(STATUS "<<< Building WHAM >>>")
endif()
endif()
if(ENABLE_TESTING)
message(STATUS "<<< Building Unit Tests >>>")

22
cmake/Modules/Packages/KOKKOS.cmake
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@ -7,26 +7,13 @@ endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
option(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC "CUDA asynchronous malloc support" OFF)
mark_as_advanced(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
if(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
message(STATUS "KOKKOS: CUDA malloc async support enabled")
else()
message(STATUS "KOKKOS: CUDA malloc async support disabled")
endif()
endif()
if(Kokkos_ENABLE_HIP)
option(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS "Enable multiple kernel instantiations with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS)
option(Kokkos_ENABLE_ROCTHRUST "Use RoCThrust library" ON)
mark_as_advanced(Kokkos_ENABLE_ROCTHRUST)
if(Kokkos_ARCH_AMD_GFX942 OR Kokkos_ARCH_AMD_GFX940)
option(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY "Enable unified memory with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY)
endif()
endif()
# Adding OpenMP compiler flags without the checks done for
# BUILD_OMP can result in compile failures. Enforce consistency.
if(Kokkos_ENABLE_OPENMP)
@ -70,8 +57,8 @@ 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/4.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "de6ee80d00b6212b02bfb7f1e71a8392" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.5.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "4d832aa0284169d9e3fbae3165286bc6" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -96,7 +83,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.4.01 REQUIRED CONFIG)
find_package(Kokkos 4.5.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -130,6 +117,7 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/group_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp

98
cmake/Modules/Packages/ML-PACE.cmake
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@ -1,50 +1,62 @@
# PACE library support for ML-PACE package
find_package(pace QUIET)
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
# to make it easier to check local build without going through the public github releases
if(LOCAL_ML-PACE)
set(lib-pace "${LOCAL_ML-PACE}")
if(pace_FOUND)
find_package(pace)
target_link_libraries(lammps PRIVATE pace::pace)
else()
# download library sources to build folder
if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
message(STATUS "Downloading ${PACELIB_URL}")
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "a53bd87cfee8b07d9f44bc17aad69c3f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
# to make it easier to check local build without going through the public github releases
if(LOCAL_ML-PACE)
set(lib-pace "${LOCAL_ML-PACE}")
else()
# download library sources to build folder
if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
message(STATUS "Downloading ${PACELIB_URL}")
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
endif()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
# uncompress downloaded sources
execute_process(
COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
# uncompress downloaded sources
execute_process(
COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
endif()
# some preinstalled yaml-cpp versions don't provide a namespaced target
find_package(yaml-cpp QUIET)
if(TARGET yaml-cpp AND NOT TARGET yaml-cpp::yaml-cpp)
add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
endif()
endif()

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

@ -1,3 +1,5 @@
# FindVTK requires that C support is enabled when looking for MPI support
enable_language(C)
find_package(VTK REQUIRED NO_MODULE)
target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
if (VTK_MAJOR_VERSION VERSION_LESS 9.0)

9
doc/documentation_conventions.md
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@ -10,7 +10,7 @@ Last change: 2022-12-30
In fall 2019, the LAMMPS documentation file format has changed from a
home grown markup designed to generate HTML format files only, to
[reStructuredText](https://docutils.sourceforge.io/rst.html>. For a
[reStructuredText](https://docutils.sourceforge.io/rst.html>). For a
transition period all files in the old .txt format were transparently
converted to .rst and then processed. The `txt2rst tool` is still
included in the distribution to obtain an initial .rst file for legacy
@ -45,8 +45,7 @@ what kind of information and sections are needed.
## Formatting conventions
For headlines we try to follow the conventions posted here:
https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings
For headlines we try to follow the conventions posted [here](https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings).
It seems to be sufficient to have this consistent only within
any single file and it is not (yet) enforced strictly, but making
this globally consistent makes it easier to move sections around.
@ -64,7 +63,7 @@ Groups of shell commands or LAMMPS input script or C/C++/Python source
code should be typeset into a `.. code-block::` section. A syntax
highlighting extension for LAMMPS input scripts is provided, so `LAMMPS`
can be used to indicate the language in the code block in addition to
`bash`, `c`, `c++`, `console`, `csh`, `diff', `fortran`, `json`, `make`,
`bash`, `c`, `c++`, `console`, `csh`, `diff`, `fortran`, `json`, `make`,
`perl`, `powershell`, `python`, `sh`, or `tcl`, `text`, or `yaml`. When
no syntax style is indicated, no syntax highlighting is performed. When
typesetting commands executed on the shell, please do not prefix
@ -84,7 +83,7 @@ block can be used, followed by multiple `.. tab::` blocks, one
for each alternative. This is only used for HTML output. For other
outputs, the `.. tabs::` directive is transparently removed and
the individual `.. tab::` blocks will be replaced with an
`.. admonition::`` block. Thus in PDF and ePUB output those will
`.. admonition::` block. Thus in PDF and ePUB output those will
be realized as sequential and plain notes.
Special remarks can be highlighted with a `.. note::` block and

2
doc/doxygen/Doxyfile.in
View File

@ -2,7 +2,7 @@
DOXYFILE_ENCODING = UTF-8
PROJECT_NAME = "LAMMPS Programmer's Guide"
PROJECT_NUMBER = "4 May 2022"
PROJECT_NUMBER = "19 November 2024"
PROJECT_BRIEF = "Documentation of the LAMMPS library interface and Python wrapper"
PROJECT_LOGO = lammps-logo.png
CREATE_SUBDIRS = NO

15
doc/github-development-workflow.md
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@ -6,7 +6,9 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
tools, but do not set policies, so it is up to the developers to come to
an agreement as to how to define and interpret policies. This document
is likely to change as our experiences and needs change, and we try to
adapt it accordingly. Last change 2023-02-10.
adapt it accordingly.
Last change: 2023-02-10
## Table of Contents
@ -72,7 +74,7 @@ be assigned to signal urgency to merge this pull request quickly.
People can be assigned to review a pull request in two ways:
* They can be assigned manually to review a pull request
by the submitter or a LAMMPS developer
by the submitter or a LAMMPS developer.
* They can be automatically assigned, because a developer's GitHub
handle matches a file pattern in the `.github/CODEOWNERS` file,
which associates developers with the code they contributed and
@ -86,9 +88,9 @@ required before merging, in addition to passing all automated
compilation and unit tests. Merging counts as implicit approval, so
does submission of a pull request (by a LAMMPS developer). So the person
doing the merge may not also submit an approving review. The GitHub
feature, that reviews from code owners are "hard" reviews (i.e. they
must all approve before merging is allowed), is currently disabled.
It is in the discretion of the merge maintainer to assess when a
feature that reviews from code owners are "hard" reviews (i.e. they
must all approve before merging is allowed) is currently disabled.
It is at the discretion of the merge maintainer to assess when a
sufficient degree of approval has been reached, especially from external
collaborators. Reviews may be (automatically) dismissed, when the
reviewed code has been changed. Review may be requested a second time.
@ -147,7 +149,8 @@ only contain bug fixes, feature additions to peripheral functionality,
and documentation updates. In between stable releases, bug fixes and
infrastructure updates are back-ported from the "develop" branch to the
"maintenance" branch and occasionally merged into "stable" and published
as update releases.
as update releases. Further explanation of LAMMPS versions can be found
[in the documentation](https://docs.lammps.org/Manual_version.html).
## Project Management

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "29 August 2024" "2024-08-29"
.TH LAMMPS "1" "19 November 2024" "2024-11-19"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 29 August 2024
\- Molecular Dynamics Simulator. Version 19 November 2024
.SH SYNOPSIS
.B lmp

12
doc/src/Build.rst
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@ -1,10 +1,14 @@
Build LAMMPS
============
LAMMPS is built as a library and an executable from source code using
either traditional makefiles for use with GNU make (which may require
manual editing), or using a build environment generated by CMake (Unix
Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
LAMMPS is built as a library and an executable from source code using a
build environment generated by CMake (Unix Makefiles, Ninja, Xcode,
Visual Studio, KDevelop, CodeBlocks and more depending on the platform).
Using CMake is the preferred way to build LAMMPS. In addition, LAMMPS
can be compiled using the legacy build system based on traditional
makefiles for use with GNU make (which may require manual editing).
Support for the legacy build system is slowly being phased out and may
not be available for all optional features.
As an alternative, you can download a package with pre-built executables
or automated build trees, as described in the :doc:`Install <Install>`

4
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@ -160,7 +160,7 @@ with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility
with compiler versions in use. If compilation with OpenMP enabled fails
because of your compiler requiring strict OpenMP 4.0 semantics, you can
change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the
``LMP_INC`` variable in your makefile, or add it to the command line
``LMP_INC`` variable in your makefile, or add it to the command-line flags
while configuring with CMake. LAMMPS will auto-detect a suitable setting
for most GNU, Clang, and Intel compilers.
@ -502,6 +502,8 @@ using CMake or Make.
# chain.x, micelle2d.x, msi2lmp, phana,
# stl_bin2txt
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build LAMMPS-GUI
-D BUILD_WHAM=value # yes (default). Download and build WHAM;
# only available for BUILD_LAMMPS_GUI=yes
The generated binaries will also become part of the LAMMPS installation
(see below).

28
doc/src/Build_cmake.rst
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@ -8,7 +8,7 @@ packages. Links to those pages on the :doc:`Build overview <Build>`
page.
The following text assumes some familiarity with CMake and focuses on
using the command line tool ``cmake`` and what settings are supported
using the command-line tool ``cmake`` and what settings are supported
for building LAMMPS. A more detailed tutorial on how to use CMake
itself, the text mode or graphical user interface, to change the
generated output files for different build tools and development
@ -16,7 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
.. note::
LAMMPS currently requires that CMake version 3.16 or later is available.
LAMMPS currently requires that CMake version 3.20 or later is available.
.. warning::
@ -32,22 +32,22 @@ environments is on a :doc:`separate page <Howto_cmake>`.
Advantages of using CMake
^^^^^^^^^^^^^^^^^^^^^^^^^
CMake is an alternative to compiling LAMMPS in the traditional way
through :doc:`(manually customized) makefiles <Build_make>`. Using
CMake has multiple advantages that are specifically helpful for
people with limited experience in compiling software or for people
that want to modify or extend LAMMPS.
CMake is the preferred way of compiling LAMMPS in contrast to the legacy
build system based on GNU make and through :doc:`(manually customized)
makefiles <Build_make>`. Using CMake has multiple advantages that are
specifically helpful for people with limited experience in compiling
software or for people that want to modify or extend LAMMPS.
- CMake can detect available hardware, tools, features, and libraries
and adapt the LAMMPS default build configuration accordingly.
- CMake can generate files for different build tools and integrated
development environments (IDE).
- CMake supports customization of settings with a command line, text
- CMake supports customization of settings with a command-line, text
mode, or graphical user interface. No manual editing of files,
knowledge of file formats or complex command line syntax is required.
knowledge of file formats or complex command-line syntax is required.
- All enabled components are compiled in a single build operation.
- Automated dependency tracking for all files and configuration options.
- Support for true out-of-source compilation. Multiple configurations
- Support for true out-of-source compilation. Multiple configurations
and settings with different choices of LAMMPS packages, settings, or
compilers can be configured and built concurrently from the same
source tree.
@ -68,7 +68,7 @@ that purpose you can use either the command-line utility ``cmake`` (or
graphical utility ``cmake-gui``, or use them interchangeably. The
second step is then the compilation and linking of all objects,
libraries, and executables using the selected build tool. Here is a
minimal example using the command line version of CMake to build LAMMPS
minimal example using the command-line version of CMake to build LAMMPS
with no add-on packages enabled and no customization:
.. code-block:: bash
@ -131,7 +131,7 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
configuration step. The cache file contains all current CMake settings.
To modify settings, enable or disable features, you need to set
*variables* with either the ``-D`` command line flag (``-D
*variables* with either the ``-D`` command-line flag (``-D
VARIABLE1_NAME=value``) or change them in the text mode of the graphical
user interface. The ``-D`` flag can be used several times in one command.
@ -141,11 +141,11 @@ a different compiler tool chain. Those are loaded with the ``-C`` flag
(``-C ../cmake/presets/basic.cmake``). This step would only be needed
once, as the settings from the preset files are stored in the
``CMakeCache.txt`` file. It is also possible to customize the build
by adding one or more ``-D`` flags to the CMake command line.
by adding one or more ``-D`` flags to the CMake command.
Generating files for alternate build tools (e.g. Ninja) and project files
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
command line flag. A list of available generator settings for your
command-line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
.. _cmake_multiconfig:

10
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@ -263,9 +263,9 @@ will be skipped if prerequisite features are not available in LAMMPS.
time. Preference is given to parts of the code base that are easy to
test or commonly used.
Tests as shown by the ``ctest`` program are command lines defined in the
Tests as shown by the ``ctest`` program are commands defined in the
``CMakeLists.txt`` files in the ``unittest`` directory tree. A few
tests simply execute LAMMPS with specific command line flags and check
tests simply execute LAMMPS with specific command-line flags and check
the output to the screen for expected content. A large number of unit
tests are special tests programs using the `GoogleTest framework
<https://github.com/google/googletest/>`_ and linked to the LAMMPS
@ -420,7 +420,7 @@ during MD timestepping and manipulate per-atom properties like
positions, velocities, and forces. For those fix styles, testing can be
done in a very similar fashion as for force fields and thus there is a
test program `test_fix_timestep` that shares a lot of code, properties,
and command line flags with the force field style testers described in
and command-line flags with the force field style testers described in
the previous section.
This tester will set up a small molecular system run with verlet run
@ -642,10 +642,10 @@ The following target are available for both, GNU make and CMake:
.. _gh-cli:
GitHub command line interface
GitHub command-line interface
-----------------------------
GitHub has developed a `command line tool <https://cli.github.com>`_
GitHub has developed a `command-line tool <https://cli.github.com>`_
to interact with the GitHub website via a command called ``gh``.
This is extremely convenient when working with a Git repository hosted
on GitHub (like LAMMPS). It is thus highly recommended to install it

149
doc/src/Build_extras.rst
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@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
* :ref:`LEPTON <lepton>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MISC <misc>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
@ -209,7 +210,7 @@ necessary for ``hipcc`` and the linker to work correctly.
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero back ends. To use
CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
command-line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne.
@ -232,7 +233,7 @@ option in preparations to run on Aurora system at Argonne.
.. code:: bash
# CUDA target (not recommended, use GPU_ARCH=cuda)
# CUDA target (not recommended, use GPU_API=cuda)
# !!! DO NOT set CMAKE_CXX_COMPILER !!!
export HIP_PLATFORM=nvcc
export HIP_PATH=/path/to/HIP/install
@ -421,9 +422,10 @@ minutes to hours) to build. Of course you only need to do that once.)
cmake build system. The ``lib/kim/Install.py`` script supports a
``CMAKE`` environment variable if the cmake executable is named other
than ``cmake`` on your system. Additional environment variables may be
provided on the command line for use by cmake. For example, to use the
``cmake3`` executable and tell it to use the gnu version 11 compilers
to build KIM, one could use the following command line.
set with the ``make`` command for use by cmake. For example, to use the
``cmake3`` executable and tell it to use the GNU version 11 compilers
called ``g++-11``, ``gcc-11`` and ``gfortran-11`` to build KIM, one
could use the following command.
.. code-block:: bash
@ -546,16 +548,7 @@ They must be specified in uppercase.
- Local machine
* - AMDAVX
- HOST
- AMD 64-bit x86 CPU (AVX 1)
* - ZEN
- HOST
- AMD Zen class CPU (AVX 2)
* - ZEN2
- HOST
- AMD Zen2 class CPU (AVX 2)
* - ZEN3
- HOST
- AMD Zen3 class CPU (AVX 2)
- AMD chip
* - ARMV80
- HOST
- ARMv8.0 Compatible CPU
@ -571,105 +564,126 @@ They must be specified in uppercase.
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - ARMV9_GRACE
- HOST
- ARMv9 NVIDIA Grace CPU
* - SNB
- HOST
- Intel Sandy/Ivy Bridge CPU (AVX 1)
- Intel Sandy/Ivy Bridge CPUs
* - HSW
- HOST
- Intel Haswell CPU (AVX 2)
- Intel Haswell CPUs
* - BDW
- HOST
- Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
* - SKL
- HOST
- Intel Skylake Client CPU
* - SKX
- HOST
- Intel Skylake Xeon Server CPU (AVX512)
- Intel Broadwell Xeon E-class CPUs
* - ICL
- HOST
- Intel Ice Lake Client CPU (AVX512)
- Intel Ice Lake Client CPUs (AVX512)
* - ICX
- HOST
- Intel Ice Lake Xeon Server CPU (AVX512)
* - SPR
- Intel Ice Lake Xeon Server CPUs (AVX512)
* - SKL
- HOST
- Intel Sapphire Rapids Xeon Server CPU (AVX512)
- Intel Skylake Client CPUs
* - SKX
- HOST
- Intel Skylake Xeon Server CPUs (AVX512)
* - KNC
- HOST
- Intel Knights Corner Xeon Phi
* - KNL
- HOST
- Intel Knights Landing Xeon Phi
* - SPR
- HOST
- Intel Sapphire Rapids Xeon Server CPUs (AVX512)
* - POWER8
- HOST
- IBM POWER8 CPU
- IBM POWER8 CPUs
* - POWER9
- HOST
- IBM POWER9 CPU
- IBM POWER9 CPUs
* - ZEN
- HOST
- AMD Zen architecture
* - ZEN2
- HOST
- AMD Zen2 architecture
* - ZEN3
- HOST
- AMD Zen3 architecture
* - RISCV_SG2042
- HOST
- SG2042 (RISC-V) CPU
- SG2042 (RISC-V) CPUs
* - RISCV_RVA22V
- HOST
- RVA22V (RISC-V) CPUs
* - KEPLER30
- GPU
- NVIDIA Kepler generation CC 3.0 GPU
- NVIDIA Kepler generation CC 3.0
* - KEPLER32
- GPU
- NVIDIA Kepler generation CC 3.2 GPU
- NVIDIA Kepler generation CC 3.2
* - KEPLER35
- GPU
- NVIDIA Kepler generation CC 3.5 GPU
- NVIDIA Kepler generation CC 3.5
* - KEPLER37
- GPU
- NVIDIA Kepler generation CC 3.7 GPU
- NVIDIA Kepler generation CC 3.7
* - MAXWELL50
- GPU
- NVIDIA Maxwell generation CC 5.0 GPU
- NVIDIA Maxwell generation CC 5.0
* - MAXWELL52
- GPU
- NVIDIA Maxwell generation CC 5.2 GPU
- NVIDIA Maxwell generation CC 5.2
* - MAXWELL53
- GPU
- NVIDIA Maxwell generation CC 5.3 GPU
- NVIDIA Maxwell generation CC 5.3
* - PASCAL60
- GPU
- NVIDIA Pascal generation CC 6.0 GPU
- NVIDIA Pascal generation CC 6.0
* - PASCAL61
- GPU
- NVIDIA Pascal generation CC 6.1 GPU
- NVIDIA Pascal generation CC 6.1
* - VOLTA70
- GPU
- NVIDIA Volta generation CC 7.0 GPU
- NVIDIA Volta generation CC 7.0
* - VOLTA72
- GPU
- NVIDIA Volta generation CC 7.2 GPU
- NVIDIA Volta generation CC 7.2
* - TURING75
- GPU
- NVIDIA Turing generation CC 7.5 GPU
- NVIDIA Turing generation CC 7.5
* - AMPERE80
- GPU
- NVIDIA Ampere generation CC 8.0 GPU
- NVIDIA Ampere generation CC 8.0
* - AMPERE86
- GPU
- NVIDIA Ampere generation CC 8.6 GPU
- NVIDIA Ampere generation CC 8.6
* - ADA89
- GPU
- NVIDIA Ada Lovelace generation CC 8.9 GPU
- NVIDIA Ada generation CC 8.9
* - HOPPER90
- GPU
- NVIDIA Hopper generation CC 9.0 GPU
- NVIDIA Hopper generation CC 9.0
* - AMD_GFX906
- GPU
- AMD GPU MI50/MI60
- AMD GPU MI50/60
* - AMD_GFX908
- GPU
- AMD GPU MI100
* - AMD_GFX90A
- GPU
- AMD GPU MI200
* - AMD_GFX940
- GPU
- AMD GPU MI300
* - AMD_GFX942
- GPU
- AMD GPU MI300
* - AMD_GFX942_APU
- GPU
- AMD APU MI300A
* - AMD_GFX1030
- GPU
- AMD GPU V620/W6800
@ -678,7 +692,7 @@ They must be specified in uppercase.
- AMD GPU RX7900XTX
* - AMD_GFX1103
- GPU
- AMD Phoenix APU with Radeon 740M/760M/780M/880M/890M
- AMD APU Phoenix
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
@ -701,7 +715,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.3.0 of the Kokkos library.
This list was last updated for version 4.5.1 of the Kokkos library.
.. tabs::
@ -2018,7 +2032,7 @@ TBB and MKL.
.. _mdi:
MDI package
-----------------------------
-----------
.. tabs::
@ -2045,6 +2059,37 @@ MDI package
----------
.. _misc:
MISC package
------------
The :doc:`fix imd <fix_imd>` style in this package can be run either
synchronously (communication with IMD clients is done in the main
process) or asynchronously (the fix spawns a separate thread that can
communicate with IMD clients concurrently to the LAMMPS execution).
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D LAMMPS_ASYNC_IMD=value # Run IMD server asynchronously
# value = no (default) or yes
.. tab:: Traditional make
To enable asynchronous mode the ``-DLAMMPS_ASYNC_IMD`` define
needs to be added to the ``LMP_INC`` variable in the
``Makefile.machine`` you are using. For example:
.. code-block:: make
LMP_INC = -DLAMMPS_ASYNC_IMD -DLAMMPS_MEMALIGN=64
----------
.. _molfile:
MOLFILE package
@ -2191,7 +2236,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
from the sources in the *lib* folder (including the essential
libqmmm.a) are not included in the static LAMMPS library and
(currently) not installed, while their code is included in the
shared LAMMPS library. Thus a typical command line to configure
shared LAMMPS library. Thus a typical command to configure
building LAMMPS for QMMM would be:
.. code-block:: bash

