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Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.6.1

Browse Source
This commit is contained in:
Stan Moore
2025-06-27 09:50:48 -06:00
parent 011f05f9ff b7be53f3fc
commit f1d19c96cb
444 changed files with 118668 additions and 4551 deletions
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10
.github/release_steps.md vendored
View File

@ -104,13 +104,13 @@ with a future release) from the `lammps-static` folder.
rm -rf release-packages
mkdir release-packages
cd release-packages
wget https://download.lammps.org/static/fedora41_musl.sif
apptainer shell fedora41_musl.sif
wget https://download.lammps.org/static/fedora41_musl_mingw.sif
apptainer shell fedora41_musl_mingw.sif
git clone -b release --depth 10 https://github.com/lammps/lammps.git lammps-release
cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
cmake --build build-release --target all
cmake --build build-release --target install
/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
/usr/musl/bin/x86_64-linux-musl-strip -g lammps-static/bin/*
tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
exit # fedora 41 container
cd ..
@ -204,7 +204,7 @@ cd ..
rm -r release-packages
```
#### Build Multi-arch App-bundle for macOS
#### Build Multi-arch App-bundle with GUI for macOS
Building app-bundles for macOS is not as easily automated and portable
as some of the other steps. It requires a machine actually running
@ -251,7 +251,7 @@ attached to the GitHub release page.
We are currently building the application images on macOS 12 (aka Monterey).
#### Build Linux x86_64 binary tarball on Ubuntu 20.04LTS
#### Build Linux x86_64 binary tarball with GUI on Ubuntu 20.04LTS
While the flatpak Linux version uses portable runtime libraries provided
by the flatpak environment, we also build regular Linux executables that

23
.github/workflows/check-cpp23.yml vendored
View File

@ -1,4 +1,4 @@
# GitHub action to build LAMMPS on Linux with gcc and C++23
# GitHub action to build LAMMPS on Linux with gcc or clang and C++23
name: "Check for C++23 Compatibility"
on:
@ -11,11 +11,19 @@ on:
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Build with C++23 support enabled
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
strategy:
max-parallel: 2
matrix:
idx: [ gcc, clang ]
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
@ -29,8 +37,11 @@ jobs:
run: |
sudo apt-get update
sudo apt-get install -y ccache \
libeigen3-dev \
clang \
libcurl4-openssl-dev \
libeigen3-dev \
libfftw3-dev \
libomp-dev \
mold \
mpi-default-bin \
mpi-default-dev \
@ -44,8 +55,8 @@ jobs:
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-cpp23-ccache-${{ github.sha }}
restore-keys: linux-cpp23-ccache-
key: linux-cpp23-ccache-${{ matrix.idx }}-${{ github.sha }}
restore-keys: linux-cpp23-ccache-${{ matrix.idx }}
- name: Building LAMMPS via CMake
shell: bash
@ -58,14 +69,14 @@ jobs:
cmake -S cmake -B build \
-C cmake/presets/most.cmake \
-C cmake/presets/kokkos-openmp.cmake \
-C cmake/presets/${{ matrix.idx }}.cmake \
-D CMAKE_CXX_STANDARD=23 \
-D CMAKE_CXX_COMPILER=g++ \
-D CMAKE_C_COMPILER=gcc \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D CMAKE_BUILD_TYPE=Debug \
-D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
-D DOWNLOAD_POTENTIALS=off \
-D FFT=KISS \
-D BUILD_MPI=on \
-D BUILD_SHARED_LIBS=on \
-D BUILD_TOOLS=off \

37
cmake/CMakeLists.txt
View File

@ -7,6 +7,10 @@ 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()
########################################
# initialize version variables with project command
if(POLICY CMP0048)
cmake_policy(SET CMP0048 NEW)
endif()
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
@ -27,7 +31,10 @@ endif()
########################################
project(lammps CXX)
project(lammps
DESCRIPTION "The LAMMPS Molecular Dynamics Simulator"
HOMEPAGE_URL "https://www.lammps.org"
LANGUAGES CXX C)
set(SOVERSION 0)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
@ -131,7 +138,9 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")))
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
endif()
@ -194,6 +203,10 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
endif()