4
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@ -8,6 +8,10 @@ Building LAMMPS with traditional makefiles requires that you have a
for customizing your LAMMPS build with a number of global compilation
options and features.
This build system is slowly being phased out and may not support all
optional features and packages in LAMMPS. It is recommended to switch
to the :doc:`CMake based build system <Build_cmake>`.
Requirements
^^^^^^^^^^^^

1
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@ -49,6 +49,7 @@ packages:
* :ref:`LEPTON <lepton>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MISC <misc>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`

6
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@ -100,9 +100,9 @@ procedure.
It is possible to use both the integrated CMake support of the Visual
Studio IDE or use an external CMake installation (e.g. downloaded from
cmake.org) to create build files and compile LAMMPS from the command line.
cmake.org) to create build files and compile LAMMPS from the command-line.
Compilation via command line and unit tests are checked automatically
Compilation via command-line and unit tests are checked automatically
for the LAMMPS development branch through
`GitHub Actions <https://github.com/lammps/lammps/actions/workflows/compile-msvc.yml>`_.
@ -115,7 +115,7 @@ for the LAMMPS development branch through
Please note, that for either approach CMake will create a so-called
:ref:`"multi-configuration" build environment <cmake_multiconfig>`, and
the command lines for building and testing LAMMPS must be adjusted
the commands for building and testing LAMMPS must be adjusted
accordingly.
The LAMMPS cmake folder contains a ``CMakeSettings.json`` file with

2
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@ -4,7 +4,7 @@ LAMMPS Class
The LAMMPS class is encapsulating an MD simulation state and thus it is
the class that needs to be created when starting a new simulation system
state. The LAMMPS executable essentially creates one instance of this
class and passes the command line flags and tells it to process the
class and passes the command-line flags and tells it to process the
provided input (a file or ``stdin``). It shuts the class down when
control is returned to it and then exits. When using LAMMPS as a
library from another code it is required to create an instance of this

1
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@ -90,6 +90,7 @@ OPT.
* :doc:`lepton (o) <angle_lepton>`
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`mwlc <angle_mwlc>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`spica (ko) <angle_spica>`
* :doc:`table (o) <angle_table>`

10
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@ -43,7 +43,7 @@ OPT.
* :doc:`brownian/asphere <fix_brownian>`
* :doc:`brownian/sphere <fix_brownian>`
* :doc:`charge/regulation <fix_charge_regulation>`
* :doc:`cmap <fix_cmap>`
* :doc:`cmap (k) <fix_cmap>`
* :doc:`colvars <fix_colvars>`
* :doc:`controller <fix_controller>`
* :doc:`damping/cundall <fix_damping_cundall>`
@ -58,6 +58,7 @@ OPT.
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield (k) <fix_efield>`
* :doc:`efield/lepton <fix_efield_lepton>`
* :doc:`efield/tip4p <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode>`
@ -134,7 +135,7 @@ OPT.
* :doc:`nve/dot <fix_nve_dot>`
* :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
* :doc:`nve/eff <fix_nve_eff>`
* :doc:`nve/limit <fix_nve_limit>`
* :doc:`nve/limit (k) <fix_nve_limit>`
* :doc:`nve/line <fix_nve_line>`
* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`nve/noforce <fix_nve_noforce>`
@ -187,10 +188,11 @@ OPT.
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`
* :doc:`qtb <fix_qtb>`
* :doc:`qtpie/reaxff <fix_qtpie_reaxff>`
* :doc:`rattle <fix_shake>`
* :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`recenter (k) <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rheo <fix_rheo>`
* :doc:`rheo/oxidation <fix_rheo_oxidation>`
@ -270,7 +272,7 @@ OPT.
* :doc:`wall/piston <fix_wall_piston>`
* :doc:`wall/reflect (k) <fix_wall_reflect>`
* :doc:`wall/reflect/stochastic <fix_wall_reflect_stochastic>`
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region (k) <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
* :doc:`wall/table <fix_wall>`

2
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@ -69,7 +69,7 @@ WARNING message is printed. The :doc:`Errors <Errors>` page gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
You can use the :ref:`-skiprun <skiprun>` command line flag
You can use the :ref:`-skiprun <skiprun>` command-line flag
to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar
commands to check the entire input for correct syntax to avoid crashes
on typos or syntax errors in long runs.

1
doc/src/Commands_pair.rst
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@ -80,6 +80,7 @@ OPT.
* :doc:`coul/tt <pair_coul_tt>`
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dispersion/d3 <pair_dispersion_d3>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`

182
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@ -1,6 +1,10 @@
Removed commands and packages
=============================
.. contents::
------
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or
replacements. LAMMPS has special dummy styles implemented, that will
@ -8,47 +12,60 @@ stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
restart2data tool
-----------------
LAMMPS shell
------------
.. versionchanged:: 23Nov2013
.. versionchanged:: 29Aug2024
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
i-PI tool
---------
.. deprecated:: 11Dec2015
.. versionchanged:: 27Jun2024
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPI via pip are provided.
Box command
-----------
USER-REAXC package
------------------
.. deprecated:: 22Dec2022
.. deprecated:: 7Feb2024
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use
the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
backward compatibility by providing aliases for the styles. These have
been removed, so using "reaxff" is now *required*.
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
MPIIO package
-------------
.. deprecated:: 22Dec2022
.. deprecated:: 21Nov2023
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
present, LAMMPS will replace the commands accordingly and print a
warning.
The MPIIO package has been removed from LAMMPS since it was unmaintained
for many years and thus not updated to incorporate required changes that
had been applied to the corresponding non-MPIIO commands. As a
consequence the MPIIO commands had become unreliable and sometimes
crashing LAMMPS or corrupting data. Similar functionality is available
through the :ref:`ADIOS package <PKG-ADIOS>` and the :ref:`NETCDF
package <PKG-NETCDF>`. Also, the :doc:`dump_modify nfile or dump_modify
fileper <dump_modify>` keywords may be used for an efficient way of
writing out dump files when running on large numbers of processors.
Similarly, the "nfile" and "fileper" keywords exist for restarts:
see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
:doc:`write_restart <write_restart>`.
MSCG package
------------
.. deprecated:: 21Nov2023
The MSCG package has been removed from LAMMPS since it was unmaintained
for many years and instead superseded by the `OpenMSCG software
<https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
University of Chicago, which can be used independent from LAMMPS.
LATTE package
-------------
@ -64,18 +81,6 @@ packages, including LATTE. See the ``examples/QUANTUM`` dir and the
with LATTE as a plugin library (similar to the way fix latte worked), as
well as on a different set of MPI processors.
MEAM package
------------
The MEAM package in Fortran has been replaced by a C++ implementation.
The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
Minimize style fire/old
-----------------------
@ -97,38 +102,38 @@ The same functionality is available through
:doc:`bond style mesocnt <bond_mesocnt>` and
:doc:`angle style mesocnt <angle_mesocnt>`.
MPIIO package
-------------
Box command
-----------
.. deprecated:: 21Nov2023
.. deprecated:: 22Dec2022
The MPIIO package has been removed from LAMMPS since it was unmaintained
for many years and thus not updated to incorporate required changes that
had been applied to the corresponding non-MPIIO commands. As a
consequence the MPIIO commands had become unreliable and sometimes
crashing LAMMPS or corrupting data. Similar functionality is available
through the :ref:`ADIOS package <PKG-ADIOS>` and the :ref:`NETCDF
package <PKG-NETCDF>`. Also, the :doc:`dump_modify nfile or dump_modify
fileper <dump_modify>` keywords may be used for an efficient way of
writing out dump files when running on large numbers of processors.
Similarly, the "nfile" and "fileper" keywords exist for restarts:
see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
:doc:`write_restart <write_restart>`.
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
MSCG package
------------
.. deprecated:: 22Dec2022
.. deprecated:: 21Nov2023
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
present, LAMMPS will replace the commands accordingly and print a
warning.
The MSCG package has been removed from LAMMPS since it was unmaintained
for many years and instead superseded by the `OpenMSCG software
<https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
University of Chicago, which can be used independent from LAMMPS.
MESSAGE package
---------------
.. deprecated:: 4May2022
The MESSAGE package has been removed since it was superseded by the
:ref:`MDI package <PKG-MDI>`. MDI implements the same functionality
and in a more general way with direct support for more applications.
REAX package
------------
.. deprecated:: 4Jan2019
The REAX package has been removed since it was superseded by the
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF package has been tested
to yield equivalent results to the REAX package, offers better
@ -138,20 +143,25 @@ syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-REAXC package
------------------
MEAM package
------------
.. deprecated:: 7Feb2024
.. deprecated:: 4Jan2019
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use
the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
backward compatibility by providing aliases for the styles. These have
been removed, so using "reaxff" is now *required*.
The MEAM package in Fortran has been replaced by a C++ implementation.
The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
USER-CUDA package
-----------------
.. deprecated:: 31May2016
The USER-CUDA package had been removed, since it had been unmaintained
for a long time and had known bugs and problems. Significant parts of
the design were transferred to the
@ -160,19 +170,27 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
and the :ref:`GPU package <PKG-GPU>` are maintained
and allow running LAMMPS with GPU acceleration.
i-PI tool
---------
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
.. versionchanged:: 27Jun2024
.. deprecated:: 11Dec2015
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPI via pip are provided.
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
LAMMPS shell
------------
restart2data tool
-----------------
.. versionchanged:: 29Aug2024
.. deprecated:: 23Nov2013
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command-line flags <Run_options>`

16
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@ -79,19 +79,19 @@ containing ``double`` values. To correctly store integers that may be
64-bit (bigint, tagint, imageint) in the buffer, you need to use the
:ref:`ubuf union <communication_buffer_coding_with_ubuf>` construct.
The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
of forward and reverse communication operations using the same *Comm*
class methods. Likewise, the same pack/unpack methods and
The *Fix*, *Bond*, *Compute*, and *Dump* classes can also invoke the
same kind of forward and reverse communication operations using the
same *Comm* class methods. Likewise, the same pack/unpack methods and
comm_forward/comm_reverse variables must be defined by the calling
*Fix*, *Compute*, or *Dump* class.
*Fix*, *Bond*, *Compute*, or *Dump* class.
For *Fix* classes, there is an optional second argument to the
For all of these classes, there is an optional second argument to the
*forward_comm()* and *reverse_comm()* call which can be used when the
fix performs multiple modes of communication, with different numbers
of values per atom. The fix should set the *comm_forward* and
class performs multiple modes of communication, with different numbers
of values per atom. The class should set the *comm_forward* and
*comm_reverse* variables to the maximum value, but can invoke the
communication for a particular mode with a smaller value. For this
to work, the *pack_forward_comm()*, etc methods typically use a class
to work, the *pack_forward_comm()*, etc. methods typically use a class
member variable to choose which values to pack/unpack into/from the
buffer.

4
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@ -94,12 +94,12 @@ represents what is generally referred to as an "instance of LAMMPS". It
is a composite holding pointers to instances of other core classes
providing the core functionality of the MD engine in LAMMPS and through
them abstractions of the required operations. The constructor of the
LAMMPS class will instantiate those instances, process the command line
LAMMPS class will instantiate those instances, process the command-line
flags, initialize MPI (if not already done) and set up file pointers for
input and output. The destructor will shut everything down and free all
associated memory. Thus code for the standalone LAMMPS executable in
``main.cpp`` simply initializes MPI, instantiates a single instance of
LAMMPS while passing it the command line flags and input script. It
LAMMPS while passing it the command-line flags and input script. It
deletes the LAMMPS instance after the method reading the input returns
and shuts down the MPI environment before it exits the executable.

76
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@ -227,12 +227,12 @@ Tests for the C-style library interface
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tests for validating the LAMMPS C-style library interface are in the
``unittest/c-library`` folder. They are implemented either to be used
for utility functions or for LAMMPS commands, but use the functions
implemented in the ``src/library.cpp`` file as much as possible. There
may be some overlap with other tests, but only in as much as is required
to test the C-style library API. The tests are distributed over
multiple test programs which try to match the grouping of the
``unittest/c-library`` folder. They text either utility functions or
LAMMPS commands, but use the functions implemented in
``src/library.cpp`` as much as possible. There may be some overlap with
other tests as far as the LAMMPS functionality is concerned, but the
focus is on testing the C-style library API. The tests are distributed
over multiple test programs which try to match the grouping of the
functions in the source code and :ref:`in the manual <lammps_c_api>`.
This group of tests also includes tests invoking LAMMPS in parallel
@ -258,7 +258,7 @@ Tests for the Python module and package
The ``unittest/python`` folder contains primarily tests for classes and
functions in the LAMMPS python module but also for commands in the
PYTHON package. These tests are only enabled if the necessary
PYTHON package. These tests are only enabled, if the necessary
prerequisites are detected or enabled during configuration and
compilation of LAMMPS (shared library build enabled, Python interpreter
found, Python development files found).
@ -272,29 +272,30 @@ Tests for the Fortran interface
Tests for using the Fortran module are in the ``unittest/fortran``
folder. Since they are also using the GoogleTest library, they require
implementing test wrappers in C++ that will call fortran functions
which provide a C function interface through ISO_C_BINDINGS that will in
turn call the functions in the LAMMPS Fortran module.
test wrappers written in C++ that will call fortran functions with a C
function interface through ISO_C_BINDINGS which will in turn call the
functions in the LAMMPS Fortran module.
Tests for the C++-style library interface
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tests in the ``unittest/cplusplus`` folder are somewhat similar to
the tests for the C-style library interface, but do not need to test the
several convenience and utility functions that are only available through
the C-style interface. Instead it can focus on the more generic features
that are used internally. This part of the unit tests is currently still
mostly in the planning stage.
convenience and utility functions that are only available through the
C-style library interface. Instead they focus on the more generic
features that are used in LAMMPS internally. This part of the unit
tests is currently still mostly in the planning stage.
Tests for reading and writing file formats
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The ``unittest/formats`` folder contains test programs for reading and
writing files like data files, restart files, potential files or dump files.
This covers simple things like the file i/o convenience functions in the
``utils::`` namespace to complex tests of atom styles where creating and
deleting atoms with different properties is tested in different ways
and through script commands or reading and writing of data or restart files.
writing files like data files, restart files, potential files or dump
files. This covers simple things like the file i/o convenience
functions in the ``utils::`` namespace to complex tests of atom styles
where creating and deleting of atoms with different properties is tested
in different ways and through script commands or reading and writing of
data or restart files.
Tests for styles computing or modifying forces
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -443,7 +444,7 @@ file for a style that is similar to one to be tested. The file name should
follow the naming conventions described above and after copying the file,
the first step is to replace the style names where needed. The coefficient
values do not have to be meaningful, just in a reasonable range for the
given system. It does not matter if some forces are large, as long as
given system. It does not matter if some forces are large, for as long as
they do not diverge.
The template input files define a large number of index variables at the top
@ -476,7 +477,7 @@ the tabulated coulomb, to test both code paths. The reference results in the YA
files then should be compared manually, if they agree well enough within the limits
of those two approximations.
The ``test_pair_style`` and equivalent programs have special command line options
The ``test_pair_style`` and equivalent programs have special command-line options
to update the YAML files. Running a command like
.. code-block:: bash
@ -531,19 +532,20 @@ Python module.
Troubleshooting failed unit tests
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The are by default no unit tests for newly added features (e.g. pair, fix,
or compute styles) unless your pull request also includes tests for the
added features. If you are modifying some features, you may see failures
for existing tests, if your modifications have some unexpected side effects
or your changes render the existing test invalid. If you are adding an
accelerated version of an existing style, then only tests for INTEL,
KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
Tests for the GPU package are time consuming and thus are only run
*after* a merge, or when a special label, ``gpu_unit_tests`` is added
to the pull request. After the test has started, it is often best to
remove the label since every PR activity will re-trigger the test (that
is a limitation of triggering a test with a label). Support for unit
tests when using KOKKOS with GPU acceleration is currently not supported.
There are by default no unit tests for newly added features (e.g. pair,
fix, or compute styles) unless your pull request also includes tests for
these added features. If you are modifying some existing LAMMPS
features, you may see failures for existing tests, if your modifications
have some unexpected side effects or your changes render the existing
test invalid. If you are adding an accelerated version of an existing
style, then only tests for INTEL, KOKKOS (with OpenMP only), OPENMP, and
OPT will be run automatically. Tests for the GPU package are time
consuming and thus are only run *after* a merge, or when a special
label, ``gpu_unit_tests`` is added to the pull request. After the test
has started, it is often best to remove the label since every PR
activity will re-trigger the test (that is a limitation of triggering a
test with a label). Support for unit tests using KOKKOS with GPU
acceleration is currently not supported.
When you see a failed build on GitHub, click on ``Details`` to be taken
to the corresponding LAMMPS Jenkins CI web page. Click on the "Exit"
@ -588,7 +590,7 @@ While the epsilon (relative precision) for a single, `IEEE 754 compliant
<https://en.wikipedia.org/wiki/IEEE_754>`_, double precision floating
point operation is at about 2.2e-16, the achievable precision for the
tests is lower due to most numbers being sums over intermediate results
and the non-associativity of floating point math leading to larger
for which the non-associativity of floating point math leads to larger
errors. As a rule of thumb, the test epsilon can often be in the range
5.0e-14 to 1.0e-13. But for "noisy" force kernels, e.g. those a larger
amount of arithmetic operations involving `exp()`, `log()` or `sin()`
@ -602,14 +604,14 @@ of floating point operations or that some or most intermediate operations
may be done using approximations or with single precision floating point
math.
To rerun the failed unit test individually, change to the ``build`` directory
To rerun a failed unit test individually, change to the ``build`` directory
and run the test with verbose output. For example,
.. code-block:: bash
env TEST_ARGS=-v ctest -R ^MolPairStyle:lj_cut_coul_long -V
``ctest`` with the ``-V`` flag also shows the exact command line
``ctest`` with the ``-V`` flag also shows the exact command
of the test. One can then use ``gdb --args`` to further debug and
catch exceptions with the test command, for example,

10
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@ -310,7 +310,7 @@ the constructor and the destructor.
Pair styles are different from most classes in LAMMPS that define a
"style", as their constructor only uses the LAMMPS class instance
pointer as an argument, but **not** the command line arguments of the
pointer as an argument, but **not** the arguments of the
:doc:`pair_style command <pair_style>`. Instead, those arguments are
processed in the ``Pair::settings()`` function (or rather the version in
the derived class). The constructor is the place where global defaults
@ -891,7 +891,7 @@ originally created from mixing or not).
These data file output functions are only useful for true pair-wise
additive potentials, where the potential parameters can be entered
through *multiple* :doc:`pair_coeff commands <pair_coeff>`. Pair styles
that require a single "pair_coeff \* \*" command line are not compatible
that require a single "pair_coeff \* \*" command are not compatible
with reading their parameters from data files. For pair styles like
*born/gauss* that do support writing to data files, the potential
parameters will be read from the data file, if present, and
@ -1122,7 +1122,7 @@ once. Thus, the ``coeff()`` function has to do three tasks, each of
which is delegated to a function in the ``PairTersoff`` class:
#. map elements to atom types. Those follow the potential file name in the
command line arguments and are processed by the ``map_element2type()`` function.
command arguments and are processed by the ``map_element2type()`` function.
#. read and parse the potential parameter file in the ``read_file()`` function.
#. Build data structures where the original and derived parameters are
indexed by all possible triples of atom types and thus can be looked
@ -1356,8 +1356,8 @@ either 0 or 1.
The ``morseflag`` variable defaults to 0 and is set to 1 in the
``PairAIREBOMorse::settings()`` function which is called by the
:doc:`pair_style <pair_style>` command. This function delegates
all command line processing and setting of other parameters to the
:doc:`pair_style <pair_style>` command. This function delegates all
command argument processing and setting of other parameters to the
``PairAIREBO::settings()`` function of the base class.
.. code-block:: c++

54
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@ -83,7 +83,7 @@ Run LAMMPS from within the debugger
Running LAMMPS under the control of the debugger as shown below only
works for a single MPI rank (for debugging a program running in parallel
you usually need a parallel debugger program). A simple way to launch
GDB is to prefix the LAMMPS command line with ``gdb --args`` and then
GDB is to prefix the LAMMPS command-line with ``gdb --args`` and then
type the command "run" at the GDB prompt. This will launch the
debugger, load the LAMMPS executable and its debug info, and then run
it. When it reaches the code causing the segmentation fault, it will
@ -180,7 +180,7 @@ inspect the behavior of a compiled program by essentially emulating a
CPU and instrumenting the program while running. This slows down
execution quite significantly, but can also report issues that are not
resulting in a crash. The default valgrind tool is a memory checker and
you can use it by prefixing the normal command line with ``valgrind``.
you can use it by prefixing the normal command-line with ``valgrind``.
Unlike GDB, this will also work for parallel execution, but it is
recommended to redirect the valgrind output to a file (e.g. with
``--log-file=crash-%p.txt``, the %p will be substituted with the
@ -235,3 +235,53 @@ from GDB. In addition you get a more specific hint about what cause the
segmentation fault, i.e. that it is a NULL pointer dereference. To find
out which pointer exactly was NULL, you need to use the debugger, though.
Debugging when LAMMPS appears to be stuck
=========================================
Sometimes the LAMMPS calculation appears to be stuck, that is the LAMMPS
process or processes are active, but there is no visible progress. This
can have multiple reasons:
- The selected styles are slow and require a lot of CPU time and the
system is large. When extrapolating the expected speed from smaller
systems, one has to factor in that not all models scale linearly with
system size, e.g. :doc:`kspace styles like ewald or pppm
<kspace_style>`. There is very little that can be done in this case.
- The output interval is not set or set to a large value with the
:doc:`thermo <thermo>` command. I the first case, there will be output
only at the first and last step.
- The output is block-buffered and instead of line-buffered. The output
will only be written to the screen after 4096 or 8192 characters of
output have accumulated. This most often happens for files but also
with MPI parallel executables for output to the screen, since the
output to the screen is handled by the MPI library so that output from
all processes can be shown. This can be suppressed by using the
``-nonblock`` or ``-nb`` command-line flag, which turns off buffering
for screen and logfile output.
- An MPI parallel calculation has a bug where a collective MPI function
is called (e.g. ``MPI_Barrier()``, ``MPI_Bcast()``,
``MPI_Allreduce()`` and so on) before pending point-to-point
communications are completed or when the collective function is only
called from a subset of the MPI processes. This also applies to some
internal LAMMPS functions like ``Error::all()`` which uses
``MPI_Barrier()`` and thus ``Error::one()`` must be called, if the
error condition does not happen on all MPI processes simultaneously.
- Some function in LAMMPS has a bug where a ``for`` or ``while`` loop
does not trigger the exit condition and thus will loop forever. This
can happen when the wrong variable is incremented or when one value in
a comparison becomes ``NaN`` due to an overflow.
In the latter two cases, further information and stack traces (see above)
can be obtain by attaching a debugger to a running process. For that the
process ID (PID) is needed; this can be found on Linux machines with the
``top``, ``htop``, ``ps``, or ``pstree`` commands.
Then running the (GNU) debugger ``gdb`` with the ``-p`` flag followed by
the process id will attach the process to the debugger and stop
execution of that specific process. From there on it is possible to
issue all debugger commands in the same way as when LAMMPS was started
from the debugger (see above). Most importantly it is possible to
obtain a stack trace with the ``where`` command and thus determine where
in the execution of a timestep this process is. Also internal data can
be printed and execution single stepped or continued. When the debugger
is exited, the calculation will resume normally.

23
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@ -54,3 +54,26 @@ header of a data file (e.g. the number of atoms) is larger than the
number of lines provided (e.g. in the corresponding Atoms section)
and then LAMMPS will continue reading into the next section and that
would have a completely different format.
.. _err0003:
Illegal variable command: expected X arguments but found Y
----------------------------------------------------------
This error indicates that there are the wrong number of arguments for a
specific variable command, but a common reason for that is a variable
expression that has whitespace but is not enclosed in single or double
quotes.
To explain, the LAMMPS input parser reads and processes lines. The
resulting line is broken down into "words". Those are usually
individual commands, labels, names, values separated by whitespace (a
space or tab character). For "words" that may contain whitespace, they
have to be enclosed in single (') or double (") quotes. The parser will
then remove the outermost pair of quotes and then pass that string as
"word" to the variable command.
Thus missing quotes or accidental extra whitespace will lead to the
error shown in the header because the unquoted whitespace will result
in the text being broken into more "words", i.e. the variable expression
being split.

2
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@ -7774,7 +7774,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Too few values in body section of molecule file*
Self-explanatory.
*Too many -pk arguments in command line*
*Too many -pk arguments in command-line*
The string formed by concatenating the arguments is too long. Use a
package command in the input script instead.

2
doc/src/Examples.rst
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@ -146,6 +146,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| streitz | use of Streitz/Mintmire potential with charge equilibration |
+-------------+------------------------------------------------------------------+
| stress_vcm | removing binned rigid body motion from binned stress profile |
+-------------+------------------------------------------------------------------+
| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
+-------------+------------------------------------------------------------------+
| threebody | regression test input for a variety of manybody potentials |

14
doc/src/Fortran.rst
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@ -16,7 +16,7 @@ compiled alongside the code using it from the source code in
``fortran/lammps.f90`` *and* with the same compiler used to build the
rest of the Fortran code that interfaces to LAMMPS. When linking, you
also need to :doc:`link to the LAMMPS library <Build_link>`. A typical
command line for a simple program using the Fortran interface would be:
command for a simple program using the Fortran interface would be:
.. code-block:: bash
@ -91,12 +91,12 @@ function and triggered with the optional logical argument set to
CALL lmp%close(.TRUE.)
END PROGRAM testlib
It is also possible to pass command line flags from Fortran to C/C++ and
It is also possible to pass command-line flags from Fortran to C/C++ and
thus make the resulting executable behave similarly to the standalone
executable (it will ignore the `-in/-i` flag, though). This allows
using the command line to configure accelerator and suffix settings,
using the command-line to configure accelerator and suffix settings,
configure screen and logfile output, or to set index style variables
from the command line and more. Here is a correspondingly adapted
from the command-line and more. Here is a correspondingly adapted
version of the previous example:
.. code-block:: fortran
@ -108,7 +108,7 @@ version of the previous example:
CHARACTER(LEN=128), ALLOCATABLE :: command_args(:)
INTEGER :: i, argc
! copy command line flags to `command_args()`
! copy command-line flags to `command_args()`
argc = COMMAND_ARGUMENT_COUNT()
ALLOCATE(command_args(0:argc))
DO i=0, argc
@ -321,6 +321,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype set_string_variable: subroutine
:f set_internal_variable: :f:subr:`set_internal_variable`
:ftype set_internal_variable: subroutine
:f eval: :f:func:`eval`
:ftype eval: function
:f gather_atoms: :f:subr:`gather_atoms`
:ftype gather_atoms: subroutine
:f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@ -448,7 +450,7 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
compiled with MPI support, it will also initialize MPI, if it has
not already been initialized before.
The *args* argument with the list of command line parameters is
The *args* argument with the list of command-line parameters is
optional and so it the *comm* argument with the MPI communicator.
If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For
more details please see the documentation of :cpp:func:`lammps_open`.

1
doc/src/Howto.rst
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@ -104,6 +104,7 @@ Tutorials howto
Howto_github
Howto_lammps_gui
Howto_moltemplate
Howto_python
Howto_pylammps
Howto_wsl

6
doc/src/Howto_bpm.rst
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@ -5,7 +5,11 @@ The BPM package implements bonded particle models which can be used to
simulate mesoscale solids. Solids are constructed as a collection of
particles, which each represent a coarse-grained region of space much
larger than the atomistic scale. Particles within a solid region are
then connected by a network of bonds to provide solid elasticity.
then connected by a network of bonds to model solid elasticity.
There are many names for methods that are based on similar (or
equivalent) capabilities to those in this package, including, but not
limited to, cohesive beam models, bonded DEMs, lattice spring models,
mass spring models, and lattice particle methods.
Unlike traditional bonds in molecular dynamics, the equilibrium bond
length can vary between bonds. Bonds store the reference state. This

8
doc/src/Howto_cmake.rst
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@ -56,7 +56,7 @@ using a shell like Bash or Zsh.
Visual Studio IDE with the bundled CMake or from the Windows command prompt using
a separately installed CMake package, both using the native Microsoft Visual C++
compilers and (optionally) the Microsoft MPI SDK. This tutorial, however, only
covers unix-like command line interfaces.
covers unix-like command-line interfaces.
We also assume that you have downloaded and unpacked a recent LAMMPS source code package
or used Git to create a clone of the LAMMPS sources on your compilation machine.
@ -277,7 +277,7 @@ Setting options
---------------
Options that enable, disable or modify settings are modified by setting
the value of CMake variables. This is done on the command line with the
the value of CMake variables. This is done on the command-line with the
*-D* flag in the format ``-D VARIABLE=value``, e.g. ``-D
CMAKE_BUILD_TYPE=Release`` or ``-D BUILD_MPI=on``. There is one quirk:
when used before the CMake directory, there may be a space between the
@ -376,7 +376,7 @@ Using presets
-------------
Since LAMMPS has a lot of optional features and packages, specifying
them all on the command line can be tedious. Or when selecting a
them all on the command-line can be tedious. Or when selecting a
different compiler toolchain, multiple options have to be changed
consistently and that is rather error prone. Or when enabling certain
packages, they require consistent settings to be operated in a
@ -384,7 +384,7 @@ particular mode. For this purpose, we are providing a selection of
"preset files" for CMake in the folder ``cmake/presets``. They
represent a way to pre-load or override the CMake configuration cache by
setting or changing CMake variables. Preset files are loaded using the
*-C* command line flag. You can combine loading multiple preset files or
*-C* command-line flag. You can combine loading multiple preset files or
change some variables later with additional *-D* flags. A few examples:
.. code-block:: bash

2
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@ -163,7 +163,7 @@ After everything is done, add the files to the branch and commit them:
*git rm*, *git mv* for adding, removing, renaming individual files,
respectively, and then *git commit* to finalize the commit.
Carefully check all pending changes with *git status* before
committing them. If you find doing this on the command line too
committing them. If you find doing this on the command-line too
tedious, consider using a GUI, for example the one included in git
distributions written in Tk, i.e. use *git gui* (on some Linux
distributions it may be required to install an additional package to

68
doc/src/Howto_lammps_gui.rst
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@ -20,8 +20,11 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
(Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
Sur or later), and Windows (version 10 or later) :ref:`are available
<lammps_gui_install>` for download. Non-MPI LAMMPS executables (as
``lmp``) for running LAMMPS from the command line and :doc:`some
``lmp``) for running LAMMPS from the command-line and :doc:`some
LAMMPS tools <Tools>` compiled executables are also included.
Also, the pre-compiled LAMMPS-GUI packages include the WHAM executables
from http://membrane.urmc.rochester.edu/content/wham/ for use with
LAMMPS tutorials.
The source code for LAMMPS-GUI is included in the LAMMPS source code
distribution and can be found in the ``tools/lammps-gui`` folder. It
@ -29,16 +32,16 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
<Build_cmake>`.
LAMMPS-GUI tries to provide an experience similar to what people
traditionally would have running LAMMPS using a command line window and
traditionally would have running LAMMPS using a command-line window and
the console LAMMPS executable but just rolled into a single executable:
- writing & editing LAMMPS input files with a text editor
- run LAMMPS on those input file with selected command line flags
- run LAMMPS on those input file with selected command-line flags
- extract data from the created files and visualize it with and
external software
That procedure is quite effective for people proficient in using the
command line, as that allows them to use tools for the individual steps
command-line, as that allows them to use tools for the individual steps
that they are most comfortable with. In fact, it is often *required* to
adopt this workflow when running LAMMPS simulations on high-performance
computing facilities.
@ -61,13 +64,18 @@ simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
since you only need to learn how to use a single program for most tasks
and thus time can be saved and people can focus on learning LAMMPS.
The tutorials at https://lammpstutorials.github.io/ are specifically
updated for use with LAMMPS-GUI.
updated for use with LAMMPS-GUI and can their tutorial materials can
be downloaded and loaded directly from the GUI.
Another design goal is to keep the barrier low when replacing part of
the functionality of LAMMPS-GUI with external tools. That said, LAMMPS-GUI
has some unique functionality that is not found elsewhere:
- auto-adapting to features available in the integrated LAMMPS library
- auto-completion for LAMMPS commands and options
- context-sensitive online help
- start and stop of simulations via mouse or keyboard
- monitoring of simulation progress
- interactive visualization using the :doc:`dump image <dump_image>`
command with the option to copy-paste the resulting settings
- automatic slide show generation from dump image out at runtime
@ -100,10 +108,11 @@ MacOS 11 and later
^^^^^^^^^^^^^^^^^^
After downloading the ``LAMMPS-macOS-multiarch-GUI-<version>.dmg``
installer package, you need to double-click it and then, in the window
that opens, drag the app bundle as indicated into the "Applications"
folder. The follow the instructions in the "README.txt" file to
get access to the other included executables.
application bundle disk image, you need to double-click it and then, in
the window that opens, drag the app bundle as indicated into the
"Applications" folder. Afterwards, the disk image can be unmounted.
Then follow the instructions in the "README.txt" file to get access to
the other included command-line executables.
Linux on x86\_64
^^^^^^^^^^^^^^^^
@ -117,15 +126,25 @@ into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly.
The second variant uses `flatpak <https://www.flatpak.org>`_ and
requires the flatpak management and runtime software to be installed.
After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``
After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak``
flatpak bundle, you can install it with ``flatpak install --user
LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``. After installation,
LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak``. After installation,
LAMMPS-GUI should be integrated into your desktop environment under
"Applications > Science" but also can be launched from the console with
``flatpak run org.lammps.lammps-gui``. The flatpak bundle also includes
the console LAMMPS executable ``lmp`` which can be launched to run
simulations with, for example: ``flatpak run --command=lmp
org.lammps.lammps-gui -in in.melt``.
simulations with, for example with:
.. code-block:: sh
flatpak run --command=lmp org.lammps.lammps-gui -in in.melt
Other bundled command-line executables are run the same way and can be
listed with:
.. code-block:: sh
ls $(flatpak info --show-location org.lammps.lammps-gui )/files/bin
Compiling from Source
@ -165,9 +184,9 @@ window is stored when exiting and restored when starting again.
Opening Files
^^^^^^^^^^^^^
The LAMMPS-GUI application can be launched without command line arguments
The LAMMPS-GUI application can be launched without command-line arguments
and then starts with an empty buffer in the *Editor* window. If arguments
are given LAMMPS will use first command line argument as the file name for
are given LAMMPS will use first command-line argument as the file name for
the *Editor* buffer and reads its contents into the buffer, if the file
exists. All further arguments are ignored. Files can also be opened via
the *File* menu, the `Ctrl-O` (`Command-O` on macOS) keyboard shortcut
@ -261,14 +280,21 @@ Output Window
By default, when starting a run, an *Output* window opens that displays
the screen output of the running LAMMPS calculation, as shown below.
This text would normally be seen in the command line window.
This text would normally be seen in the command-line window.
.. image:: JPG/lammps-gui-log.png
:align: center
:scale: 50%
LAMMPS-GUI captures the screen output from LAMMPS as it is generated and
updates the *Output* window regularly during a run.
updates the *Output* window regularly during a run. If there are any
warnings or errors in the LAMMPS output, they are highlighted by using
bold text colored in red. There is a small panel at the bottom center
of the *Output* window showing how many warnings and errors were
detected and how many lines the entire output has. By clicking on the
button on the right with the warning symbol or by using the keyboard
shortcut `Ctrl-N` (`Command-N` on macOS), you can jump to the next
line with a warning or error.
By default, the *Output* window is replaced each time a run is started.
The runs are counted and the run number for the current run is displayed
@ -398,7 +424,7 @@ below.
Like for the *Output* and *Charts* windows, its content is continuously
updated during a run. It will show "(none)" if there are no variables
defined. Note that it is also possible to *set* :doc:`index style
variables <variable>`, that would normally be set via command line
variables <variable>`, that would normally be set via command-line
flags, via the "Set Variables..." dialog from the *Run* menu.
LAMMPS-GUI automatically defines the variable "gui_run" to the current
value of the run counter. That way it is possible to automatically
@ -775,11 +801,11 @@ General Settings:
- *Echo input to log:* when checked, all input commands, including
variable expansions, are echoed to the *Output* window. This is
equivalent to using `-echo screen` at the command line. There is no
equivalent to using `-echo screen` at the command-line. There is no
log *file* produced by default, since LAMMPS-GUI uses `-log none`.
- *Include citation details:* when checked full citation info will be
included to the log window. This is equivalent to using `-cite
screen` on the command line.
screen` on the command-line.
- *Show log window by default:* when checked, the screen output of a
LAMMPS run will be collected in a log window during the run
- *Show chart window by default:* when checked, the thermodynamic
@ -828,7 +854,7 @@ Accelerators:
This tab enables selection of an accelerator package for LAMMPS to use
and is equivalent to using the `-suffix` and `-package` flags on the
command line. Only settings supported by the LAMMPS library and local
command-line. Only settings supported by the LAMMPS library and local
hardware are available. The `Number of threads` field allows setting
the maximum number of threads for the accelerator packages that use
threads.

4
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@ -738,8 +738,8 @@ command.
This can be done, for example, by using the built-in visualizer of the
:doc:`dump image or dump movie <dump_image>` command to create snapshot
images or a movie. Below are example command lines for using dump image
with the :ref:`example listed below <periexample>` and a set of images
images or a movie. Below are example command for using dump image with
the :ref:`example listed below <periexample>` and a set of images
created for steps 300, 600, and 2000 this way.
.. code-block:: LAMMPS