# do not include the (obsolete) MPI C++ bindings which makes for leaner object files
# and avoids namespace conflicts. Put this early to increase its visbility.
set(MPI_CXX_SKIP_MPICXX TRUE CACHE BOOL "Skip MPI C++ Bindings" FORCE)
########################################################################
# User input options #
########################################################################
@ -231,15 +244,6 @@ option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared lib
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
# Support using clang-tidy for C++ files with selected options
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
else()
unset(CMAKE_CXX_CLANG_TIDY CACHE)
endif()
file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@ -264,6 +268,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES
ADIOS
AMOEBA
APIP
ASPHERE
ATC
AWPMD
@ -377,7 +382,6 @@ if(PKG_ADIOS)
# The search for ADIOS2 must come before MPI because
# it includes its own MPI search with the latest FindMPI.cmake
# script that defines the MPI::MPI_C target
enable_language(C)
find_package(ADIOS2 REQUIRED)
if(BUILD_MPI)
if(NOT ADIOS2_HAVE_MPI)
@ -392,21 +396,18 @@ if(PKG_ADIOS)
endif()
if(NOT CMAKE_CROSSCOMPILING)
find_package(MPI QUIET)
find_package(MPI QUIET COMPONENTS CXX)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
include(MPI4WIN)
else()
find_package(MPI REQUIRED)
find_package(MPI REQUIRED COMPONENTS CXX)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
@ -467,6 +468,7 @@ pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
pkg_depends(MESONT MOLECULE)
pkg_depends(RHEO BPM)
pkg_depends(APIP ML-PACE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -533,7 +535,6 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
endif()
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
find_package(BLAS)

102
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -62,6 +62,9 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
endif()
set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
# skip over obsolete MPI-2 C++ bindings
set(MPI_CXX_SKIP_MPICXX TRUE)
#######
# helper functions from LAMMPSUtils.cmake
function(validate_option name values)
@ -128,8 +131,7 @@ endif()
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
find_package(MPI QUIET COMPONENTS CXX)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
@ -141,78 +143,38 @@ if(BUILD_MPI)
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
else()
find_package(MPI REQUIRED)
find_package(MPI REQUIRED COMPONENTS CXX)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)

22
cmake/Modules/LAMMPSUtils.cmake
View File

@ -75,13 +75,25 @@ function(get_lammps_version version_header variable)
list(FIND MONTHS "${month}" month)
string(LENGTH ${day} day_length)
string(LENGTH ${month} month_length)
if(day_length EQUAL 1)
set(day "0${day}")
# no leading zero needed for new version string with dots
# if(day_length EQUAL 1)
# set(day "0${day}")
# endif()
# if(month_length EQUAL 1)
# set(month "0${month}")
#endif()
file(STRINGS ${version_header} line REGEX LAMMPS_UPDATE)
string(REGEX REPLACE "#define LAMMPS_UPDATE \"Update ([0-9]+)\"" "\\1" tweak "${line}")
if (line MATCHES "#define LAMMPS_UPDATE \"(Maintenance|Development)\"")
set(tweak "99")
endif()
if(month_length EQUAL 1)
set(month "0${month}")
if(NOT tweak)
set(tweak "0")
endif()
set(${variable} "${year}${month}${day}" PARENT_SCOPE)
# new version string with dots
set(${variable} "${year}.${month}.${day}.${tweak}" PARENT_SCOPE)
# old version string without dots
# set(${variable} "${year}${month}${day}" PARENT_SCOPE)
endfunction()
function(check_for_autogen_files source_dir)

99
cmake/Modules/MPI4WIN.cmake
View File

@ -1,74 +1,31 @@
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
# set-up MS-MPI library for Windows with MinGW compatibility
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")

1
cmake/Modules/Packages/COLVARS.cmake
View File

@ -27,7 +27,6 @@ if(BUILD_OMP)
endif()
if(BUILD_MPI)
target_compile_definitions(colvars PUBLIC -DCOLVARS_MPI)
target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
endif()

4
cmake/Modules/Packages/GPU.cmake
View File

@ -189,7 +189,7 @@ if(GPU_API STREQUAL "CUDA")
endif()
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR -DLAMMPS_${LAMMPS_SIZES})
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
@ -489,7 +489,7 @@ else()
target_link_libraries(gpu PRIVATE mpi_stubs)
endif()
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
target_sources(lammps PRIVATE ${GPU_SOURCES})
target_include_directories(lammps PRIVATE ${GPU_SOURCES_DIR})

10
cmake/Modules/Packages/MC.cmake
View File

@ -7,3 +7,13 @@ if(NOT PKG_MANYBODY)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()
# fix neighbor/swap may only be installed if also the VORONOI package is installed
if(NOT PKG_VORONOI)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_neighbor_swap.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_neighbor_swap.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

8
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -53,7 +53,13 @@ else()
add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
endif()
add_subdirectory(${lib-pace} build-pace)
# fixup yaml-cpp/emitterutils.cpp for GCC 15+ until patch is applied
file(READ ${lib-pace}/yaml-cpp/src/emitterutils.cpp yaml_emitterutils)
string(REPLACE "#include <sstream>" "#include <sstream>\n#include <cinttypes>" yaml_tmp_emitterutils "${yaml_emitterutils}")