564
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View File

@ -1,564 +1,6 @@
PyLammps Tutorial
=================
.. contents::
Overview
--------
:py:class:`PyLammps <lammps.PyLammps>` is a Python wrapper class for
LAMMPS which can be created on its own or use an existing
:py:class:`lammps Python <lammps.lammps>` object. It creates a simpler,
more "pythonic" interface to common LAMMPS functionality, in contrast to
the :py:class:`lammps <lammps.lammps>` wrapper for the LAMMPS :ref:`C
language library interface API <lammps_c_api>` which is written using
`Python ctypes <ctypes_>`_. The :py:class:`lammps <lammps.lammps>`
wrapper is discussed on the :doc:`Python_head` doc page.
Unlike the flat `ctypes <ctypes_>`_ interface, PyLammps exposes a
discoverable API. It no longer requires knowledge of the underlying C++
code implementation. Finally, the :py:class:`IPyLammps
<lammps.IPyLammps>` wrapper builds on top of :py:class:`PyLammps
<lammps.PyLammps>` and adds some additional features for `IPython
integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for
embedded visualization output from :doc:`dump style image <dump_image>`.
.. _ctypes: https://docs.python.org/3/library/ctypes.html
.. _ipython: https://ipython.org/
.. _jupyter: https://jupyter.org/
Comparison of lammps and PyLammps interfaces
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
lammps.lammps
"""""""""""""
* uses `ctypes <ctypes_>`_
* direct memory access to native C++ data with optional support for NumPy arrays
* provides functions to send and receive data to LAMMPS
* interface modeled after the LAMMPS :ref:`C language library interface API <lammps_c_api>`
* requires knowledge of how LAMMPS internally works (C pointers, etc)
* full support for running Python with MPI using `mpi4py <https://mpi4py.readthedocs.io>`_
* no overhead from creating a more Python-like interface
lammps.PyLammps
"""""""""""""""
* higher-level abstraction built on *top* of the original :py:class:`ctypes based interface <lammps.lammps>`
* manipulation of Python objects
* communication with LAMMPS is hidden from API user
* shorter, more concise Python
* better IPython integration, designed for quick prototyping
* designed for serial execution
* additional overhead from capturing and parsing the LAMMPS screen output
Quick Start
-----------
System-wide Installation
^^^^^^^^^^^^^^^^^^^^^^^^
Step 1: Building LAMMPS as a shared library
"""""""""""""""""""""""""""""""""""""""""""
To use LAMMPS inside of Python it has to be compiled as shared
library. This library is then loaded by the Python interface. In this
example we enable the MOLECULE package and compile LAMMPS with PNG, JPEG
and FFMPEG output support enabled.
Step 1a: For the CMake based build system, the steps are:
.. code-block:: bash
mkdir $LAMMPS_DIR/build-shared
cd $LAMMPS_DIR/build-shared
# MPI, PNG, Jpeg, FFMPEG are auto-detected
cmake ../cmake -DPKG_MOLECULE=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
make
Step 1b: For the legacy, make based build system, the steps are:
.. code-block:: bash
cd $LAMMPS_DIR/src
# add packages if necessary
make yes-MOLECULE
# compile shared library using Makefile
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
Step 2: Installing the LAMMPS Python package
""""""""""""""""""""""""""""""""""""""""""""
PyLammps is part of the lammps Python package. To install it simply install
that package into your current Python installation with:
.. code-block:: bash
make install-python
.. note::
Recompiling the shared library requires re-installing the Python package
Installation inside of a virtualenv
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can use virtualenv to create a custom Python environment specifically tuned
for your workflow.
Benefits of using a virtualenv
""""""""""""""""""""""""""""""
* isolation of your system Python installation from your development installation
* installation can happen in your user directory without root access (useful for HPC clusters)
* installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
* you can even install specific old versions of a package if necessary
**Prerequisite (e.g. on Ubuntu)**
.. code-block:: bash
apt-get install python-virtualenv
Creating a virtualenv with lammps installed
"""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
# create virtualenv named 'testing'
virtualenv $HOME/python/testing
# activate 'testing' environment
source $HOME/python/testing/bin/activate
Now configure and compile the LAMMPS shared library as outlined above.
When using CMake and the shared library has already been build, you
need to re-run CMake to update the location of the python executable
to the location in the virtual environment with:
.. code-block:: bash
cmake . -DPython_EXECUTABLE=$(which python)
# install LAMMPS package in virtualenv
(testing) make install-python
# install other useful packages
(testing) pip install matplotlib jupyter mpi4py
...
# return to original shell
(testing) deactivate
Creating a new instance of PyLammps
-----------------------------------
To create a PyLammps object you need to first import the class from the lammps
module. By using the default constructor, a new *lammps* instance is created.
.. code-block:: python
from lammps import PyLammps
L = PyLammps()
You can also initialize PyLammps on top of this existing *lammps* object:
.. code-block:: python
from lammps import lammps, PyLammps
lmp = lammps()
L = PyLammps(ptr=lmp)
Commands
--------
Sending a LAMMPS command with the existing library interfaces is done using
the command method of the lammps object instance.
For instance, let's take the following LAMMPS command:
.. code-block:: LAMMPS
region box block 0 10 0 5 -0.5 0.5
In the original interface this command can be executed with the following
Python code if *L* was a lammps instance:
.. code-block:: python
L.command("region box block 0 10 0 5 -0.5 0.5")
With the PyLammps interface, any command can be split up into arbitrary parts
separated by white-space, passed as individual arguments to a region method.
.. code-block:: python
L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
Note that each parameter is set as Python literal floating-point number. In the
PyLammps interface, each command takes an arbitrary parameter list and transparently
merges it to a single command string, separating individual parameters by white-space.
The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the original interface parameterization needed to be done
manually by creating formatted strings.
.. code-block:: python
L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
System state
------------
In addition to dispatching commands directly through the PyLammps object, it
also provides several properties which allow you to query the system state.
L.system
Is a dictionary describing the system such as the bounding box or number of atoms
L.system.xlo, L.system.xhi
bounding box limits along x-axis
L.system.ylo, L.system.yhi
bounding box limits along y-axis
L.system.zlo, L.system.zhi
bounding box limits along z-axis
L.communication
configuration of communication subsystem, such as the number of threads or processors
L.communication.nthreads
number of threads used by each LAMMPS process
L.communication.nprocs
number of MPI processes used by LAMMPS
L.fixes
List of fixes in the current system
L.computes
List of active computes in the current system
L.dump
List of active dumps in the current system
L.groups
List of groups present in the current system
Working with LAMMPS variables
-----------------------------
LAMMPS variables can be both defined and accessed via the PyLammps interface.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: python
L.variable("a index 2")
A dictionary of all variables is returned by L.variables
you can access an individual variable by retrieving a variable object from the
L.variables dictionary by name
.. code-block:: python
a = L.variables['a']
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: python
print(a.value)
a.value = 4
Retrieving the value of an arbitrary LAMMPS expressions
-------------------------------------------------------
LAMMPS expressions can be immediately evaluated by using the eval method. The
passed string parameter can be any expression containing global thermo values,
variables, compute or fix data.
.. code-block:: python
result = L.eval("ke") # kinetic energy
result = L.eval("pe") # potential energy
result = L.eval("v_t/2.0")
Accessing atom data
-------------------
All atoms in the current simulation can be accessed by using the L.atoms list.
Each element of this list is an object which exposes its properties (id, type,
position, velocity, force, etc.).
.. code-block:: python
# access first atom
L.atoms[0].id
L.atoms[0].type
# access second atom
L.atoms[1].position
L.atoms[1].velocity
L.atoms[1].force
Some properties can also be used to set:
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)
# set position in 3D simulation
L.atoms[0].position = (1.0, 0.0, 1.)
Evaluating thermo data
----------------------
Each simulation run usually produces thermo output based on system state,
computes, fixes or variables. The trajectories of these values can be queried
after a run via the L.runs list. This list contains a growing list of run data.
The first element is the output of the first run, the second element that of
the second run.
.. code-block:: python
L.run(1000)
L.runs[0] # data of first 1000 time steps
L.run(1000)
L.runs[1] # data of second 1000 time steps
Each run contains a dictionary of all trajectories. Each trajectory is
accessible through its thermo name:
.. code-block:: python
L.runs[0].thermo.Step # list of time steps in first run
L.runs[0].thermo.Ke # list of kinetic energy values in first run
Together with matplotlib plotting data out of LAMMPS becomes simple:
.. code-block:: python
import matplotlib.plot as plt
steps = L.runs[0].thermo.Step
ke = L.runs[0].thermo.Ke
plt.plot(steps, ke)
Error handling with PyLammps
----------------------------
Using C++ exceptions in LAMMPS for errors allows capturing them on the
C++ side and rethrowing them on the Python side. This way you can handle
LAMMPS errors through the Python exception handling mechanism.
.. warning::
Capturing a LAMMPS exception in Python can still mean that the
current LAMMPS process is in an illegal state and must be
terminated. It is advised to save your data and terminate the Python
instance as quickly as possible.
Using PyLammps in IPython notebooks and Jupyter
-----------------------------------------------
If the LAMMPS Python package is installed for the same Python interpreter as
IPython, you can use PyLammps directly inside of an IPython notebook inside of
Jupyter. Jupyter is a powerful integrated development environment (IDE) for
many dynamic languages like Python, Julia and others, which operates inside of
any web browser. Besides auto-completion and syntax highlighting it allows you
to create formatted documents using Markup, mathematical formulas, graphics and
animations intermixed with executable Python code. It is a great format for
tutorials and showcasing your latest research.
To launch an instance of Jupyter simply run the following command inside your
Python environment (this assumes you followed the Quick Start instructions):
.. code-block:: bash
jupyter notebook
IPyLammps Examples
------------------
Examples of IPython notebooks can be found in the python/examples/pylammps
subdirectory. To open these notebooks launch *jupyter notebook* inside this
directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.
Validating a dihedral potential
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
This example showcases how an IPython Notebook can be used to compare a simple
LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
Four atoms are placed in the simulation and the dihedral potential is applied on
them using a datafile. Then one of the atoms is rotated along the central axis by
setting its position from Python, which changes the dihedral angle.
.. code-block:: python
phi = [d \* math.pi / 180 for d in range(360)]
pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]
pe = []
for p in pos:
L.atoms[3].position = p
L.run(0)
pe.append(L.eval("pe"))
By evaluating the potential energy for each position we can verify that
trajectory with the analytical formula. To compare both solutions, we plot
both trajectories over each other using matplotlib, which embeds the generated
plot inside the IPython notebook.
.. image:: JPG/pylammps_dihedral.jpg
:align: center
Running a Monte Carlo relaxation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation
simulation, computing and plotting energy terms and even embedding video output.
Initially, a 2D system is created in a state with minimal energy.
.. image:: JPG/pylammps_mc_minimum.jpg
:align: center
It is then disordered by moving each atom by a random delta.
.. code-block:: python
random.seed(27848)
deltaperturb = 0.2
for i in range(L.system.natoms):
x, y = L.atoms[i].position
dx = deltaperturb \* random.uniform(-1, 1)
dy = deltaperturb \* random.uniform(-1, 1)
L.atoms[i].position = (x+dx, y+dy)
L.run(0)
.. image:: JPG/pylammps_mc_disordered.jpg
:align: center
Finally, the Monte Carlo algorithm is implemented in Python. It continuously
moves random atoms by a random delta and only accepts certain moves.
.. code-block:: python
estart = L.eval("pe")
elast = estart
naccept = 0
energies = [estart]
niterations = 3000
deltamove = 0.1
kT = 0.05
natoms = L.system.natoms
for i in range(niterations):
iatom = random.randrange(0, natoms)
current_atom = L.atoms[iatom]
x0, y0 = current_atom.position
dx = deltamove \* random.uniform(-1, 1)
dy = deltamove \* random.uniform(-1, 1)
current_atom.position = (x0+dx, y0+dy)
L.run(1, "pre no post no")
e = L.eval("pe")
energies.append(e)
if e <= elast:
naccept += 1
elast = e
elif random.random() <= math.exp(natoms\*(elast-e)/kT):
naccept += 1
elast = e
else:
current_atom.position = (x0, y0)
The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
.. image:: JPG/pylammps_mc_energies_plot.jpg
:align: center
The IPython notebook also shows how to use dump commands and embed video files
inside of the IPython notebook.
Using PyLammps and mpi4py (Experimental)
----------------------------------------
PyLammps can be run in parallel using `mpi4py
<https://mpi4py.readthedocs.io>`_. This python package can be installed
using
.. code-block:: bash
pip install mpi4py
.. warning::
Usually, any :py:class:`PyLammps <lammps.PyLammps>` command must be
executed by *all* MPI processes. However, evaluations and querying
the system state is only available on MPI rank 0. Using these
functions from other MPI ranks will raise an exception.
The following is a short example which reads in an existing LAMMPS input
file and executes it in parallel. You can find in.melt in the
examples/melt folder. Please take note that the
:py:meth:`PyLammps.eval() <lammps.PyLammps.eval>` is called only from
MPI rank 0.
.. code-block:: python
from mpi4py import MPI
from lammps import PyLammps
L = PyLammps()
L.file("in.melt")
if MPI.COMM_WORLD.rank == 0:
print("Potential energy: ", L.eval("pe"))
MPI.Finalize()
To run this script (melt.py) in parallel using 4 MPI processes we invoke the
following mpirun command:
.. code-block:: bash
mpirun -np 4 python melt.py
Feedback and Contributing
-------------------------
If you find this Python interface useful, please feel free to provide feedback
and ideas on how to improve it to Richard Berger (richard.berger@outlook.com). We also
want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
and maybe their latest research results.
The PyLammps interface is deprecated and will be removed in a future release of
LAMMPS. As such, the PyLammps version of this tutorial has been removed and is
replaced by the :doc:`Python_head`.

441
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@ -0,0 +1,441 @@
LAMMPS Python Tutorial
======================
.. contents::
-----
Overview
--------
The :py:class:`lammps <lammps.lammps>` Python module is a wrapper class for the
LAMMPS :ref:`C language library interface API <lammps_c_api>` which is written using
`Python ctypes <ctypes_>`_. The design choice of this wrapper class is to
follow the C language API closely with only small changes related to Python
specific requirements and to better accommodate object oriented programming.
In addition to this flat `ctypes <ctypes_>`_ interface, the
:py:class:`lammps <lammps.lammps>` wrapper class exposes a discoverable
API that doesn't require as much knowledge of the underlying C language
library interface or LAMMPS C++ code implementation.
Finally, the API exposes some additional features for `IPython integration
<ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for embedded
visualization output from :doc:`dump style image <dump_image>`.
.. _ctypes: https://docs.python.org/3/library/ctypes.html
.. _ipython: https://ipython.org/
.. _jupyter: https://jupyter.org/
-----
Quick Start
-----------
System-wide or User Installation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step 1: Building LAMMPS as a shared library
"""""""""""""""""""""""""""""""""""""""""""
To use LAMMPS inside of Python it has to be compiled as shared library.
This library is then loaded by the Python interface. In this example we
enable the :ref:`MOLECULE package <PKG-MOLECULE>` and compile LAMMPS
with :ref:`PNG, JPEG and FFMPEG output support <graphics>` enabled.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
mkdir $LAMMPS_DIR/build-shared
cd $LAMMPS_DIR/build-shared
# MPI, PNG, Jpeg, FFMPEG are auto-detected
cmake ../cmake -DPKG_MOLECULE=yes -DPKG_PYTHON=on -DBUILD_SHARED_LIBS=yes
make
.. tab:: Traditional make
.. code-block:: bash
cd $LAMMPS_DIR/src
# add packages if necessary
make yes-MOLECULE
make yes-PYTHON
# compile shared library using Makefile
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
Step 2: Installing the LAMMPS Python package
""""""""""""""""""""""""""""""""""""""""""""
Next install the LAMMPS Python package into your current Python installation with:
.. code-block:: bash
make install-python
This will create a so-called `"wheel"
<https://packaging.python.org/en/latest/discussions/package-formats/#what-is-a-wheel>`_
and then install the LAMMPS Python module from that "wheel" into either
into a system folder (provided the command is executed with root
privileges) or into your personal Python module folder.
.. note::
Recompiling the shared library requires re-installing the Python
package.
Installation inside of a virtual environment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can use virtual environments to create a custom Python environment
specifically tuned for your workflow.
Benefits of using a virtualenv
""""""""""""""""""""""""""""""
* isolation of your system Python installation from your development installation
* installation can happen in your user directory without root access (useful for HPC clusters)
* installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
* you can even install specific old versions of a package if necessary
**Prerequisite (e.g. on Ubuntu)**
.. code-block:: bash
apt-get install python-venv
Creating a virtualenv with lammps installed
"""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
# create virtual envrionment named 'testing'
python3 -m venv $HOME/python/testing
# activate 'testing' environment
source $HOME/python/testing/bin/activate
Now configure and compile the LAMMPS shared library as outlined above.
When using CMake and the shared library has already been build, you
need to re-run CMake to update the location of the python executable
to the location in the virtual environment with:
.. code-block:: bash
cmake . -DPython_EXECUTABLE=$(which python)
# install LAMMPS package in virtualenv
(testing) make install-python
# install other useful packages
(testing) pip install matplotlib jupyter mpi4py pandas
...
# return to original shell
(testing) deactivate
-------
Creating a new lammps instance
------------------------------
To create a lammps object you need to first import the class from the lammps
module. By using the default constructor, a new :py:class:`lammps
<lammps.lammps>` instance is created.
.. code-block:: python
from lammps import lammps
L = lammps()
See the :doc:`LAMMPS Python documentation <Python_create>` for how to customize
the instance creation with optional arguments.
-----
Commands
--------
Sending a LAMMPS command with the library interface is done using
the ``command`` method of the lammps object.
For instance, let's take the following LAMMPS command:
.. code-block:: LAMMPS
region box block 0 10 0 5 -0.5 0.5
This command can be executed with the following Python code if ``L`` is a ``lammps``
instance:
.. code-block:: python
L.command("region box block 0 10 0 5 -0.5 0.5")
For convenience, the ``lammps`` class also provides a command wrapper ``cmd``
that turns any LAMMPS command into a regular function call:
.. code-block:: python
L.cmd.region("box block", 0, 10, 0, 5, -0.5, 0.5)
Note that each parameter is set as Python number literal. With
the wrapper each command takes an arbitrary parameter list and transparently
merges it to a single command string, separating individual parameters by
white-space.
The benefit of this approach is avoiding redundant command calls and easier
parameterization. With the ``command`` function each call needs to be assembled
manually using formatted strings.
.. code-block:: python
L.command(f"region box block {xlo} {xhi} {ylo} {yhi} {zlo} {zhi}")
The wrapper accepts parameters directly and will convert
them automatically to a final command string.
.. code-block:: python
L.cmd.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
.. note::
When running in IPython you can use Tab-completion after ``L.cmd.`` to see
all available LAMMPS commands.
-----
Accessing atom data
-------------------
All per-atom properties that are part of the :doc:`atom style
<atom_style>` in the current simulation can be accessed using the
:py:meth:`extract_atoms() <lammps.lammps.extract_atoms()>` method. This
can be retrieved as ctypes objects or as NumPy arrays through the
lammps.numpy module. Those represent the *local* atoms of the
individual sub-domain for the current MPI process and may contain
information for the local ghost atoms or not depending on the property.
Both can be accessed as lists, but for the ctypes list object the size
is not known and hast to be retrieved first to avoid out-of-bounds
accesses.
.. code-block:: python
nlocal = L.extract_setting("nlocal")
nall = L.extract_setting("nall")
print("Number of local atoms ", nlocal, " Number of local and ghost atoms ", nall);
# access via ctypes directly
atom_id = L.extract_atom("id")
print("Atom IDs", atom_id[0:nlocal])
# access through numpy wrapper
atom_type = L.numpy.extract_atom("type")
print("Atom types", atom_type)
x = L.numpy.extract_atom("x")
v = L.numpy.extract_atom("v")
print("positions array shape", x.shape)
print("velocity array shape", v.shape)
# turn on communicating velocities to ghost atoms
L.cmd.comm_modify("vel", "yes")
v = L.numpy.extract_atom('v')
print("velocity array shape", v.shape)
Some properties can also be set from Python since internally the
data of the C++ code is accessed directly:
.. code-block:: python
# set position in 2D simulation
x[0] = (1.0, 0.0)
# set position in 3D simulation
x[0] = (1.0, 0.0, 1.)
------
Retrieving the values of thermodynamic data and variables
---------------------------------------------------------
To access thermodynamic data from the last completed timestep,
you can use the :py:meth:`get_thermo() <lammps.lammps.get_thermo>`
method, and to extract the value of (compatible) variables, you
can use the :py:meth:`extract_variable() <lammps.lammps.extract_variable>`
method.
.. code-block:: python
result = L.get_thermo("ke") # kinetic energy
result = L.get_thermo("pe") # potential energy
result = L.extract_variable("t") / 2.0
Error handling
--------------
We are using C++ exceptions in LAMMPS for errors and the C language
library interface captures and records them. This allows checking
whether errors have happened in Python during a call into LAMMPS and
then re-throw the error as a Python exception. This way you can handle
LAMMPS errors in the conventional way through the Python exception
handling mechanism.
.. warning::
Capturing a LAMMPS exception in Python can still mean that the
current LAMMPS process is in an illegal state and must be
terminated. It is advised to save your data and terminate the Python
instance as quickly as possible.
Using LAMMPS in IPython notebooks and Jupyter
---------------------------------------------
If the LAMMPS Python package is installed for the same Python
interpreter as IPython, you can use LAMMPS directly inside of an IPython
notebook inside of Jupyter. Jupyter is a powerful integrated development
environment (IDE) for many dynamic languages like Python, Julia and
others, which operates inside of any web browser. Besides
auto-completion and syntax highlighting it allows you to create
formatted documents using Markup, mathematical formulas, graphics and
animations intermixed with executable Python code. It is a great format
for tutorials and showcasing your latest research.
To launch an instance of Jupyter simply run the following command inside your
Python environment (this assumes you followed the Quick Start instructions):
.. code-block:: bash
jupyter notebook
Interactive Python Examples
---------------------------
Examples of IPython notebooks can be found in the ``python/examples/ipython``
subdirectory. To open these notebooks launch ``jupyter notebook`` inside this
directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.
Validating a dihedral potential
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
This example showcases how an IPython Notebook can be used to compare a simple
LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
Four atoms are placed in the simulation and the dihedral potential is applied on
them using a datafile. Then one of the atoms is rotated along the central axis by
setting its position from Python, which changes the dihedral angle.
.. code-block:: python
phi = [d \* math.pi / 180 for d in range(360)]
pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]
x = L.numpy.extract_atom("x")
pe = []
for p in pos:
x[3] = p
L.cmd.run(0, "post", "no")
pe.append(L.get_thermo("pe"))
By evaluating the potential energy for each position we can verify that
trajectory with the analytical formula. To compare both solutions, we plot
both trajectories over each other using matplotlib, which embeds the generated
plot inside the IPython notebook.
.. image:: JPG/pylammps_dihedral.jpg
:align: center
Running a Monte Carlo relaxation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
This second example shows how to use the `lammps` Python interface to create a
2D Monte Carlo Relaxation simulation, computing and plotting energy terms and
even embedding video output.
Initially, a 2D system is created in a state with minimal energy.
.. image:: JPG/pylammps_mc_minimum.jpg
:align: center
It is then disordered by moving each atom by a random delta.
.. code-block:: python
random.seed(27848)
deltaperturb = 0.2
x = L.numpy.extract_atom("x")
natoms = x.shape[0]
for i in range(natoms):
dx = deltaperturb \* random.uniform(-1, 1)
dy = deltaperturb \* random.uniform(-1, 1)
x[i][0] += dx
x[i][1] += dy
L.cmd.run(0, "post", "no")
.. image:: JPG/pylammps_mc_disordered.jpg
:align: center
Finally, the Monte Carlo algorithm is implemented in Python. It continuously
moves random atoms by a random delta and only accepts certain moves.
.. code-block:: python
estart = L.get_thermo("pe")
elast = estart
naccept = 0
energies = [estart]
niterations = 3000
deltamove = 0.1
kT = 0.05
for i in range(niterations):
x = L.numpy.extract_atom("x")
natoms = x.shape[0]
iatom = random.randrange(0, natoms)
current_atom = x[iatom]
x0 = current_atom[0]
y0 = current_atom[1]
dx = deltamove \* random.uniform(-1, 1)
dy = deltamove \* random.uniform(-1, 1)
current_atom[0] = x0 + dx
current_atom[1] = y0 + dy
L.cmd.run(1, "pre no post no")
e = L.get_thermo("pe")
energies.append(e)
if e <= elast:
naccept += 1
elast = e
elif random.random() <= math.exp(natoms\*(elast-e)/kT):
naccept += 1
elast = e
else:
current_atom[0] = x0
current_atom[1] = y0
The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
.. image:: JPG/pylammps_mc_energies_plot.jpg
:align: center
The IPython notebook also shows how to use dump commands and embed video files
inside of the IPython notebook.

17
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@ -15,8 +15,9 @@ details of the system, or develop new capabilities. For instance, the numerics
associated with calculating gradients, reproducing kernels, etc. are separated
into distinct classes to simplify the development of new integration schemes
which can call these calculations. Additional numerical details can be found in
:ref:`(Clemmer) <howto_rheo_clemmer>`. Example movies illustrating some of these
capabilities are found at https://www.lammps.org/movies.html#rheopackage.
:ref:`(Palermo) <howto_rheo_palermo>` and :ref:`(Clemmer) <howto_rheo_clemmer>`.
Example movies illustrating some of these capabilities are found at
https://www.lammps.org/movies.html#rheopackage.
Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
<PKG-SPH>` package is likely better suited for your application. It has fewer advanced
@ -70,7 +71,7 @@ particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
pair rheo/solid considers a particles fluid/solid phase to determine whether to
pair rheo/solid considers a particle's fluid/solid phase to determine whether to
apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
settings such that contact forces do not have to be calculated between two bonded
solid particles in the same elastic body.
@ -79,10 +80,10 @@ In systems with thermal evolution, fix rheo/thermal can optionally set a
melting/solidification temperature allowing particles to dynamically swap their
state between fluid and solid when the temperature exceeds or drops below the
critical temperature, respectively. Using the *react* option, one can specify a maximum
bond length and a bond type. Then, when solidifying, particles will search their
bond length and a bond type. Then, when solidifying, particles search their
local neighbors and automatically create bonds with any neighboring solid particles
in range. For BPM bond styles, bonds will then use the immediate position of the two
particles to calculate a reference state. When melting, particles will delete any
in range. For BPM bond styles, bonds then use the immediate position of the two
particles to calculate a reference state. When melting, particles delete any
bonds of the specified type when reverting to a fluid state. Special bonds are updated
as bonds are created/broken.
@ -107,6 +108,10 @@ criteria for creating/deleting a bond or altering force calculations).
----------
.. _howto_rheo_palermo:
**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, Phys. Fluids, 36, 113337 (2024).
.. _howto_rheo_clemmer:
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

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@ -260,7 +260,7 @@ Switch into the :code:`examples/melt` folder:
cd ../examples/melt
To run this example in serial, use the following command line:
To run this example in serial, use the following command:
.. code-block::

2
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@ -60,7 +60,7 @@ between them at any time using "git checkout <branch name>".)
files (mostly by accident). If you do not need access to the entire
commit history (most people don't), you can speed up the "cloning"
process and reduce local disk space requirements by using the
``--depth`` git command line flag. That will create a "shallow clone"
``--depth`` git command-line flag. That will create a "shallow clone"
of the repository, which contains only a subset of the git history.
Using a depth of 1000 is usually sufficient to include the head
commits of the *develop*, the *release*, and the *maintenance*

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@ -8,6 +8,8 @@ send an email to all of them at this address: "developers at
lammps.org". General questions about LAMMPS should be posted in the
`LAMMPS forum on MatSci <https://matsci.org/lammps/>`_.
.. We need to keep this file in sync with https://www.lammps.org/authors.html
.. raw:: latex
\small
@ -27,7 +29,7 @@ lammps.org". General questions about LAMMPS should be posted in the
* - `Steve Plimpton <sjp_>`_
- SNL (retired)
- sjplimp at gmail.com
- MD kernels, parallel algorithms & scalability, code structure and design
- original author, MD kernels, parallel algorithms & scalability, code structure and design
* - `Aidan Thompson <at_>`_
- SNL
- athomps at sandia.gov

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@ -131,16 +131,15 @@ run LAMMPS in serial mode.
.. _lammps_python_api:
LAMMPS Python APIs
==================
LAMMPS Python API
=================
The LAMMPS Python module enables calling the LAMMPS C library API from
Python by dynamically loading functions in the LAMMPS shared library through
the `Python ctypes module <https://docs.python.org/3/library/ctypes.html>`_.
Because of the dynamic loading, it is **required** that LAMMPS is compiled
in :ref:`"shared" mode <exe>`. The Python interface is object-oriented, but
otherwise tries to be very similar to the C library API. Three different
Python classes to run LAMMPS are available and they build on each other.
otherwise tries to be very similar to the C library API.
More information on this is in the :doc:`Python_head`
section of the manual. Use of the LAMMPS Python module is described in
:doc:`Python_module`.

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doc/src/Library_execute.rst
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@ -7,6 +7,7 @@ This section documents the following functions:
- :cpp:func:`lammps_command`
- :cpp:func:`lammps_commands_list`
- :cpp:func:`lammps_commands_string`
- :cpp:func:`lammps_expand`
--------------------
@ -79,3 +80,8 @@ Below is a short example using some of these functions.
.. doxygenfunction:: lammps_commands_string
:project: progguide
-----------------------
.. doxygenfunction:: lammps_expand
:project: progguide

10
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@ -1,5 +1,5 @@
Compute, fixes, variables
=========================
Computes, fixes, variables
==========================
This section documents accessing or modifying data stored by computes,
fixes, or variables in LAMMPS using the following functions:
@ -12,6 +12,7 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_set_string_variable`
- :cpp:func:`lammps_set_internal_variable`
- :cpp:func:`lammps_variable_info`
- :cpp:func:`lammps_eval`
-----------------------
@ -55,6 +56,11 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_eval
:project: progguide
-----------------------
.. doxygenenum:: _LMP_DATATYPE_CONST
.. doxygenenum:: _LMP_STYLE_CONST

17
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@ -208,20 +208,21 @@ Build system (strict)
LAMMPS currently supports two build systems: one that is based on
:doc:`traditional Makefiles <Build_make>` and one that is based on
:doc:`CMake <Build_cmake>`. Therefore, your contribution must be
compatible with and support both build systems.
:doc:`CMake <Build_cmake>`. As of fall 2024, it is no longer required
to support the traditional make build system. New packages may choose
to only support building with CMake. Additions to existing packages
must follow the requirements set by that package.
For a single pair of header and implementation files that are an
independent feature, it is usually only required to add them to
``src/.gitignore``.
For traditional make, if your contributed files or package depend on
other LAMMPS style files or packages also being installed
(e.g. because your file is a derived class from the other LAMMPS
class), then an ``Install.sh`` file is also needed to check for those
dependencies and modifications to ``src/Depend.sh`` to trigger the checks.
See other README and Install.sh files in other directories as
examples.
other LAMMPS style files or packages also being installed (e.g. because
your file is a derived class from the other LAMMPS class), then an
``Install.sh`` file is also needed to check for those dependencies and
modifications to ``src/Depend.sh`` to trigger the checks. See other
README and Install.sh files in other directories as examples.
Similarly, for CMake support, changes may need to be made to
``cmake/CMakeLists.txt``, some of the files in ``cmake/presets``, and

2
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@ -46,7 +46,7 @@ Include files (varied)
but instead should be initialized either in the initializer list of
the constructor or explicitly assigned in the body of the constructor.
If the member variable is relevant to the functionality of a class
(for example when it stores a value from a command line argument), the
(for example when it stores a value from a command-line argument), the
member variable declaration is followed by a brief comment explaining
its purpose and what its values can be. Class members that are
pointers should always be initialized to ``nullptr`` in the

33
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@ -995,6 +995,7 @@ Additional pair styles that are less commonly used.
* ``src/EXTRA-PAIR``: filenames -> commands
* :doc:`pair_style <pair_style>`
* ``examples/PACKAGES/dispersion``
----------
@ -2197,8 +2198,8 @@ the :doc:`Build extras <Build_extras>` page.
* ``src/OPENMP/README``
* :doc:`Accelerator packages <Speed_packages>`
* :doc:`OPENMP package <Speed_omp>`
* :doc:`Command line option -suffix/-sf omp <Run_options>`
* :doc:`Command line option -package/-pk omp <Run_options>`
* :doc:`Command-line option -suffix/-sf omp <Run_options>`
* :doc:`Command-line option -package/-pk omp <Run_options>`
* :doc:`package omp <package>`
* 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>`,
@ -2815,14 +2816,15 @@ implements smoothed particle hydrodynamics (SPH) for liquids. See the
related :ref:`MACHDYN package <PKG-MACHDYN>` package for smooth Mach dynamics
(SMD) for solids.
This package contains ideal gas, Lennard-Jones equation of states,
Tait, and full support for complete (i.e. internal-energy dependent)
equations of state. It allows for plain or Monaghans XSPH integration
of the equations of motion. It has options for density continuity or
density summation to propagate the density field. It has
:doc:`set <set>` command options to set the internal energy and density
of particles from the input script and allows the same quantities to
be output with thermodynamic output or to dump files via the :doc:`compute property/atom <compute_property_atom>` command.
This package contains ideal gas, Lennard-Jones equation of states, Tait,
and full support for complete (i.e. internal-energy dependent) equations
of state. It allows for plain or Monaghans XSPH integration of the
equations of motion. It has options for density continuity or density
summation to propagate the density field. It has :doc:`set <set>`
command options to set the internal energy and density of particles from
the input script and allows the same quantities to be output with
thermodynamic output or to dump files via the :doc:`compute
property/atom <compute_property_atom>` command.
**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
@ -2835,6 +2837,17 @@ Dynamics, Ernst Mach Institute, Germany).
* ``examples/PACKAGES/sph``
* https://www.lammps.org/movies.html#sph
.. note::
Please note that the SPH PDF guide file has not been updated for
many years and thus does not reflect the current *syntax* of the
SPH package commands. For that please refer to the LAMMPS manual.
.. note::
Please also note, that the :ref:`RHEO package <PKG-RHEO>` offers
similar functionality in a more modern and flexible implementation.
----------
.. _PKG-SPIN:

74
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@ -2,14 +2,8 @@ Per-atom properties
===================
Similar to what is described in :doc:`Library_atoms`, the instances of
:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`, or
:py:class:`IPyLammps <lammps.IPyLammps>` can be used to extract atom quantities
and modify some of them. The main difference between the interfaces is how the information
is exposed.
While the :py:class:`lammps <lammps.lammps>` is just a thin layer that wraps C API calls,
:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps <lammps.IPyLammps>` expose
information as objects and properties.
:py:class:`lammps <lammps.lammps>` can be used to extract atom quantities
and modify some of them.
In some cases the data returned is a direct reference to the original data
inside LAMMPS cast to ``ctypes`` pointers. Where possible, the wrappers will
@ -25,57 +19,41 @@ against invalid accesses.
accordingly. These arrays can change sizes and order at every neighbor list
rebuild and atom sort event as atoms are migrating between subdomains.
.. tabs::
.. code-block:: python
.. tab:: lammps API
from lammps import lammps
.. code-block:: python
lmp = lammps()
lmp.file("in.sysinit")
from lammps import lammps
lmp = lammps()
lmp.file("in.sysinit")
# Read/Write access via ctypes
nlocal = lmp.extract_global("nlocal")
x = lmp.extract_atom("x")
nlocal = lmp.extract_global("nlocal")
x = lmp.extract_atom("x")
for i in range(nlocal):
print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
for i in range(nlocal):
print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
# Read/Write access via NumPy arrays
atom_id = L.numpy.extract_atom("id")
atom_type = L.numpy.extract_atom("type")
x = L.numpy.extract_atom("x")
v = L.numpy.extract_atom("v")
f = L.numpy.extract_atom("f")
lmp.close()
# set position in 2D simulation
x[0] = (1.0, 0.0)
**Methods**:
# set position in 3D simulation
x[0] = (1.0, 0.0, 1.)
* :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
lmp.close()
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
**Methods**:
.. tab:: PyLammps/IPyLammps API
* :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
All atoms in the current simulation can be accessed by using the :py:attr:`PyLammps.atoms <lammps.PyLammps.atoms>` property.
Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
these objects provide access to their data (id, type, position, velocity, force, etc.):
.. code-block:: python
# access first atom
L.atoms[0].id
L.atoms[0].type
# access second atom
L.atoms[1].position
L.atoms[1].velocity
L.atoms[1].force
Some attributes can be changed:
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)
# set position in 3D simulation
L.atoms[0].position = (1.0, 0.0, 1.0)
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array

116
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@ -6,11 +6,10 @@ Creating or deleting a LAMMPS object
====================================
With the Python interface the creation of a :cpp:class:`LAMMPS
<LAMMPS_NS::LAMMPS>` instance is included in the constructors for the
:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`,
and :py:class:`IPyLammps <lammps.IPyLammps>` classes.
Internally it will call either :cpp:func:`lammps_open` or :cpp:func:`lammps_open_no_mpi` from the C
library API to create the class instance.
<LAMMPS_NS::LAMMPS>` instance is included in the constructor for the
:py:class:`lammps <lammps.lammps>` class. Internally it will call either
:cpp:func:`lammps_open` or :cpp:func:`lammps_open_no_mpi` from the C library
API to create the class instance.
All arguments are optional. The *name* argument allows loading a
LAMMPS shared library that is named ``liblammps_machine.so`` instead of
@ -26,108 +25,25 @@ to run the Python module like the library interface on a subset of the
MPI ranks after splitting the communicator.
Here are simple examples using all three Python interfaces:
Here is a simple example using the LAMMPS Python interface:
.. tabs::
.. code-block:: python
.. tab:: lammps API
from lammps import lammps
.. code-block:: python
# NOTE: argv[0] is set by the lammps class constructor
args = ["-log", "none"]
from lammps import lammps
# create LAMMPS instance
lmp = lammps(cmdargs=args)
# NOTE: argv[0] is set by the lammps class constructor
args = ["-log", "none"]
# get and print numerical version code
print("LAMMPS Version: ", lmp.version())
# create LAMMPS instance
lmp = lammps(cmdargs=args)
# explicitly close and delete LAMMPS instance (optional)
lmp.close()
# get and print numerical version code
print("LAMMPS Version: ", lmp.version())
# explicitly close and delete LAMMPS instance (optional)
lmp.close()
.. tab:: PyLammps API
The :py:class:`PyLammps <lammps.PyLammps>` class is a wrapper around the
:py:class:`lammps <lammps.lammps>` class and all of its lower level functions.
By default, it will create a new instance of :py:class:`lammps <lammps.lammps>` passing
along all arguments to the constructor of :py:class:`lammps <lammps.lammps>`.
.. code-block:: python
from lammps import PyLammps
# NOTE: argv[0] is set by the lammps class constructor
args = ["-log", "none"]
# create LAMMPS instance
L = PyLammps(cmdargs=args)
# get and print numerical version code
print("LAMMPS Version: ", L.version())
# explicitly close and delete LAMMPS instance (optional)
L.close()
:py:class:`PyLammps <lammps.PyLammps>` objects can also be created on top of an existing
:py:class:`lammps <lammps.lammps>` object:
.. code-block:: python
from lammps import lammps, PyLammps
...
# create LAMMPS instance
lmp = lammps(cmdargs=args)
# create PyLammps instance using previously created LAMMPS instance
L = PyLammps(ptr=lmp)
This is useful if you have to create the :py:class:`lammps <lammps.lammps>`
instance is a specific way, but want to take advantage of the
:py:class:`PyLammps <lammps.PyLammps>` interface.
.. tab:: IPyLammps API
The :py:class:`IPyLammps <lammps.IPyLammps>` class is an extension of the
:py:class:`PyLammps <lammps.PyLammps>` class. It has the same construction behavior. By
default, it will create a new instance of :py:class:`lammps` passing
along all arguments to the constructor of :py:class:`lammps`.
.. code-block:: python
from lammps import IPyLammps
# NOTE: argv[0] is set by the lammps class constructor
args = ["-log", "none"]
# create LAMMPS instance
L = IPyLammps(cmdargs=args)
# get and print numerical version code
print("LAMMPS Version: ", L.version())
# explicitly close and delete LAMMPS instance (optional)
L.close()
You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object:
.. code-block:: python
from lammps import lammps, IPyLammps
...
# create LAMMPS instance
lmp = lammps(cmdargs=args)
# create PyLammps instance using previously created LAMMPS instance
L = PyLammps(ptr=lmp)
This is useful if you have to create the :py:class:`lammps <lammps.lammps>`
instance is a specific way, but want to take advantage of the
:py:class:`IPyLammps <lammps.IPyLammps>` interface.
In all of the above cases, same as with the :ref:`C library API <lammps_c_api>`, this will use the
Same as with the :ref:`C library API <lammps_c_api>`, this will use the
``MPI_COMM_WORLD`` communicator for the MPI library that LAMMPS was
compiled with.

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@ -1,127 +1,123 @@
Executing commands
==================
Once an instance of the :py:class:`lammps <lammps.lammps>`,
:py:class:`PyLammps <lammps.PyLammps>`, or
:py:class:`IPyLammps <lammps.IPyLammps>` class is created, there are
Once an instance of the :py:class:`lammps <lammps.lammps>` class is created, there are
multiple ways to "feed" it commands. In a way that is not very different from
running a LAMMPS input script, except that Python has many more facilities
for structured programming than the LAMMPS input script syntax. Furthermore
it is possible to "compute" what the next LAMMPS command should be.
.. tabs::
Same as in the equivalent :doc:`C library functions <Library_execute>`,
commands can be read from a file, a single string, a list of strings and a
block of commands in a single multi-line string. They are processed under the
same boundary conditions as the C library counterparts. The example below
demonstrates the use of :py:func:`lammps.file()`, :py:func:`lammps.command()`,
:py:func:`lammps.commands_list()`, and :py:func:`lammps.commands_string()`:
.. tab:: lammps API
.. code-block:: python
Same as in the equivalent
:doc:`C library functions <Library_execute>`, commands can be read from a file, a
single string, a list of strings and a block of commands in a single
multi-line string. They are processed under the same boundary conditions
as the C library counterparts. The example below demonstrates the use
of :py:func:`lammps.file()`, :py:func:`lammps.command()`,
:py:func:`lammps.commands_list()`, and :py:func:`lammps.commands_string()`:
from lammps import lammps
lmp = lammps()
.. code-block:: python
# read commands from file 'in.melt'
lmp.file('in.melt')
from lammps import lammps
lmp = lammps()
# issue a single command
lmp.command('variable zpos index 1.0')
# read commands from file 'in.melt'
lmp.file('in.melt')
# create 10 groups with 10 atoms each
cmds = [f"group g{i} id {10*i+1}:{10*(i+1)}" for i in range(10)]
lmp.commands_list(cmds)
# issue a single command
lmp.command('variable zpos index 1.0')
# run commands from a multi-line string
block = """
clear
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 single 1.0 1.0 ${zpos}
"""
lmp.commands_string(block)
# create 10 groups with 10 atoms each
cmds = ["group g{} id {}:{}".format(i,10*i+1,10*(i+1)) for i in range(10)]
lmp.commands_list(cmds)
For convenience, the :py:class:`lammps <lammps.lammps>` class also provides a
command wrapper ``cmd`` that turns any LAMMPS command into a regular function
call.
# run commands from a multi-line string
block = """
clear
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 single 1.0 1.0 ${zpos}
"""
lmp.commands_string(block)
For instance, the following LAMMPS command
.. tab:: PyLammps/IPyLammps API
.. code-block:: LAMMPS
Unlike the lammps API, the PyLammps/IPyLammps APIs allow running LAMMPS
commands by calling equivalent member functions of :py:class:`PyLammps <lammps.PyLammps>`
and :py:class:`IPyLammps <lammps.IPyLammps>` instances.
region box block 0 10 0 5 -0.5 0.5
For instance, the following LAMMPS command
would normally be executed with the following Python code:
.. code-block:: LAMMPS
.. code-block:: python
region box block 0 10 0 5 -0.5 0.5
from lammps import lammps
can be executed using with the lammps API with the following Python code if ``lmp`` is an
instance of :py:class:`lammps <lammps.lammps>`:
lmp = lammps()
lmp.command("region box block 0 10 0 5 -0.5 0.5")
.. code-block:: python
With the ``cmd`` wrapper, any LAMMPS command can be split up into arbitrary parts.
These parts are then passed to a member function with the name of the :doc:`command <Commands_all>`.
For the :doc:`region <region>` command that means the :code:`region()` method can be called.
The arguments of the command can be passed as one string, or
individually.
from lammps import lammps
.. code-block:: python
lmp = lammps()
lmp.command("region box block 0 10 0 5 -0.5 0.5")
from lammps import lammps
With the PyLammps interface, any LAMMPS command can be split up into arbitrary parts.
These parts are then passed to a member function with the name of the :doc:`command <Commands_all>`.
For the :doc:`region <region>` command that means the :code:`region()` method can be called.
The arguments of the command can be passed as one string, or
individually.
L = lammps()
.. code-block:: python
# pass command parameters as one string
L.cmd.region("box block 0 10 0 5 -0.5 0.5")
from lammps import PyLammps
# OR pass them individually
L.cmd.region("box block", 0, 10, 0, 5, -0.5, 0.5)
L = PyLammps()
In the latter example, all parameters except the first are Python floating-point literals. The
member function takes the entire parameter list and transparently merges it to a single command
string.
# pass command parameters as one string
L.region("box block 0 10 0 5 -0.5 0.5")
The benefit of this approach is avoiding redundant command calls and easier
parameterization. With `command`, `commands_list`, and `commands_string` the
parameterization needed to be done manually by creating formatted command
strings.
# OR pass them individually
L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
.. code-block:: python
In the latter example, all parameters except the first are Python floating-point literals. The
member function takes the entire parameter list and transparently merges it to a single command
string.
lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the lammps API parameterization needed to be done
manually by creating formatted command strings.
In contrast, methods of the `cmd` wrapper accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: python
.. code-block:: python
lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
L.cmd.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. note::
.. code-block:: python
When running in IPython you can use Tab-completion after ``L.cmd.`` to see
all available LAMMPS commands.
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
Using these facilities, the previous example shown above can be rewritten as follows:
Using these facilities, the example shown for the lammps API can be rewritten as follows:
.. code-block:: python
.. code-block:: python
from lammps import lammps
L = lammps()
from lammps import PyLammps
L = PyLammps()
# read commands from file 'in.melt'
L.file('in.melt')
# read commands from file 'in.melt'
L.file('in.melt')
# issue a single command
L.cmd.variable('zpos', 'index', 1.0)
# issue a single command
L.variable('zpos', 'index', 1.0)
# create 10 groups with 10 atoms each
for i in range(10):
L.cmd.group(f"g{i}", "id", f"{10*i+1}:{10*(i+1)}")
# create 10 groups with 10 atoms each
for i in range(10):
L.group(f"g{i}", "id", f"{10*i+1}:{10*(i+1)}")
L.clear()
L.region("box block", 0, 2, 0, 2, 0, 2)
L.create_box(1, "box")
L.create_atoms(1, "single", 1.0, 1.0, "${zpos}")
L.cmd.clear()
L.cmd.region("box block", 0, 2, 0, 2, 0, 2)
L.cmd.create_box(1, "box")
L.cmd.create_atoms(1, "single", 1.0, 1.0, "${zpos}")