string(REPLACE "#include <cinttypes>\n#include <cinttypes>" "#include <cinttypes>" yaml_emitterutils "${yaml_tmp_emitterutils}")
file(WRITE ${lib-pace}/yaml-cpp/src/emitterutils.cpp "${yaml_emitterutils}")
add_subdirectory(${lib-pace} build-pace EXCLUDE_FROM_ALL)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
if(CMAKE_PROJECT_NAME STREQUAL "lammps")

15
cmake/Modules/Testing.cmake
View File

@ -21,11 +21,11 @@ if(ENABLE_TESTING)
# also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04))
OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
include(CheckCXXCompilerFlag)
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
check_cxx_compiler_flag(--ld-path=${CMAKE_LINKER} HAVE_LD_PATH_FLAG)
check_cxx_compiler_flag(-fuse-ld=mold HAVE_MOLD_LINKER_FLAG)
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
@ -50,6 +50,17 @@ if(ENABLE_TESTING)
if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
endif()
if(HAVE_LD_PATH_FLAG)
if("${CMAKE_CUSTOM_LINKER}" STREQUAL "mold")
target_link_options(lammps PUBLIC --ld-path=${HAVE_MOLD_LINKER_BIN})
elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "lld")
target_link_options(lammps PUBLIC --ld-path=${HAVE_LLD_LINKER_BIN})
elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "gold")
target_link_options(lammps PUBLIC --ld-path=${HAVE_GOLD_LINKER_BIN})
elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "bfd")
target_link_options(lammps PUBLIC --ld-path=${HAVE_BFD_LINKER_BIN})
endif()
endif()
endif()
endif()

4
cmake/Modules/Tools.cmake
View File

@ -6,6 +6,10 @@ if(BUILD_TOOLS)
add_executable(stl_bin2txt ${LAMMPS_TOOLS_DIR}/stl_bin2txt.cpp)
install(TARGETS stl_bin2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
add_executable(reformat-json ${LAMMPS_TOOLS_DIR}/json/reformat-json.cpp)
target_include_directories(reformat-json PRIVATE ${LAMMPS_SOURCE_DIR})
install(TARGETS reformat-json DESTINATION ${CMAKE_INSTALL_BINDIR})
include(CheckGeneratorSupport)
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
include(CheckLanguage)

1
cmake/presets/all_off.cmake
View File

@ -4,6 +4,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
APIP
ASPHERE
ATC
AWPMD

1
cmake/presets/all_on.cmake
View File

@ -6,6 +6,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
APIP
ASPHERE
ATC
AWPMD

11
cmake/presets/hip_amd.cmake
View File

@ -19,12 +19,19 @@ set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
set(MPI_C "hipcc" CACHE STRING "" FORCE)
set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
# change as needed. This is for Fedora Linux 41 and 42
set(_libomp_root "/usr/lib/clang/18")
# we need to explicitly specify the include dir, since hipcc will
# compile each file twice and doesn't find omp.h the second time
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "hipcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

3
cmake/presets/kokkos-cuda.cmake
View File

@ -1,9 +1,8 @@
# preset that enables KOKKOS and selects CUDA compilation with OpenMP
# enabled as well. The GPU architecture *must* match your hardware
# enabled as well. The GPU architecture *must* match your hardware (If not manually set, Kokkos will try to autodetect it).
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

10
cmake/presets/kokkos-hip.cmake
View File

@ -1,8 +1,8 @@
# preset that enables KOKKOS and selects HIP compilation with OpenMP
# enabled as well. Also sets some performance related compiler flags.
# preset that enables KOKKOS and selects HIP compilation withOUT OpenMP.
# Kokkos OpenMP is not compatible with the second pass of hipcc.
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_HIP ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_VEGA90A on CACHE BOOL "" FORCE)
@ -11,11 +11,11 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -munsafe-fp-atomics" CACHE STRING "" FORCE)
# If KSPACE is also enabled, use CUFFT for FFTs
# If KSPACE is also enabled, use HIPFFT for FFTs
set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
#set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
# these flags are needed to build with Cray MPICH on OLCF Crusher
#-D CMAKE_CXX_FLAGS="-I/${MPICH_DIR}/include"

1
cmake/presets/nolib.cmake
View File

@ -3,6 +3,7 @@
set(PACKAGES_WITH_LIB
ADIOS
APIP
ATC
AWPMD
COMPRESS

6
doc/Makefile
View File

@ -99,8 +99,6 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
ln -sf Manual.html html/index.html;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
@ -162,8 +160,6 @@ epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
deactivate ;\
)
@ -183,8 +179,6 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
rst_anchor_check src/*.rst ;\

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "2 April 2025" "2025-04-02"
.TH LAMMPS "1" "12 June 2025" "2025-06-12"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 2 April 2025
\- Molecular Dynamics Simulator. Version 12 June 2025
.SH SYNOPSIS
.B lmp

22
doc/src/Build_development.rst
View File

@ -28,28 +28,6 @@ variable VERBOSE set to 1:
----------
.. _clang-tidy:
Enable static code analysis with clang-tidy (CMake only)
--------------------------------------------------------
The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
static code analysis tool to diagnose (and potentially fix) typical
programming errors or coding style violations. It has a modular framework
of tests that can be adjusted to help identifying problems before they
become bugs and also assist in modernizing large code bases (like LAMMPS).
It can be enabled for all C++ code with the following CMake flag
.. code-block:: bash
-D ENABLE_CLANG_TIDY=value # value = no (default) or yes
With this flag enabled all source files will be processed twice, first to
be compiled and then to be analyzed. Please note that the analysis can be
significantly more time-consuming than the compilation itself.
----------
.. _iwyu_processing:
Report missing and unneeded '#include' statements (CMake only)

29
doc/src/Build_extras.rst
View File

@ -35,6 +35,7 @@ This is the list of packages that may require additional steps.
:columns: 6
* :ref:`ADIOS <adios>`
* :ref:`APIP <apip>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvar>`
@ -1284,6 +1285,34 @@ systems.
----------
.. _apip:
APIP package
-----------------------------
The APIP package depends on the library of the
:ref:`ML-PACE <ml-pace>` package.
The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_APIP=yes``
and ``-D PKG_ML-PACE=yes``.
One can use a local version of the ML-PACE library instead of
automatically downloading the library as described :ref:`here <ml-pace>`.
.. tab:: Traditional make
You need to install the ML-PACE package *first* and follow
the instructions :ref:`here <ml-pace>` before installing
the APIP package.
----------
.. _atc:
ATC package

5
doc/src/Commands_fix.rst
View File

@ -22,6 +22,7 @@ OPT.
* :doc:`append/atoms <fix_append_atoms>`
* :doc:`atc <fix_atc>`
* :doc:`atom/swap <fix_atom_swap>`
* :doc:`atom_weight/apip <fix_atom_weight_apip>`
* :doc:`ave/atom <fix_ave_atom>`
* :doc:`ave/chunk <fix_ave_chunk>`
* :doc:`ave/correlate <fix_ave_correlate>`
@ -29,6 +30,7 @@ OPT.
* :doc:`ave/grid <fix_ave_grid>`
* :doc:`ave/histo <fix_ave_histo>`
* :doc:`ave/histo/weight <fix_ave_histo>`
* :doc:`ave/moments <fix_ave_moments>`
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
@ -90,6 +92,8 @@ OPT.
* :doc:`imd <fix_imd>`
* :doc:`indent <fix_indent>`
* :doc:`ipi <fix_ipi>`
* :doc:`lambda/apip <fix_lambda_apip>`
* :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>`
* :doc:`langevin (k) <fix_langevin>`
* :doc:`langevin/drude <fix_langevin_drude>`
* :doc:`langevin/eff <fix_langevin_eff>`
@ -217,6 +221,7 @@ OPT.
* :doc:`rigid/small (o) <fix_rigid>`
* :doc:`rx (k) <fix_rx>`
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`set <fix_set>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`sgcmc <fix_sgcmc>`

2
doc/src/Commands_kspace.rst
View File

@ -31,3 +31,5 @@ OPT.
* :doc:`pppm/dielectric <kspace_style>`
* :doc:`pppm/electrode (i) <kspace_style>`
* :doc:`scafacos <kspace_style>`
* :doc:`zero <kspace_style>`

8
doc/src/Commands_pair.rst
View File

@ -96,7 +96,9 @@ OPT.
* :doc:`eam/cd <pair_eam>`
* :doc:`eam/cd/old <pair_eam>`
* :doc:`eam/fs (gikot) <pair_eam>`
* :doc:`eam/fs/apip <pair_eam_apip>`
* :doc:`eam/he <pair_eam>`
* :doc:`eam/apip <pair_eam_apip>`
* :doc:`edip (o) <pair_edip>`
* :doc:`edip/multi <pair_edip>`
* :doc:`edpd (g) <pair_mesodpd>`
@ -124,6 +126,9 @@ OPT.
* :doc:`ilp/tmd (t) <pair_ilp_tmd>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
* :doc:`lambda/input/apip <pair_lambda_input_apip>`
* :doc:`lambda/input/csp/apip <pair_lambda_input_apip>`
* :doc:`lambda/zone/apip <pair_lambda_zone_apip>`
* :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
@ -237,6 +242,9 @@ OPT.
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pace/apip <pair_pace_apip>`
* :doc:`pace/fast/apip <pair_pace_apip>`
* :doc:`pace/precise/apip <pair_pace_apip>`
* :doc:`pedone (o) <pair_pedone>`
* :doc:`pod (k) <pair_pod>`
* :doc:`peri/eps <pair_peri>`

2
doc/src/Commands_removed.rst
View File

@ -15,7 +15,7 @@ with the direct alternative (if available) and print a warning.