1
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@ -15,6 +15,7 @@ together.
Python_call
Python_formats
Python_examples
Python_jupyter
Python_error
Python_trouble

45
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@ -0,0 +1,45 @@
Using LAMMPS in IPython notebooks and Jupyter
=============================================
If the LAMMPS Python package is installed for the same Python interpreter as
`IPython <ipython>`_, you can use LAMMPS directly inside of an IPython notebook inside of
Jupyter. `Jupyter <juypter>`_ is a powerful integrated development environment (IDE) for
many dynamic languages like Python, Julia and others, which operates inside of
any web browser. Besides auto-completion and syntax highlighting it allows you
to create formatted documents using Markup, mathematical formulas, graphics and
animations intermixed with executable Python code. It is a great format for
tutorials and showcasing your latest research.
The easiest way to install it is via ``pip``:
.. code-block:: bash
pip install --user jupyter
To launch an instance of Jupyter simply run the following command inside your
Python environment:
.. code-block:: bash
jupyter notebook
Interactive Python Examples
---------------------------
Examples of IPython notebooks can be found in the ``python/examples/ipython``
subdirectory. They require LAMMPS to be compiled as shared library with PYTHON,
PNG, JPEG and FFMPEG support.
To open these notebooks launch ``jupyter notebook index.ipynb`` inside this
directory. The opened file provides an overview of the available examples.
- Example 1: Using LAMMPS with Python (``simple.ipynb``)
- Example 2: Analyzing LAMMPS thermodynamic data (``thermo.ipynb``)
- Example 3: Working with Per-Atom Data (``atoms.ipynb``)
- Example 4: Working with LAMMPS variables (``variables.ipynb``)
- Example 5: Validating a dihedral potential (``dihedrals/dihedral.ipynb``)
- Example 6: Running a Monte Carlo relaxation (``montecarlo/mc.ipynb``)
.. note::
Typically clicking a link in Jupyter will open a new tab, which might be blocked by your pop-up blocker.

53
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@ -10,19 +10,11 @@ be installed into a Python system folder or a user folder with ``make
install-python``. Components of the module can then loaded into a Python
session with the ``import`` command.
There are multiple Python interface classes in the :py:mod:`lammps` module:
.. warning::
- the :py:class:`lammps <lammps.lammps>` class. This is a wrapper around
the C-library interface and its member functions try to replicate the
:ref:`C-library API <lammps_c_api>` closely. This is the most
feature-complete Python API.
- the :py:class:`PyLammps <lammps.PyLammps>` class. This is a more high-level
and more Python style class implemented on top of the
:py:class:`lammps <lammps.lammps>` class.
- the :py:class:`IPyLammps <lammps.IPyLammps>` class is derived from
:py:class:`PyLammps <lammps.PyLammps>` and adds embedded graphics
features to conveniently include LAMMPS into `Jupyter
<https://jupyter.org/>`_ notebooks.
Alternative interfaces such as :py:class:`PyLammps <lammps.PyLammps>` and
:py:class:`IPyLammps <lammps.IPyLammps>` classes have been deprecated and
will be removed in a future version of LAMMPS.
.. _mpi4py_url: https://mpi4py.readthedocs.io
@ -49,7 +41,7 @@ The ``lammps`` class API
========================
The :py:class:`lammps <lammps.lammps>` class is the core of the LAMMPS
Python interfaces. It is a wrapper around the :ref:`LAMMPS C library
Python interface. It is a wrapper around the :ref:`LAMMPS C library
API <lammps_c_api>` using the `Python ctypes module
<https://docs.python.org/3/library/ctypes.html>`_ and a shared library
compiled from the LAMMPS sources code. The individual methods in this
@ -64,40 +56,7 @@ functions. Below is a detailed documentation of the API.
.. autoclass:: lammps.numpy_wrapper::numpy_wrapper
:members:
----------
The ``PyLammps`` class API
==========================
The :py:class:`PyLammps <lammps.PyLammps>` class is a wrapper that creates a
simpler, more "Pythonic" interface to common LAMMPS functionality. LAMMPS
data structures are exposed through objects and properties. This makes Python
scripts shorter and more concise. See the :doc:`PyLammps Tutorial
<Howto_pylammps>` for an introduction on how to use this interface.
.. autoclass:: lammps.PyLammps
:members:
.. autoclass:: lammps.AtomList
:members:
.. autoclass:: lammps.Atom
:members:
.. autoclass:: lammps.Atom2D
:members:
----------
The ``IPyLammps`` class API
===========================
The :py:class:`IPyLammps <lammps.PyLammps>` class is an extension of
:py:class:`PyLammps <lammps.PyLammps>`, adding additional functions to
quickly display visualizations such as images and videos inside of IPython.
See the :doc:`PyLammps Tutorial <Howto_pylammps>` for examples.
.. autoclass:: lammps.IPyLammps
.. autoclass:: lammps.ipython::wrapper
:members:
----------

123
doc/src/Python_objects.rst
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@ -4,95 +4,52 @@ Compute, fixes, variables
This section documents accessing or modifying data from objects like
computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
.. tabs::
For :py:meth:`lammps.extract_compute() <lammps.lammps.extract_compute()>` and
:py:meth:`lammps.extract_fix() <lammps.lammps.extract_fix()>`, the global, per-atom,
or local data calculated by the compute or fix can be accessed. What is returned
depends on whether the compute or fix calculates a scalar or vector or array.
For a scalar, a single double value is returned. If the compute or fix calculates
a vector or array, a pointer to the internal LAMMPS data is returned, which you can
use via normal Python subscripting.
.. tab:: lammps API
The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices.
See the :doc:`Howto output <Howto_output>` page for a discussion of
global, per-atom, and local data, and of scalar, vector, and array
data types. See the doc pages for individual :doc:`computes <compute>`
and :doc:`fixes <fix>` for a description of what they calculate and
store.
For :py:meth:`lammps.extract_compute() <lammps.lammps.extract_compute()>` and
:py:meth:`lammps.extract_fix() <lammps.lammps.extract_fix()>`, the global, per-atom,
or local data calculated by the compute or fix can be accessed. What is returned
depends on whether the compute or fix calculates a scalar or vector or array.
For a scalar, a single double value is returned. If the compute or fix calculates
a vector or array, a pointer to the internal LAMMPS data is returned, which you can
use via normal Python subscripting.
For :py:meth:`lammps.extract_variable() <lammps.lammps.extract_variable()>`,
an :doc:`equal-style or atom-style variable <variable>` is evaluated and
its result returned.
The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices.
See the :doc:`Howto output <Howto_output>` page for a discussion of
global, per-atom, and local data, and of scalar, vector, and array
data types. See the doc pages for individual :doc:`computes <compute>`
and :doc:`fixes <fix>` for a description of what they calculate and
store.
For equal-style variables a single ``c_double`` value is returned and the
group argument is ignored. For atom-style variables, a vector of
``c_double`` is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.
For :py:meth:`lammps.extract_variable() <lammps.lammps.extract_variable()>`,
an :doc:`equal-style or atom-style variable <variable>` is evaluated and
its result returned.
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
For equal-style variables a single ``c_double`` value is returned and the
group argument is ignored. For atom-style variables, a vector of
``c_double`` is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.
The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
existing string-style variable to a new string value, so that subsequent LAMMPS
commands can access the variable.
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
**Methods**:
The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
existing string-style variable to a new string value, so that subsequent LAMMPS
commands can access the variable.
* :py:meth:`lammps.extract_compute() <lammps.lammps.extract_compute()>`: extract value(s) from a compute
* :py:meth:`lammps.extract_fix() <lammps.lammps.extract_fix()>`: extract value(s) from a fix
* :py:meth:`lammps.extract_variable() <lammps.lammps.extract_variable()>`: extract value(s) from a variable
* :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>`: set existing named string-style variable to value
**Methods**:
**NumPy Methods**:
* :py:meth:`lammps.extract_compute() <lammps.lammps.extract_compute()>`: extract value(s) from a compute
* :py:meth:`lammps.extract_fix() <lammps.lammps.extract_fix()>`: extract value(s) from a fix
* :py:meth:`lammps.extract_variable() <lammps.lammps.extract_variable()>`: extract value(s) from a variable
* :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>`: set existing named string-style variable to value
**NumPy Methods**:
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
.. tab:: PyLammps/IPyLammps API
PyLammps and IPyLammps classes currently do not add any additional ways of
retrieving information out of computes and fixes. This information can still be accessed by using the lammps API:
.. code-block:: python
L.lmp.extract_compute(...)
L.lmp.extract_fix(...)
# OR
L.lmp.numpy.extract_compute(...)
L.lmp.numpy.extract_fix(...)
LAMMPS variables can be both defined and accessed via the :py:class:`PyLammps <lammps.PyLammps>` interface.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: python
L.variable("a index 2")
A dictionary of all variables is returned by the :py:attr:`PyLammps.variables <lammps.PyLammps.variables>` property:
you can access an individual variable by retrieving a variable object from the
``L.variables`` dictionary by name
.. code-block:: python
a = L.variables['a']
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: python
print(a.value)
a.value = 4
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays

19
doc/src/Python_overview.rst
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@ -56,7 +56,7 @@ Below is an example output for Python version 3.8.5.
---------
LAMMPS can work together with Python in three ways. First, Python can
LAMMPS can work together with Python in two ways. First, Python can
wrap LAMMPS through the its :doc:`library interface <Library>`, so
that a Python script can create one or more instances of LAMMPS and
launch one or more simulations. In Python terms, this is referred to as
@ -67,22 +67,7 @@ launch one or more simulations. In Python terms, this is referred to as
Launching LAMMPS via Python
Second, the lower-level Python interface in the :py:class:`lammps Python
class <lammps.lammps>` can be used indirectly through the provided
:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps
<lammps.IPyLammps>` wrapper classes, also written in Python. These
wrappers try to simplify the usage of LAMMPS in Python by providing a
more object-based interface to common LAMMPS functionality. They also
reduce the amount of code necessary to parameterize LAMMPS scripts
through Python and make variables and computes directly accessible.
.. figure:: JPG/pylammps-invoke-lammps.png
:figclass: align-center
Using the PyLammps / IPyLammps wrappers
Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
script or styles can invoke Python code directly, and pass information
back-and-forth between the input script and Python functions you write.
This Python code can also call back to LAMMPS to query or change its

135
doc/src/Python_properties.rst
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@ -2,14 +2,8 @@ System properties
=================
Similar to what is described in :doc:`Library_properties`, the instances of
:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`, or
:py:class:`IPyLammps <lammps.IPyLammps>` can be used to extract different kinds
of information about the active LAMMPS instance and also to modify some of it. The
main difference between the interfaces is how the information is exposed.
While the :py:class:`lammps <lammps.lammps>` is just a thin layer that wraps C API calls,
:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps <lammps.IPyLammps>` expose
information as objects and properties.
:py:class:`lammps <lammps.lammps>` can be used to extract different kinds
of information about the active LAMMPS instance and also to modify some of it.
In some cases the data returned is a direct reference to the original data
inside LAMMPS cast to ``ctypes`` pointers. Where possible, the wrappers will
@ -25,113 +19,38 @@ against invalid accesses.
accordingly. These arrays can change sizes and order at every neighbor list
rebuild and atom sort event as atoms are migrating between subdomains.
.. tabs::
.. code-block:: python
.. tab:: lammps API
from lammps import lammps
.. code-block:: python
lmp = lammps()
lmp.file("in.sysinit")
from lammps import lammps
natoms = lmp.get_natoms()
print(f"running simulation with {natoms} atoms")
lmp = lammps()
lmp.file("in.sysinit")
lmp.command("run 1000 post no");
natoms = lmp.get_natoms()
print(f"running simulation with {natoms} atoms")
for i in range(10):
lmp.command("run 100 pre no post no")
pe = lmp.get_thermo("pe")
ke = lmp.get_thermo("ke")
print(f"PE = {pe}\nKE = {ke}")
lmp.command("run 1000 post no");
lmp.close()
for i in range(10):
lmp.command("run 100 pre no post no")
pe = lmp.get_thermo("pe")
ke = lmp.get_thermo("ke")
print(f"PE = {pe}\nKE = {ke}")
**Methods**:
lmp.close()
* :py:meth:`version() <lammps.lammps.version()>`: return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
* :py:meth:`get_thermo() <lammps.lammps.get_thermo()>`: return current value of a thermo keyword
* :py:meth:`last_thermo() <lammps.lammps.last_thermo()>`: return a dictionary of the last thermodynamic output
* :py:meth:`get_natoms() <lammps.lammps.get_natoms()>`: total # of atoms as int
* :py:meth:`reset_box() <lammps.lammps.reset_box()>`: reset the simulation box size
* :py:meth:`extract_setting() <lammps.lammps.extract_setting()>`: return a global setting
* :py:meth:`extract_global() <lammps.lammps.extract_global()>`: extract a global quantity
* :py:meth:`extract_box() <lammps.lammps.extract_box()>`: extract box info
* :py:meth:`create_atoms() <lammps.lammps.create_atoms()>`: create N atoms with IDs, types, x, v, and image flags
**Methods**:
**Properties**:
* :py:meth:`version() <lammps.lammps.version()>`: return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
* :py:meth:`get_thermo() <lammps.lammps.get_thermo()>`: return current value of a thermo keyword
* :py:meth:`last_thermo() <lammps.lammps.last_thermo()>`: return a dictionary of the last thermodynamic output
* :py:meth:`get_natoms() <lammps.lammps.get_natoms()>`: total # of atoms as int
* :py:meth:`reset_box() <lammps.lammps.reset_box()>`: reset the simulation box size
* :py:meth:`extract_setting() <lammps.lammps.extract_setting()>`: return a global setting
* :py:meth:`extract_global() <lammps.lammps.extract_global()>`: extract a global quantity
* :py:meth:`extract_box() <lammps.lammps.extract_box()>`: extract box info
* :py:meth:`create_atoms() <lammps.lammps.create_atoms()>`: create N atoms with IDs, types, x, v, and image flags
**Properties**:
* :py:attr:`last_thermo_step <lammps.lammps.last_thermo_step>`: the last timestep thermodynamic output was computed
.. tab:: PyLammps/IPyLammps API
In addition to the functions provided by :py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>` objects
have several properties which allow you to query the system state:
L.system
Is a dictionary describing the system such as the bounding box or number of atoms
L.system.xlo, L.system.xhi
bounding box limits along x-axis
L.system.ylo, L.system.yhi
bounding box limits along y-axis
L.system.zlo, L.system.zhi
bounding box limits along z-axis
L.communication
configuration of communication subsystem, such as the number of threads or processors
L.communication.nthreads
number of threads used by each LAMMPS process
L.communication.nprocs
number of MPI processes used by LAMMPS
L.fixes
List of fixes in the current system
L.computes
List of active computes in the current system
L.dump
List of active dumps in the current system
L.groups
List of groups present in the current system
**Retrieving the value of an arbitrary LAMMPS expressions**
LAMMPS expressions can be immediately evaluated by using the ``eval`` method. The
passed string parameter can be any expression containing global :doc:`thermo` values,
variables, compute or fix data (see :doc:`Howto_output`):
.. code-block:: python
result = L.eval("ke") # kinetic energy
result = L.eval("pe") # potential energy
result = L.eval("v_t/2.0")
**Example**
.. code-block:: python
from lammps import PyLammps
L = PyLammps()
L.file("in.sysinit")
print(f"running simulation with {L.system.natoms} atoms")
L.run(1000, "post no");
for i in range(10):
L.run(100, "pre no post no")
pe = L.eval("pe")
ke = L.eval("ke")
print(f"PE = {pe}\nKE = {ke}")
* :py:attr:`last_thermo_step <lammps.lammps.last_thermo_step>`: the last timestep thermodynamic output was computed

6
doc/src/Run_basics.rst
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@ -1,8 +1,8 @@
Basics of running LAMMPS
========================
LAMMPS is run from the command line, reading commands from a file via
the ``-in`` command line flag, or from standard input. Using the ``-in
LAMMPS is run from the command-line, reading commands from a file via
the ``-in`` command-line flag, or from standard input. Using the ``-in
in.file`` variant is recommended (see note below). The name of the
LAMMPS executable is either ``lmp`` or ``lmp_<machine>`` with
`<machine>` being the machine string used when compiling LAMMPS. This
@ -25,7 +25,7 @@ build LAMMPS:
You normally run the LAMMPS command in the directory where your input
script is located. That is also where output files are produced by
default, unless you provide specific other paths in your input script or
on the command line. As in some of the examples above, the LAMMPS
on the command-line. As in some of the examples above, the LAMMPS
executable itself can be placed elsewhere.
.. note::

2
doc/src/Run_options.rst
View File

@ -632,7 +632,7 @@ the ``-package omp`` command-line switch or the :doc:`package omp <package>` com
The :doc:`suffix <suffix>` command can also be used within an input
script to set a suffix, or to turn off or back on any suffix setting
made via the command line.
made via the command-line.
----------

2
doc/src/Run_windows.rst
View File

@ -20,7 +20,7 @@ To run with 4 threads, you can type this:
lmp -in in.lj.lmp -k on t 4 -sf kk
Alternately, you can also install a package with LAMMPS-GUI included and
open the LAMMPS-GUI app (the package includes the command line version
open the LAMMPS-GUI app (the package includes the command-line version
of LAMMPS as well) and open the input file in the GUI and run it from
there. For details on LAMMPS-GUI, see :doc:`Howto_lammps_gui`.