GJF formulation in fix langevin
-------------------------------
.. deprecated:: TBD
.. deprecated:: 12Jun2025
The *gjf* keyword in fix langevin is deprecated and will be removed
soon. The GJF functionality has been moved to its own fix style

42
doc/src/Developer_plugins.rst
View File

@ -68,24 +68,25 @@ Members of ``lammpsplugin_t``
* - author
- String with the name and email of the author
* - creator.v1
- Pointer to factory function for pair, bond, angle, dihedral, improper, kspace, or command styles
- Pointer to factory function for pair, bond, angle, dihedral, improper, kspace, command, or minimize styles
* - creator.v2
- Pointer to factory function for compute, fix, or region styles
- Pointer to factory function for compute, fix, region, or run styles
* - handle
- Pointer to the open DSO file handle
Only one of the two alternate creator entries can be used at a time and
which of those is determined by the style of plugin. The "creator.v1"
element is for factory functions of supported styles computing forces
(i.e. pair, bond, angle, dihedral, or improper styles) or command styles
and the function takes as single argument the pointer to the LAMMPS
instance. The factory function is cast to the ``lammpsplugin_factory1``
type before assignment. The "creator.v2" element is for factory
functions creating an instance of a fix, compute, or region style and
takes three arguments: a pointer to the LAMMPS instance, an integer with
the length of the argument list and a ``char **`` pointer to the list of
arguments. The factory function pointer needs to be cast to the
``lammpsplugin_factory2`` type before assignment.
(i.e. pair, bond, angle, dihedral, or improper styles), command styles,
or minimize styles and the function takes as single argument the pointer
to the LAMMPS instance. The factory function is cast to the
``lammpsplugin_factory1`` type before assignment. The "creator.v2"
element is for factory functions creating an instance of a fix, compute,
region, or run style and takes three arguments: a pointer to the LAMMPS
instance, an integer with the length of the argument list and a ``char
**`` pointer to the list of arguments. The factory function pointer
needs to be cast to the ``lammpsplugin_factory2`` type before
assignment.
Pair style example
^^^^^^^^^^^^^^^^^^
@ -247,8 +248,8 @@ DSO handle. The registration function is called with a pointer to the address
of this struct and the pointer of the LAMMPS class. The registration function
will then add the factory function of the plugin style to the respective
style map under the provided name. It will also make a copy of the struct
in a list of all loaded plugins and update the reference counter for loaded
plugins from this specific DSO file.
in a global list of all loaded plugins and update the reference counter for
loaded plugins from this specific DSO file.
The pair style itself (i.e. the PairMorse2 class in this example) can be
written just like any other pair style that is included in LAMMPS. For
@ -263,6 +264,21 @@ the plugin will override the existing code. This can be used to modify
the behavior of existing styles or to debug new versions of them without
having to re-compile or re-install all of LAMMPS.
.. versionchanged:: 12Jun2025
When using the :doc:`clear <clear>` command, plugins are not unloaded
but restored to their respective style maps. This also applies when
multiple LAMMPS instances are created and deleted through the library
interface. The :doc:`plugin load <plugin>` load command may be issued
again, but for existing plugins they will be skipped. To replace
plugins they must be explicitly unloaded with :doc:`plugin unload
<plugin>`. When multiple LAMMPS instances are created concurrently, any
loaded plugins will be added to the global list of plugins, but are not
immediately available to any LAMMPS instance that was created before
loading the plugin. To "import" such plugins, the :doc:`plugin restore
<plugin>` may be used. Plugins are only removed when they are explicitly
unloaded or the LAMMPS interface is "finalized".
Compiling plugins
^^^^^^^^^^^^^^^^^

45
doc/src/Developer_updating.rst
View File

@ -29,6 +29,7 @@ Available topics in mostly chronological order are:
- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
- `FLERR as first argument to minimum image functions in Domain class`_
----
@ -610,3 +611,47 @@ KSpace solvers which use distributed FFT grids:
- ``src/KSPACE/pppm.cpp``
This change is **required** or else the code will not compile.
FLERR as first argument to minimum image functions in Domain class
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 12Jun2025
The ``Domain::minimum_image()`` and ``Domain::minimum_image_big()``
functions were changed to take the ``FLERR`` macros as first argument.
This way the error message indicates *where* the function was called
instead of pointing to the implementation of the function. Example:
Old:
.. code-block:: c++
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1, dely1, delz1);
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image_big(delx2, dely2, delz2);
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
New:
.. code-block:: c++
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(FLERR, delx1, dely1, delz1);
double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image_big(FLERR, delx2, dely2, delz2);
double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
This change is **required** or else the code will not compile.

235
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@ -1,124 +1,149 @@
Common problems
===============
Common issues that are often regarded as bugs
=============================================
If two LAMMPS runs do not produce the exact same answer on different
machines or different numbers of processors, this is typically not a
bug. In theory you should get identical answers on any number of
processors and on any machine. In practice, numerical round-off can
cause slight differences and eventual divergence of molecular dynamics
phase space trajectories within a few 100s or few 1000s of timesteps.
However, the statistical properties of the two runs (e.g. average
energy or temperature) should still be the same.
The list below are some random notes on behavior of LAMMPS that is
sometimes unexpected or even considered a bug. Most of the time, these
are just issues of understanding how LAMMPS is implemented and
parallelized. Please also have a look at the :doc:`Error details
discussions page <Errors_details>` that contains recommendations for
tracking down issues and explanations for error messages that may
sometimes be confusing or need additional explanations.
If the :doc:`velocity <velocity>` command is used to set initial atom
velocities, a particular atom can be assigned a different velocity
when the problem is run on a different number of processors or on
different machines. If this happens, the phase space trajectories of
the two simulations will rapidly diverge. See the discussion of the
*loop* option in the :doc:`velocity <velocity>` command for details and
options that avoid this issue.
- A LAMMPS simulation typically has two stages, 1) issuing commands
and 2) run or minimize. Most LAMMPS errors are detected in stage 1),
others at the beginning of stage 2), and finally others like a bond
stretching too far may or lost atoms or bonds may not occur until the
middle of a run.
Similarly, the :doc:`create_atoms <create_atoms>` command generates a
lattice of atoms. For the same physical system, the ordering and
numbering of atoms by atom ID may be different depending on the number
of processors.
- If two LAMMPS runs do not produce the exact same answer on different
machines or different numbers of processors, this is typically not a
bug. In theory you should get identical answers on any number of
processors and on any machine. In practice, numerical round-off can
cause slight differences and eventual divergence of molecular dynamics
phase space trajectories within a few 100s or few 1000s of timesteps.
This can be triggered by different ordering of atoms due to different
domain decompositions, but also through different CPU architectures,
different operating systems, different compilers or compiler versions,
different compiler optimization levels, different FFT libraries.
However, the statistical properties of the two runs (e.g. average
energy or temperature) should still be the same.
Some commands use random number generators which may be setup to
produce different random number streams on each processor and hence
will produce different effects when run on different numbers of
processors. A commonly-used example is the :doc:`fix langevin <fix_langevin>` command for thermostatting.
- If the :doc:`velocity <velocity>` command is used to set initial atom
velocities, a particular atom can be assigned a different velocity
when the problem is run on a different number of processors or on
different machines. If this happens, the phase space trajectories of
the two simulations will rapidly diverge. See the discussion of the
*loop* option in the :doc:`velocity <velocity>` command for details
and options that avoid this issue.
A LAMMPS simulation typically has two stages, setup and run. Most
LAMMPS errors are detected at setup time; others like a bond
stretching too far may not occur until the middle of a run.
- Similarly, the :doc:`create_atoms <create_atoms>` command generates a
lattice of atoms. For the same physical system, the ordering and
numbering of atoms by atom ID may be different depending on the number
of processors.
LAMMPS tries to flag errors and print informative error messages so
you can fix the problem. For most errors it will also print the last
input script command that it was processing. Of course, LAMMPS cannot
figure out your physics or numerical mistakes, like choosing too big a
timestep, specifying erroneous force field coefficients, or putting 2
atoms on top of each other! If you run into errors that LAMMPS
does not catch that you think it should flag, please send an email to
the `developers <https://www.lammps.org/authors.html>`_ or create an new
topic on the dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
- Some commands use random number generators which may be setup to
produce different random number streams on each processor and hence
will produce different effects when run on different numbers of
processors. A commonly-used example is the :doc:`fix langevin
<fix_langevin>` command for thermostatting.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by
looking in the log.lammps file or using the :doc:`echo command <echo>`
to see it on the screen. If you get an error like "Invalid ...
style", with ... being fix, compute, pair, etc, it means that you
mistyped the style name or that the command is part of an optional
package which was not compiled into your executable. The list of
available styles in your executable can be listed by using
:doc:`the -h command-line switch <Run_options>`. The installation and
compilation of optional packages is explained on the
:doc:`Build packages <Build_package>` doc page.