41
doc/src/Speed_gpu.rst
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@ -31,7 +31,8 @@ Coulombics. It has the following general features:
(for Nvidia GPUs, AMD GPUs, Intel GPUs, and multicore CPUs).
so that the same functionality is supported on a variety of hardware.
**Required hardware/software:**
Required hardware/software
""""""""""""""""""""""""""
To compile and use this package in CUDA mode, you currently need
to have an NVIDIA GPU and install the corresponding NVIDIA CUDA
@ -69,12 +70,14 @@ To compile and use this package in HIP mode, you have to have the AMD ROCm
software installed. Versions of ROCm older than 3.5 are currently deprecated
by AMD.
**Building LAMMPS with the GPU package:**
Building LAMMPS with the GPU package
""""""""""""""""""""""""""""""""""""
See the :ref:`Build extras <gpu>` page for
instructions.
**Run with the GPU package from the command line:**
Run with the GPU package from the command-line
""""""""""""""""""""""""""""""""""""""""""""""
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI
@ -133,7 +136,8 @@ affect the setting for bonded interactions (LAMMPS default is "on").
The "off" setting for pairwise interaction is currently required for
GPU package pair styles.
**Or run with the GPU package by editing an input script:**
Run with the GPU package by editing an input script
"""""""""""""""""""""""""""""""""""""""""""""""""""
The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
tasks/node, and use of multiple MPI tasks/GPU is the same.
@ -149,7 +153,8 @@ You must also use the :doc:`package gpu <package>` command to enable the
GPU package, unless the ``-sf gpu`` or ``-pk gpu`` :doc:`command-line switches <Run_options>` were used. It specifies the number of
GPUs/node to use, as well as other options.
**Speed-ups to expect:**
Speed-up to expect
""""""""""""""""""
The performance of a GPU versus a multicore CPU is a function of your
hardware, which pair style is used, the number of atoms/GPU, and the
@ -176,10 +181,13 @@ better with multiple OMP threads because the inter-process communication
is higher for these styles with the GPU package in order to allow
deterministic results.
**Guidelines for best performance:**
Guidelines for best performance
"""""""""""""""""""""""""""""""
* Using multiple MPI tasks per GPU will often give the best performance,
as allowed my most multicore CPU/GPU configurations.
* Using multiple MPI tasks (2-10) per GPU will often give the best
performance, as allowed my most multicore CPU/GPU configurations.
Using too many MPI tasks will result in worse performance due to
growing overhead with the growing number of MPI tasks.
* If the number of particles per MPI task is small (e.g. 100s of
particles), it can be more efficient to run with fewer MPI tasks per
GPU, even if you do not use all the cores on the compute node.
@ -199,12 +207,13 @@ deterministic results.
:doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
:doc:`improper <improper_style>`, and :doc:`long-range <kspace_style>`
calculations will not be included in the "Pair" time.
* Since only part of the pppm kspace style is GPU accelerated, it
may be faster to only use GPU acceleration for Pair styles with
long-range electrostatics. See the "pair/only" keyword of the
package command for a shortcut to do that. The work between kspace
on the CPU and non-bonded interactions on the GPU can be balanced
through adjusting the coulomb cutoff without loss of accuracy.
* Since only part of the pppm kspace style is GPU accelerated, it may be
faster to only use GPU acceleration for Pair styles with long-range
electrostatics. See the "pair/only" keyword of the :doc:`package
command <package>` for a shortcut to do that. The distribution of
work between kspace on the CPU and non-bonded interactions on the GPU
can be balanced through adjusting the coulomb cutoff without loss of
accuracy.
* When the *mode* setting for the package gpu command is force/neigh,
the time for neighbor list calculations on the GPU will be added into
the "Pair" time, not the "Neigh" time. An additional breakdown of the
@ -220,4 +229,6 @@ deterministic results.
Restrictions
""""""""""""
None.
When using :doc:`hybrid pair styles <pair_hybrid>`, the neighbor list
must be generated on the host instead of the GPU and thus the potential
GPU acceleration is reduced.

42
doc/src/Speed_intel.rst
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@ -1,5 +1,5 @@
INTEL package
==================
=============
The INTEL package is maintained by Mike Brown at Intel
Corporation. It provides two methods for accelerating simulations,
@ -13,18 +13,18 @@ twice, once on the CPU and once with an offload flag. This allows
LAMMPS to run on the CPU cores and co-processor cores simultaneously.
Currently Available INTEL Styles
"""""""""""""""""""""""""""""""""""""
""""""""""""""""""""""""""""""""
* Angle Styles: charmm, harmonic
* Bond Styles: fene, fourier, harmonic
* Bond Styles: fene, harmonic
* Dihedral Styles: charmm, fourier, harmonic, opls
* Fixes: nve, npt, nvt, nvt/sllod, nve/asphere
* Fixes: nve, npt, nvt, nvt/sllod, nve/asphere, electrode/conp, electrode/conq, electrode/thermo
* Improper Styles: cvff, harmonic
* Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm,
lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long,
rebo, sw, tersoff
* K-Space Styles: pppm, pppm/disp
rebo, snap, sw, tersoff
* K-Space Styles: pppm, pppm/disp, pppm/electrode
.. warning::
@ -33,7 +33,7 @@ Currently Available INTEL Styles
input requires it, LAMMPS will abort with an error message.
Speed-up to expect
"""""""""""""""""""
""""""""""""""""""
The speedup will depend on your simulation, the hardware, which
styles are used, the number of atoms, and the floating-point
@ -312,21 +312,21 @@ almost all cases.
recommended, especially when running on a machine with Intel
Hyper-Threading technology disabled.
Run with the INTEL package from the command line
"""""""""""""""""""""""""""""""""""""""""""""""""""""
Run with the INTEL package from the command-line
""""""""""""""""""""""""""""""""""""""""""""""""
To enable INTEL optimizations for all available styles used in
the input script, the ``-sf intel`` :doc:`command-line switch <Run_options>` can be used without any requirement for
editing the input script. This switch will automatically append
"intel" to styles that support it. It also invokes a default command:
:doc:`package intel 1 <package>`. This package command is used to set
options for the INTEL package. The default package command will
specify that INTEL calculations are performed in mixed precision,
that the number of OpenMP threads is specified by the OMP_NUM_THREADS
environment variable, and that if co-processors are present and the
binary was built with offload support, that 1 co-processor per node
will be used with automatic balancing of work between the CPU and the
co-processor.
To enable INTEL optimizations for all available styles used in the input
script, the ``-sf intel`` :doc:`command-line switch <Run_options>` can
be used without any requirement for editing the input script. This
switch will automatically append "intel" to styles that support it. It
also invokes a default command: :doc:`package intel 1 <package>`. This
package command is used to set options for the INTEL package. The
default package command will specify that INTEL calculations are
performed in mixed precision, that the number of OpenMP threads is
specified by the OMP_NUM_THREADS environment variable, and that if
co-processors are present and the binary was built with offload support,
that 1 co-processor per node will be used with automatic balancing of
work between the CPU and the co-processor.
You can specify different options for the INTEL package by using
the ``-pk intel Nphi`` :doc:`command-line switch <Run_options>` with

8
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@ -77,7 +77,7 @@ version 23 November 2023 and Kokkos version 4.2.
rank. When running with multiple MPI ranks, you may see segmentation
faults without GPU-aware MPI support. These can be avoided by adding
the flags :doc:`-pk kokkos gpu/aware off <Run_options>` to the
LAMMPS command line or by using the command :doc:`package kokkos
LAMMPS command-line or by using the command :doc:`package kokkos
gpu/aware off <package>` in the input file.
.. admonition:: Intel Data Center GPU support
@ -423,7 +423,7 @@ in the ``kokkos-cuda.cmake`` CMake preset file.
cmake -DKokkos_ENABLE_CUDA=yes -DKokkos_ENABLE_OPENMP=yes ../cmake
The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
using the ``-sf kk`` in the command line gives the default CUDA version
using the ``-sf kk`` in the command-line gives the default CUDA version
everywhere. However, if the "/kk/host" suffix is added to a specific
style in the input script, the Kokkos OpenMP (CPU) version of that
specific style will be used instead. Set the number of OpenMP threads
@ -439,7 +439,7 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then:
mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk
Conversely, if the ``-sf kk/host`` is used in the command line and then
Conversely, if the ``-sf kk/host`` is used in the command-line and then
the "/kk" or "/kk/device" suffix is added to a specific style in your
input script, then only that specific style will run on the GPU while
everything else will run on the CPU in OpenMP mode. Note that the
@ -451,7 +451,7 @@ on the host CPU can overlap with a pair style running on the
GPU. First compile with ``--default-stream per-thread`` added to ``CCFLAGS``
in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host"
suffix for kspace and bonds, angles, etc. in the input file and the
"kk" suffix (equal to "kk/device") on the command line. Also make
"kk" suffix (equal to "kk/device") on the command-line. Also make
sure the environment variable ``CUDA_LAUNCH_BLOCKING`` is not set to "1"
so CPU/GPU overlap can occur.

2
doc/src/Speed_omp.rst
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@ -21,7 +21,7 @@ Building LAMMPS with the OPENMP package
See the :ref:`Build extras <openmp>` page for
instructions.
Run with the OPENMP package from the command line
Run with the OPENMP package from the command-line
"""""""""""""""""""""""""""""""""""""""""""""""""""
These examples assume one or more 16-core nodes.

2
doc/src/Speed_opt.rst
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@ -17,7 +17,7 @@ Building LAMMPS with the OPT package
See the :ref:`Build extras <opt>` page for instructions.
Run with the OPT package from the command line
Run with the OPT package from the command-line
""""""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash

14
doc/src/Tools.rst
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@ -501,7 +501,7 @@ Here are a few highlights of LAMMPS-GUI
- Indicator for line that caused an error
- Visualization of current state in Image Viewer (via calling :doc:`write_dump image <dump_image>`)
- Capture of images created via :doc:`dump image <dump_image>` in Slide show window
- Dialog to set variables, similar to the LAMMPS command line flag '-v' / '-var'
- Dialog to set variables, similar to the LAMMPS command-line flag '-v' / '-var'
- Support for GPU, INTEL, KOKKOS/OpenMP, OPENMAP, and OPT and accelerator packages
Parallelization
@ -550,7 +550,7 @@ will be found automatically. 2) you can download the `Flatpak file
*flatpak* command: ``flatpak install --user
LAMMPS-Linux-x86_64-GUI-<version>.flatpak`` and run it with ``flatpak
run org.lammps.lammps-gui``. The flatpak bundle also includes the
command line version of LAMMPS and some LAMMPS tools like msi2lmp. The
command-line version of LAMMPS and some LAMMPS tools like msi2lmp. The
can be launched by using the ``--command`` flag. For example to run
LAMMPS directly on the ``in.lj`` benchmark input you would type in the
``bench`` folder: ``flatpak run --command=lmp -in in.lj`` The flatpak
@ -608,10 +608,10 @@ would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
distribution.
When compiling LAMMPS-GUI with plugin support, there is an additional
command line flag (``-p <path>`` or ``--pluginpath <path>``) which
command-line flag (``-p <path>`` or ``--pluginpath <path>``) which
allows to override the path to LAMMPS shared library used by the GUI.
This is usually auto-detected on the first run and can be changed in the
LAMMPS-GUI *Preferences* dialog. The command line flag allows to reset
LAMMPS-GUI *Preferences* dialog. The command-line flag allows to reset
this path to a valid value in case the original setting has become
invalid. An empty path ("") as argument restores the default setting.
@ -656,7 +656,7 @@ it will create a compressed ``LAMMPS-Win10-amd64.zip`` zip file with the
executables and required dependent .dll files. This zip file can be
uncompressed and ``lammps-gui.exe`` run directly from there. The
uncompressed folder can be added to the ``PATH`` environment and LAMMPS
and LAMMPS-GUI can be launched from anywhere from the command line.
and LAMMPS-GUI can be launched from anywhere from the command-line.
**MinGW64 Cross-compiler**
@ -876,7 +876,7 @@ the same ``LAMMPS_CACHING_DIR``. This script does the following:
#. 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.
commands 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.
@ -1025,7 +1025,7 @@ with those in the provided log file with the same number of processors
in the same subdirectory. If the differences between the actual and
reference values are within specified tolerances, the test is considered
passed. For each test batch, that is, a set of example input scripts,
the mpirun command, the LAMMPS command line arguments, and the
the mpirun command, the LAMMPS command-line arguments, and the
tolerances for individual thermo quantities can be specified in a
configuration file in YAML format.

94
doc/src/angle_mwlc.rst Normal file
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@ -0,0 +1,94 @@
.. index:: angle_style mwlc
angle_style mwlc command
==========================
Syntax
""""""
.. code-block:: LAMMPS
angle_style mwlc
Examples
""""""""
.. code-block:: LAMMPS
angle_style mwlc
angle_coeff * 25 1 10 1
Description
"""""""""""
.. versionadded:: TBD
The *mwlc* angle style models a meltable wormlike chain and can be used
to model non-linear bending elasticity of polymers, e.g. DNA. *mwlc*
uses a potential that is a canonical-ensemble superposition of a
non-melted and a melted state :ref:`(Farrell) <Farrell>`. The potential
is
.. math::
E = -k_{B}T\,\log [q + q^{m}] + E_{0},
where the non-melted and melted partition functions are
.. math::
q = \exp [-k_{1}(1+\cos{\theta})/k_{B}T]; \\
q^{m} = \exp [-(\mu+k_{2}(1+\cos{\theta}))/k_{B}T].
:math:`k_1` is the bending elastic constant of the non-melted state,
:math:`k_2` is the bending elastic constant of the melted state,
:math:`\mu` is the melting energy, and
:math:`T` is the reference temperature.
The reference energy,
.. math::
E_{0} = -k_{B}T\,\log [1 + \exp[-\mu/k_{B}T]],
ensures that E is zero for a fully extended chain.
This potential is a continuous version of the two-state potential
introduced by :ref:`(Yan) <Yan>`.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`k_1` (energy)
* :math:`k_2` (energy)
* :math:`\mu` (energy)
* :math:`T` (temperature)
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none
----------
.. _Farrell:
**(Farrell)** `Farrell, Dobnikar, Podgornik, Curk, Phys Rev Lett, 133, 148101 (2024). <https://doi.org/10.1103/PhysRevLett.133.148101>`_
.. _Yan:
**(Yan)** `Yan, Marko, Phys Rev Lett, 93, 108108 (2004). <https://doi.org/10.1103/PhysRevLett.93.108108>`_

1
doc/src/angle_style.rst
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@ -94,6 +94,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`lepton <angle_lepton>` - angle potential from evaluating a string
* :doc:`mesocnt <angle_mesocnt>` - piecewise harmonic and linear angle for bending-buckling of nanotubes
* :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`mwlc <angle_mwlc>` - meltable wormlike chain
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
* :doc:`table <angle_table>` - tabulated by angle

9
doc/src/bond_bpm_rotational.rst
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@ -132,8 +132,8 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`k_b` (force*distance/radians units)
* :math:`f_{r,c}` (force units)
* :math:`f_{s,c}` (force units)
* :math:`\tau_{b,c}` (force*distance units)
* :math:`\tau_{t,c}` (force*distance units)
* :math:`\tau_{b,c}` (force*distance units)
* :math:`\gamma_n` (force/velocity units)
* :math:`\gamma_s` (force/velocity units)
* :math:`\gamma_r` (force*distance/velocity units)
@ -154,8 +154,11 @@ page on BPMs.
If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond reaches a damage criterion greater than one,
it will trigger an error.
The recommended bond communication distance no longer depends on bond failure
coefficients (which are ignored) but instead corresponds to the typical heuristic
maximum strain used by typical non-bpm bond styles. Similar behavior to *break no*
can also be attained by setting arbitrarily high values for all four failure
coefficients. One cannot use *break no* with *smooth yes*.
If the *store/local* keyword is used, an internal fix will track bonds that
break during the simulation. Whenever a bond breaks, data is processed

7
doc/src/bond_bpm_spring.rst
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@ -117,8 +117,11 @@ page on BPMs.
If the *break* keyword is set to *no*, LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond reaches a strain greater than :math:`\epsilon_c`,
it will trigger an error.
The recommended bond communication distance no longer depends on the value of
:math:`\epsilon_c` (which is ignored) but instead corresponds to the typical
heuristic maximum strain used by typical non-bpm bond styles. Similar behavior
to *break no* can also be attained by setting an arbitrarily high value of
:math:`\epsilon_c`. One cannot use *break no* with *smooth yes*.
.. versionadded:: TBD

6
doc/src/compute_sph_e_atom.rst
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@ -33,6 +33,12 @@ particle.
See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
LAMMPS.
.. note::
Please note that the SPH PDF guide file has not been updated for
many years and thus does not reflect the current *syntax* of the
SPH package commands. For that please refer to the LAMMPS manual.
The value of the internal energy will be 0.0 for atoms not in the
specified compute group.

6
doc/src/compute_sph_rho_atom.rst
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@ -32,6 +32,12 @@ kernel function interpolation using "pair style sph/rhosum".
See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
LAMMPS.
.. note::
Please note that the SPH PDF guide file has not been updated for
many years and thus does not reflect the current *syntax* of the
SPH package commands. For that please refer to the LAMMPS manual.
The value of the SPH density will be 0.0 for atoms not in the
specified compute group.

6
doc/src/compute_sph_t_atom.rst
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@ -37,6 +37,12 @@ particles, i.e. a Smooth-Particle Hydrodynamics particle.
See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in
LAMMPS.
.. note::
Please note that the SPH PDF guide file has not been updated for
many years and thus does not reflect the current *syntax* of the
SPH package commands. For that please refer to the LAMMPS manual.
The value of the internal energy will be 0.0 for atoms not in the
specified compute group.

2
doc/src/compute_stress_curvilinear.rst
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@ -87,7 +87,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
.. code-block:: LAMMPS
compute 1 all stress/spherical 0 0 0 0.1 10
compute p all stress/spherical 0 0 0 0.1 10
fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
The values calculated by this compute are "intensive". The stress

21
doc/src/compute_temp_chunk.rst
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@ -184,11 +184,24 @@ temp/chunk calculation to a file is to use the
The keyword/value option pairs are used in the following ways.
The *com* keyword can be used with a value of *yes* to subtract the
velocity of the center-of-mass for each chunk from the velocity of the
atoms in that chunk, before calculating either the global or per-chunk
temperature. This can be useful if the atoms are streaming or
velocity of the center-of-mass (VCM) for each chunk from the velocity of
the atoms in that chunk, before calculating either the global or per-chunk
temperature. This can be useful if the atoms are streaming or
otherwise moving collectively, and you wish to calculate only the
thermal temperature.
thermal temperature. This per-chunk VCM bias can be used in other fixes and
computes that can incorporate a temperature bias. If this compute is used
as a temperature bias in other commands then this bias is subtracted from
each atom, the command runs with the remaining thermal velocities, and
then the bias is added back in. This includes thermostatting
fixes like :doc:`fix nvt <fix_nh>`,
:doc:`fix temp/rescale <fix_temp_rescale>`,
:doc:`fix temp/berendsen <fix_temp_berendsen>`, and
:doc:`fix langevin <fix_langevin>`, and computes like
:doc:`compute stress/atom <compute_stress_atom>` and
:doc:`compute pressure <compute_pressure>`. See the input script in
examples/stress_vcm for an example of how to use the *com* keyword in
conjunction with compute stress/atom to create a stress profile of a rigid
body while removing the overall motion of the rigid body.
For the *bias* keyword, *bias-ID* refers to the ID of a temperature
compute that removes a "bias" velocity from each atom. This also

2
doc/src/compute_temp_partial.rst
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@ -46,7 +46,7 @@ degrees of freedom.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
:doc:`compute pressure <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the

2
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@ -681,7 +681,7 @@ MPEG or other movie file you can use:
* c) Use FFmpeg
FFmpeg is a command line tool that is available on many platforms and
FFmpeg is a command-line tool that is available on many platforms and
allows extremely flexible encoding and decoding of movies.
.. code-block:: bash

2
doc/src/fix.rst
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@ -237,6 +237,7 @@ accelerated styles exist.
* :doc:`dt/reset <fix_dt_reset>` - reset the timestep based on velocity, forces
* :doc:`edpd/source <fix_dpd_source>` - add heat source to eDPD simulations
* :doc:`efield <fix_efield>` - impose electric field on system
* :doc:`efield/lepton <fix_efield_lepton>` - impose electric field on system using a Lepton expression for the potential
* :doc:`efield/tip4p <fix_efield>` - impose electric field on system with TIP4P molecules
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
* :doc:`electrode/conp <fix_electrode>` - impose electric potential
@ -366,6 +367,7 @@ accelerated styles exist.
* :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
* :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling
* :doc:`qtb <fix_qtb>` - implement quantum thermal bath scheme
* :doc:`qtpie/reaxff <fix_qtpie_reaxff>` - apply QTPIE charge equilibration
* :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
* :doc:`reaxff/bonds <fix_reaxff_bonds>` - write out ReaxFF bond information
* :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information

6
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@ -111,7 +111,8 @@ LAMMPS was built with that package. See the :doc:`Build package
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than :math:`10~\AA`.
periodic cell dimensions smaller than the non-bonded cutoff radius,
which is typically :math:`10~\AA` for ReaxFF simulations.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,
@ -122,7 +123,8 @@ components in non-periodic directions.
Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix qtpi/reaxff <fix_qtpie_reaxff>`
Default
"""""""

10
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@ -119,6 +119,14 @@ style supports it. Note that the :doc:`pair_style <pair_style>` and
to specify these parameters initially; the fix adapt command simply
overrides the parameters.
.. note::
Pair_coeff settings must be made **explicitly** in order for fix
adapt to be able to change them. Settings inferred from mixing
are not suitable. If necessary all mixed settings can be output
to a file using the :doc:`write_coeff command <write_coeff>` and
then the desired mixed pair_coeff settings copied from that file.
The *pstyle* argument is the name of the pair style. If
:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
*pstyle* should be a sub-style name. If there are multiple
@ -398,6 +406,8 @@ sub-style name. The angle styles that currently work with fix adapt are:
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`mwlc <angle_mwlc>` | k1,k2,mu,T | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+--------------------+-------------+
| :doc:`spica <angle_spica>` | k,theta0 | type angles |