- LAMMPS tries to flag errors and print informative error messages so
you can fix the problem. For most errors it will also print the last
input script command that it was processing or even point to the
keyword that is causing troubles. Of course, LAMMPS cannot figure out
your physics or numerical mistakes, like choosing too big a timestep,
specifying erroneous force field coefficients, or putting 2 atoms on
top of each other! Also, LAMMPS does not know what you *intend* to
do, but very strictly applies the syntax as described in the
documentation. If you run into errors that LAMMPS does not catch that
you think it should flag, please send an email to the `developers
<https://www.lammps.org/authors.html>`_ or create an new topic on the
dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
For a given command, LAMMPS expects certain arguments in a specified
order. If you mess this up, LAMMPS will often flag the error, but it
may also simply read a bogus argument and assign a value that is
valid, but not what you wanted. E.g. trying to read the string "abc"
as an integer value of 0. Careful reading of the associated doc page
for the command should allow you to fix these problems. In most cases,
where LAMMPS expects to read a number, either integer or floating point,
it performs a stringent test on whether the provided input actually
is an integer or floating-point number, respectively, and reject the
input with an error message (for instance, when an integer is required,
but a floating-point number 1.0 is provided):
- If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by
looking in the log.lammps file or using the :doc:`echo command <echo>`
to see it on the screen. If you get an error like "Invalid ...
style", with ... being fix, compute, pair, etc, it means that you
mistyped the style name or that the command is part of an optional
package which was not compiled into your executable. The list of
available styles in your executable can be listed by using
:doc:`the -h command-line switch <Run_options>`. The installation and
compilation of optional packages is explained on the :doc:`Build
packages <Build_package>` doc page.
.. parsed-literal::
- For a given command, LAMMPS expects certain arguments in a specified
order. If you mess this up, LAMMPS will often flag the error, but it
may also simply read a bogus argument and assign a value that is
valid, but not what you wanted. E.g. trying to read the string "abc"
as an integer value of 0. Careful reading of the associated doc page
for the command should allow you to fix these problems. In most cases,
where LAMMPS expects to read a number, either integer or floating
point, it performs a stringent test on whether the provided input
actually is an integer or floating-point number, respectively, and
reject the input with an error message (for instance, when an integer
is required, but a floating-point number 1.0 is provided):
ERROR: Expected integer parameter instead of '1.0' in input script or data file
.. parsed-literal::
Some commands allow for using variable references in place of numeric
constants so that the value can be evaluated and may change over the
course of a run. This is typically done with the syntax *v_name* for a
parameter, where name is the name of the variable. On the other hand,
immediate variable expansion with the syntax ${name} is performed while
reading the input and before parsing commands,
ERROR: Expected integer parameter instead of '1.0' in input script or data file
.. note::
- Some commands allow for using variable references in place of numeric
constants so that the value can be evaluated and may change over the
course of a run. This is typically done with the syntax *v_name* for
a parameter, where name is the name of the variable. On the other
hand, immediate variable expansion with the syntax ${name} is
performed while reading the input and before parsing commands,
Using a variable reference (i.e. *v_name*) is only allowed if
the documentation of the corresponding command explicitly says it is.
Otherwise, you will receive an error message of this kind:
.. note::
.. parsed-literal::
Using a variable reference (i.e. *v_name*) is only allowed if
the documentation of the corresponding command explicitly says it is.
Otherwise, you will receive an error message of this kind:
ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
.. parsed-literal::
Generally, LAMMPS will print a message to the screen and logfile and
exit gracefully when it encounters a fatal error. Sometimes it will
print a WARNING to the screen and logfile and continue on; you can
decide if the WARNING is important or not. A WARNING message that is
generated in the middle of a run is only printed to the screen, not to
the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
crashes or hangs without spitting out an error message first then it
could be a bug (see :doc:`this section <Errors_bugs>`) or one of the following
cases:
ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
LAMMPS runs in the available memory a processor allows to be
allocated. Most reasonable MD runs are compute limited, not memory
limited, so this should not be a bottleneck on most platforms. Almost
all large memory allocations in the code are done via C-style malloc's
which will generate an error message if you run out of memory.
Smaller chunks of memory are allocated via C++ "new" statements. If
you are unlucky you could run out of memory just when one of these
small requests is made, in which case the code will crash or hang (in
parallel), since LAMMPS does not trap on those errors.
- Generally, LAMMPS will print a message to the screen and logfile and
exit gracefully when it encounters a fatal error. When running in
parallel this message may be stuck in an I/O buffer and LAMMPS will be
terminated before that buffer is printed. In that case you can try
adding the ``-nonblock`` or ``-nb`` command-line flag to turn off that
buffering. Please note that this should not be used for production
runs, since turning off buffering usually has a significant negative
impact on performance (even worse than :doc:`thermo_modify flush yes
<thermo_modify>`). Sometimes LAMMPS will print a WARNING to the
screen and logfile and continue on; you can decide if the WARNING is
important or not, but as a general rule do not ignore warnings that
you not understand. A WARNING message that is generated in the middle
of a run is only printed to the screen, not to the logfile, to avoid
cluttering up thermodynamic output. If LAMMPS crashes or hangs
without generating an error message first then it could be a bug
(see :doc:`this section <Errors_bugs>`).