22
doc/src/fix_adapt_fep.rst
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@ -116,12 +116,22 @@ style supports it. Note that the :doc:`pair_style <pair_style>` and
to specify these parameters initially; the fix adapt command simply
overrides the parameters.
The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
a sub-style name. For example, *pstyle* could be specified as "soft"
or "lubricate". The *pparam* argument is the name of the parameter to
change. This is the current list of pair styles and parameters that
can be varied by this fix. See the doc pages for individual pair
styles and their energy formulas for the meaning of these parameters:
.. note::
Pair_coeff settings must be made **explicitly** in order for fix
adapt/fep to be able to change them. Settings inferred from mixing
are not suitable. If necessary all mixed settings can be output
to a file using the :doc:`write_coeff command <write_coeff>` and
then the desired mixed pair_coeff settings copied from that file.
The *pstyle* argument is the name of the pair style. If
:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
*pstyle* should be a sub-style name. For example, *pstyle* could be
specified as "soft" or "lubricate". The *pparam* argument is the name
of the parameter to change. This is the current list of pair styles and
parameters that can be varied by this fix. See the doc pages for
individual pair styles and their energy formulas for the meaning of
these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |

9
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@ -1,8 +1,11 @@
.. index:: fix cmap
.. index:: fix cmap/kk
fix cmap command
================
Accelerator Variants: *cmap/kk*
Syntax
""""""
@ -141,6 +144,12 @@ outermost level.
MUST not disable the :doc:`fix_modify <fix_modify>` *energy* option
for this fix.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

13
doc/src/fix_colvars.rst
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@ -1,8 +1,11 @@
.. index:: fix colvars
.. index:: fix colvars/kk
fix colvars command
===================
Accelerator Variants: *colvars/kk*
Syntax
""""""
@ -118,6 +121,16 @@ thermostat target temperature.
The *seed* keyword contains the seed for the random number generator
that will be used in the colvars module.
----------
.. note::
Fix colvars/kk is not really ported to KOKKOS, since the colvars
library has not been ported to KOKKOS. It merely has some
optimizations to reduce the data transfers between host and device
for KOKKOS with GPUs.
----------
Restarting
""""""""""

8
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@ -45,8 +45,9 @@ Description
Add a force :math:`\vec{F} = q\vec{E}` to each charged atom in the group due to an
external electric field being applied to the system. If the system
contains point-dipoles, also add a torque on the dipoles due to the
external electric field.
contains point-dipoles, also add a torque :math:`\vec{T} = \vec{p} \times \vec{E}` on the dipoles due to the
external electric field. This fix does not compute the dipole force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}`,
and the :doc:`fix efield/lepton <fix_efield_lepton>` command should be used instead.
.. versionadded:: 28Mar2023
@ -68,6 +69,7 @@ For point-dipoles, equal-style variables can be used, but atom-style
variables are not currently supported, since they imply a spatial
gradient in the electric field which means additional terms with
gradients of the field are required for the force and torque on dipoles.
The :doc:`fix efield/lepton <fix_efield_lepton>` command should be used instead.
Equal-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command
@ -229,7 +231,7 @@ Fix style *efield/tip4p* can only be used with tip4p pair styles.
Related commands
""""""""""""""""
:doc:`fix addforce <fix_addforce>`
:doc:`fix addforce <fix_addforce>`, :doc:`fix efield/lepton <fix_efield_lepton>`
Default
"""""""

143
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@ -0,0 +1,143 @@
.. index:: fix efield/lepton
fix efield/lepton command
=========================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID efield/lepton V ...
* ID, group-ID are documented in the :doc:`fix <fix>` command
* style = *efield/lepton*
* V = electric potential (electric field * distance units)
* V must be a Lepton expression (see below)
* zero or more keyword/value pairs may be appended to args
* keyword = *region* or *step*
.. parsed-literal::
*region* value = region-ID
region-ID = ID of region atoms must be in to have effect
*step* value = h
h = step size for numerical differentiation (distance units)
Examples
""""""""
.. code-block:: LAMMPS
fix ex all efield/lepton "-E*x; E=1"
fix dexx all efield/lepton "-0.5*x^2" step 1
fix yukawa all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A=1; B=1" step 1e-6
fix infp all efield/lepton "-abs(x)" step 1
variable th equal 2*PI*ramp(0,1)
fix erot all efield/lepton "-(x*cos(v_th)+y*sin(v_th))"
Description
"""""""""""
.. versionadded:: TBD
Add an electric potential :math:`V` that applies to a group of charged atoms a force :math:`\vec{F} = q \vec{E}`,
and to dipoles a force :math:`\vec{F} = (\vec{p} \cdot \nabla) \vec{E}` and torque :math:`\vec{T} = \vec{p} \times \vec{E}`,
where :math:`\vec{E} = - \nabla V`. The fix also evaluates the electrostatic energy (:math:`U_{q} = q V` and :math:`U_{p} = - \vec{p} \cdot \vec{E}`)
due to this potential when the :doc:`fix_modify energy yes <fix_modify>` command is specified (see below).
.. note::
This command should be used instead of :doc:`fix efield <fix_efield>` if you want to impose a non-uniform electric field on a system with dipoles
since the latter does not include the dipole force term. If you only have charges or if the electric field gradient is negligible,
:doc:`fix efield <fix_efield>` should be used since it is faster.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the *efield/lepton* fix style interfaces with, evaluates
the expression string at run time to compute the energy, forces, and torques. It creates an analytical representation
of :math:`V` and :math:`\vec{E}`, while the gradient force is computed using a central difference scheme
.. math::
\vec{F} = \frac{|\vec{p}|}{2h} \left[ \vec{E}(\vec{x} + h \hat{p}) - \vec{E}(\vec{x} - h \hat{p}) \right] .
The Lepton expression must be either enclosed in quotes or must not contain any whitespace so that LAMMPS
recognizes it as a single keyword. More on valid Lepton expressions below. The final Lepton expression must
be a function of only :math:`x, y, z`, which refer to the current *unwrapped* coordinates of the atoms to ensure continuity.
Special care must be taken when using this fix with periodic boundary conditions or box-changing commands.
----------
.. include:: lepton_expression.rst
----------
If the *region* keyword is used, the atom must also be in the specified
geometric :doc:`region <region>` in order to be affected by the potential.
The *step* keyword is required when :doc:`atom_style dipole <atom_style>` is used and the electric field is non-uniform.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
fix to add the potential energy defined above to the global potential energy
of the system as part of :doc:`thermodynamic output <thermo_style>`.
The default setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
fix to add the contribution due to the added ***forces*** on charges and dipoles
to both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute stress/atom
<compute_stress_atom>` commands. The former can be accessed by
:doc:`thermodynamic output <thermo_style>`. The default setting for
this fix is :doc:`fix_modify virial no <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
integrator the fix adding its forces. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the potential energy discussed above.
The vector is the total force added to the group of atoms.
The scalar and vector values calculated by this fix are "extensive".
This fix cannot be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command. You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.
.. note::
If you want the electric potential energy to be included in the
total potential energy of the system (the quantity being minimized),
you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for this fix.
----------
Restrictions
""""""""""""
Fix style *efield/lepton* is part of the LEPTON package. It is only enabled if LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix efield <fix_efield>`
Default
"""""""
none

22
doc/src/fix_external.rst
View File

@ -139,9 +139,9 @@ properties are:
void set_vector_length(int n);
void set_vector(int idx, double val);
These allow to set per-atom energy contributions, per-atom stress
contributions, the length and individual values of a global vector
of properties that the caller code may want to communicate to LAMMPS
These enable setting per-atom energy and per-atom stress contributions,
the length and individual values of a global vector of properties that
the caller code may want to communicate to LAMMPS
(e.g. for use in :doc:`fix ave/time <fix_ave_time>` or in
:doc:`equal-style variables <variable>` or for
:doc:`custom thermo output <thermo_style>`.
@ -173,9 +173,19 @@ stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
energy discussed above. The scalar stored by this fix is "extensive".
This fix computes a global scalar, a global vector, and a per-atom array
which can be accessed by various :doc:`output commands <Howto_output>`.
The scalar is the potential energy discussed above. The scalar stored
by this fix is "extensive".
The global vector has a custom length and needs to be set by the external
program using the
:cpp:func:`lammps_fix_external_set_vector() <lammps_fix_external_set_vector>`
and :cpp:func:`lammps_fix_external_set_vector_length()
<lammps_fix_external_set_vector_length>`
calls of the LAMMPS library interface or the equivalent call of the Python
or Fortran modules.
The per-atom array has 3 values for each atom and is the applied external
force.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

71
doc/src/fix_imd.rst
View File

@ -26,6 +26,29 @@ Syntax
*nowait* arg = *on* or *off*
off = LAMMPS waits to be connected to an IMD client before continuing (default)
on = LAMMPS listens for an IMD client, but continues with the run
*version* arg = *2* or *3*
2 = use IMD protocol version 2 (default)
3 = use IMD protocol version 3.
The following keywords are only supported for IMD protocol version 3.
.. parsed-literal::
*time* arg = *on* or *off*
off = simulation time is not transmitted (default)
on = simulation time is transmitted.
*box* arg = *on* or *off*
off = simulation box data is not transmitted (default)
on = simulation box data is transmitted.
*coordinates* arg = *on* or *off*
off = atomic coordinates are not transmitted (default)
on = atomic coordinates are transmitted.
*velocities* arg = *on* or *off*
off = atomic velocities are not transmitted (default)
on = atomic velocities are transmitted.
*forces* arg = *on* or *off*
off = atomic forces are not transmitted (default)
on = atomic forces are transmitted.
Examples
""""""""
@ -40,16 +63,19 @@ Description
This fix implements the "Interactive MD" (IMD) protocol which allows
realtime visualization and manipulation of MD simulations through the
IMD protocol, as initially implemented in VMD and NAMD. Specifically
it allows LAMMPS to connect an IMD client, for example the `VMD visualization program <VMD_>`_, so that it can monitor the progress of the
simulation and interactively apply forces to selected atoms.
IMD protocol, as initially implemented in VMD and NAMD. Specifically it
allows LAMMPS to connect an IMD client, for example the `VMD
visualization program <VMD_>`_ (currently only supports IMDv2) or the
`Python IMDClient <IMDClient_>`_ (supports both IMDv2 and IMDv3), so
that it can monitor the progress of the simulation and interactively
apply forces to selected atoms.
If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD
then fix imd will use POSIX threads to spawn a IMD communication
thread on MPI rank 0 in order to offload data reading and writing
from the main execution thread and potentially lower the inferred
latencies for slow communication links. This feature has only been
tested under linux.
If LAMMPS is compiled with the pre-processor flag
:ref:`-DLAMMPS_ASYNC_IMD <misc>` then fix imd will use POSIX threads to
spawn an IMD communication thread on MPI rank 0 in order to offload data
exchange with the IMD client from the main execution thread and
potentially lower the inferred latencies for slow communication
links. This feature has only been tested under linux.
The source code for this fix includes code developed by the Theoretical
and Computational Biophysics Group in the Beckman Institute for Advanced
@ -94,10 +120,19 @@ with different units or as a measure to tweak the forces generated by
the manipulation of the IMD client, this option allows to make
adjustments.
.. versionadded:: TBD
In `IMDv3 <IMDv3_>`_, the IMD protocol has been extended to allow for
the transmission of simulation time, box dimensions, atomic coordinates,
velocities, and forces. The *version* keyword allows to select the
version of the protocol to be used. The *time*, *box*, *coordinates*,
*velocities*, and *forces* keywords allow to select which data is
transmitted to the IMD client. The default is to transmit all data.
To connect VMD to a listening LAMMPS simulation on the same machine
with fix imd enabled, one needs to start VMD and load a coordinate or
topology file that matches the fix group. When the VMD command
prompts appears, one types the command line:
prompts appears, one types the command:
.. parsed-literal::
@ -129,6 +164,10 @@ screen output is active.
.. _imdvmd: https://www.ks.uiuc.edu/Research/vmd/imd/
.. _IMDClient: https://github.com/Becksteinlab/imdclient/tree/main/imdclient
.. _IMDv3: https://imdclient.readthedocs.io/en/latest/protocol_v3.html
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -147,14 +186,14 @@ This fix is part of the MISC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the
group the fix is applied to. The fix internally sorts atom IDs by
ascending integer value; in VMD (and thus the IMD protocol) those will
be assigned 0-based consecutive index numbers.
When used in combination with VMD, a topology or coordinate file has to
be loaded, which matches (in number and ordering of atoms) the group the
fix is applied to. The fix internally sorts atom IDs by ascending
integer value; in VMD (and thus the IMD protocol) those will be assigned
0-based consecutive index numbers.
When using multiple active IMD connections at the same time, each
needs to use a different port number.
fix instance needs to use a different port number.
Related commands
""""""""""""""""

9
doc/src/fix_nve_limit.rst
View File

@ -1,8 +1,11 @@
.. index:: fix nve/limit
.. index:: fix nve/limit/kk
fix nve/limit command
=====================
Accelerator Variants: *nve/limit/kk*
Syntax
""""""
@ -79,6 +82,12 @@ is "extensive".
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>`.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""
none

2
doc/src/fix_precession_spin.rst
View File

@ -135,7 +135,7 @@ directions for the forces. Only the direction of the vector is
important; its length is ignored (the entered vectors are
normalized).
Those styles can be combined within one single command line.
Those styles can be combined within one single command.
.. note::

2
doc/src/fix_qeq.rst
View File

@ -190,7 +190,7 @@ on atoms via the matrix inversion method. A tolerance of 1.0e-6 is
usually a good number. Keyword *alpha* can be used to change the Slater
type orbital exponent.
.. versionadded:: TBD
.. versionadded:: 19Nov2024
The *qeq/ctip* style describes partial charges on atoms in the same way
as style *qeq/shielded* but also enables the definition of charge

6
doc/src/fix_qeq_reaxff.rst
View File

@ -124,7 +124,8 @@ LAMMPS was built with that package. See the :doc:`Build package
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions less than 10 Angstroms.
periodic cell dimensions smaller than the non-bonded cutoff radius,
which is typically :math:`10~\AA` for ReaxFF simulations.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,
@ -138,7 +139,8 @@ as an atom-style variable using the *potential* keyword for `fix efield`.
Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`,
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`
Default
"""""""

200
doc/src/fix_qtpie_reaxff.rst Normal file
View File

@ -0,0 +1,200 @@
.. index:: fix qtpie/reaxff
fix qtpie/reaxff command
========================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID qtpie/reaxff Nevery cutlo cuthi tolerance params gfile args
* ID, group-ID are documented in :doc:`fix <fix>` command
* qtpie/reaxff = style name of this fix command
* Nevery = perform QTPIE every this many steps
* cutlo,cuthi = lo and hi cutoff for Taper radius
* tolerance = precision to which charges will be equilibrated
* params = reaxff or a filename
* gfile = the name of a file containing Gaussian orbital exponents
* one or more keywords or keyword/value pairs may be appended
.. parsed-literal::
keyword = *maxiter*
*maxiter* N = limit the number of iterations to *N*
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qtpie
fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 params.qtpie exp.qtpie maxiter 500
Description
"""""""""""
.. versionadded:: 19Nov2024
The QTPIE charge equilibration method is an extension of the QEq charge
equilibration method. With QTPIE, the partial charges on individual atoms
are computed by minimizing the electrostatic energy of the system in the
same way as the QEq method but where the absolute electronegativity,
:math:`\chi_i`, of each atom in the QEq charge equilibration scheme
:ref:`(Rappe and Goddard) <Rappe3>` is replaced with an effective
electronegativity given by :ref:`(Chen) <qtpie-Chen>`
.. math::
\chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j) S_{ij}}
{\sum_{m=1}^{N}S_{im}},
which acts to penalize long-range charge transfer seen with the QEq charge
equilibration scheme. In this equation, :math:`N` is the number of atoms in
the system and :math:`S_{ij}` is the overlap integral between atom :math:`i`
and atom :math:`j`.
The effect of an external electric field can be incorporated into the QTPIE
method by modifying the absolute or effective electronegativities of each
atom :ref:`(Chen) <qtpie-Chen>`. This fix models the effect of an external
electric field by using the effective electronegativity given in
:ref:`(Gergs) <Gergs>`:
.. math::
\chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \phi_i - \phi_j) S_{ij}}
{\sum_{m=1}^{N}S_{im}},
where :math:`\phi_i` and :math:`\phi_j` are the electric
potentials at the positions of atom :math:`i` and :math:`j`
due to the external electric field.
This fix is typically used in conjunction with the ReaxFF force
field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
command, but it can be used with any potential in LAMMPS, so long as it
defines and uses charges on each atom. For more technical details about the
charge equilibration performed by `fix qtpie/reaxff`, which is the same as in
:doc:`fix qeq/reaxff <fix_qeq_reaxff>` except for the use of
:math:`\chi_{\mathrm{eff},i}`, please refer to :ref:`(Aktulga) <qeq-Aktulga2>`.
To be explicit, this fix replaces :math:`\chi_k` of eq. 3 in
:ref:`(Aktulga) <qeq-Aktulga2>` with :math:`\chi_{\mathrm{eff},k}`.
This fix requires the absolute electronegativity, :math:`\chi`, in eV, the
self-Coulomb potential, :math:`\eta`, in eV, and the shielded Coulomb
constant, :math:`\gamma`, in :math:`\AA^{-1}`. If the *params* setting above
is the word "reaxff", then these are extracted from the
:doc:`pair_style reaxff <pair_reaxff>` command and the ReaxFF force field
file it reads in. If a file name is specified for *params*, then the
parameters are taken from the specified file and the file must contain
one line for each atom type. The latter form must be used when performing
QTPIE with a non-ReaxFF potential. Each line should be formatted as follows,
ensuring that the parameters are given in units of eV, eV, and :math:`\AA^{-1}`,
respectively:
.. parsed-literal::
itype chi eta gamma
where *itype* is the atom type from 1 to Ntypes. Note that eta is
defined here as twice the eta value in the ReaxFF file.
The overlap integrals in the equation for :math:`\chi_{\mathrm{eff},i}`
are computed by using normalized 1s Gaussian type orbitals. The Gaussian
orbital exponents, :math:`\alpha`, that are needed to compute the overlap
integrals are taken from the file given by *gfile*.
This file must contain one line for each atom type and provide the Gaussian
orbital exponent for each atom type in units of inverse square Bohr radius.
Each line should be formatted as follows:
.. parsed-literal::
itype alpha
Empty lines or any text following the pound sign (#) are ignored. An example
*gfile* for a system with two atom types is
.. parsed-literal::
# An example gfile. Exponents are taken from Table 2.2 of Chen, J. (2009).
# Theory and applications of fluctuating-charge models.
# The units of the exponents are 1 / (Bohr radius)^2 .
1 0.2240 # O
2 0.5434 # H
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
.. note::
In order to solve the self-consistent equations for electronegativity
equalization, LAMMPS imposes the additional constraint that all the
charges in the fix group must add up to zero. The initial charge
assignments should also satisfy this constraint. LAMMPS will print a
warning if that is not the case.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`. This fix computes a global scalar (the number of
iterations) and a per-atom vector (the effective electronegativity), which
can be accessed 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 invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the REAXFF package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This fix does not correctly handle interactions involving multiple
periodic images of the same atom. Hence, it should not be used for
periodic cell dimensions smaller than the non-bonded cutoff radius,
which is typically :math:`10~\AA` for ReaxFF simulations.
This fix may be used in combination with :doc:`fix efield <fix_efield>`
and will apply the external electric field during charge equilibration,
but there may be only one fix efield instance used and the electric field
must be applied to all atoms in the system. Consequently, `fix efield` must
be used with *group-ID* all and must not be used with the keyword *region*.
Equal-style variables can be used for electric field vector
components without any further settings. Atom-style variables can be used
for spatially-varying electric field vector components, but the resulting
electric potential must be specified as an atom-style variable using
the *potential* keyword for `fix efield`.
Related commands
""""""""""""""""
:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
:doc:`fix acks2/reaxff <fix_acks2_reaxff>`
Default
"""""""
maxiter 200
----------
.. _Rappe3:
**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95,
3358-3363 (1991).
.. _qtpie-Chen:
**(Chen)** Chen, Jiahao. Theory and applications of fluctuating-charge models.
University of Illinois at Urbana-Champaign, 2009.
.. _Gergs:
**(Gergs)** Gergs, Dirkmann and Mussenbrock.
Journal of Applied Physics 123.24 (2018).
.. _qeq-Aktulga2:
**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).

9
doc/src/fix_recenter.rst
View File

@ -1,8 +1,11 @@
.. index:: fix recenter
.. index:: fix recenter/kk
fix recenter command
====================
Accelerator Variants: *recenter/kk*
Syntax
""""""
@ -113,6 +116,12 @@ The scalar and vector values calculated by this fix are "extensive".
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>`.
----------
.. include:: accel_styles.rst
----------
Restrictions
""""""""""""

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