Illegal arithmetic can cause LAMMPS to run slow or crash. This is
typically due to invalid physics and numerics that your simulation is
computing. If you see wild thermodynamic values or NaN values in your
LAMMPS output, something is wrong with your simulation. If you
suspect this is happening, it is a good idea to print out
thermodynamic info frequently (e.g. every timestep) via the
:doc:`thermo <thermo>` so you can monitor what is happening.
Visualizing the atom movement is also a good idea to ensure your model
is behaving as you expect.
- LAMMPS runs in the available memory a processor allows to be
allocated. Most reasonable MD runs are compute limited, not memory
limited, so this should not be a bottleneck on most platforms. Almost
all large memory allocations in the code are done via C-style malloc's
which will generate an error message if you run out of memory.
Smaller chunks of memory are allocated via C++ "new" statements. If
you are unlucky you could run out of memory just when one of these
small requests is made, in which case the code will crash or hang (in
parallel).
In parallel, one way LAMMPS can hang is due to how different MPI
implementations handle buffering of messages. If the code hangs
without an error message, it may be that you need to specify an MPI
setting or two (usually via an environment variable) to enable
buffering or boost the sizes of messages that can be buffered.
- Illegal arithmetic can cause LAMMPS to run slow or crash. This is
typically due to invalid physics and numerics that your simulation is
computing. If you see wild thermodynamic values or NaN values in your
LAMMPS output, something is wrong with your simulation. If you
suspect this is happening, it is a good idea to print out
thermodynamic info frequently (e.g. every timestep) via the
:doc:`thermo <thermo>` so you can monitor what is happening.
Visualizing the atom movement is also a good idea to ensure your model
is behaving as you expect.
- When running in parallel with MPI, one way LAMMPS can hang is because
LAMMPS has come across an error condition, but only on one or a few
MPI processes and not all of them. LAMMPS has two different "stop
with an error message" functions and the correct one has to be called
or else it will hang.

40
doc/src/Errors_details.rst
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@ -51,8 +51,11 @@ Parallel versus serial
^^^^^^^^^^^^^^^^^^^^^^
Issues where something is "lost" or "missing" often exhibit that issue
only when running in parallel. That doesn't mean there is no problem,
only the symptoms are not triggering an error quickly. Correspondingly,
*only* when running in parallel. That doesn't mean there is no problem
when running in serial, only the symptoms are not triggering an error.
This may be because there is no domain decomposition with just one
processor and thus all atoms are accessible, or it may be because the
problem will manifest faster with smaller subdomains. Correspondingly,
errors may be triggered faster with more processors and thus smaller
sub-domains.
@ -244,6 +247,25 @@ equal style (or similar) variables can only be expanded before the box
is defined if they do not reference anything that cannot be defined
before the box (e.g. a compute or fix reference or a thermo keyword).
.. _hint13:
Illegal ... command
^^^^^^^^^^^^^^^^^^^
These are a catchall error messages that used to be used a lot in LAMMPS
(also programmers are sometimes lazy). They usually include the name of
the source file and the line where the error happened. This can be used
to track down what caused the error (most often some form of syntax error)
by looking at the source code. However, this has two disadvantages: 1. one
has to check the source file from the exact same LAMMPS version, or else
the line number would be different or the core may have been rewritten and
that specific error does not exist anymore.
The LAMMPS developers are committed to replace these too generic error
messages with more descriptive errors, e.g. listing *which* keyword was
causing the error, so that it will be much simpler to look up the
correct syntax in the manual (and without referring to the source code).
------
.. _err0001:
@ -1029,13 +1051,15 @@ Even though the LAMMPS error message recommends to increase the "one"
parameter, this may not always be the correct solution. The neighbor
list overflow can also be a symptom for some other error that cannot be
easily detected. For example, a frequent reason for an (unexpected)
high density are incorrect box boundaries (since LAMMPS wraps atoms back
high density are incorrect box dimensions (since LAMMPS wraps atoms back
into the principal box with periodic boundaries) or coordinates provided
as fractional coordinates. In both cases, LAMMPS cannot easily know
whether the input geometry has such a high density (and thus requiring
more neighbor list storage per atom) by intention. Rather than blindly
increasing the "one" parameter, it is thus worth checking if this is
justified by the combination of density and cutoff.
as fractional coordinates (LAMMPS does not support this for data files).
In both cases, LAMMPS cannot easily know whether the input geometry has
such a high density (and thus requiring more neighbor list storage per
atom) on purpose or by accident. Rather than blindly increasing the
"one" parameter, it is thus worth checking if this is justified by the
combination of density and cutoff. This is particularly recommended
when using some tool(s) to convert input or data files.
When boosting (= increasing) the "one" parameter, it is recommended to
also increase the value for the "page" parameter to maintain the ratio

31
doc/src/Fortran.rst
View File

@ -69,10 +69,11 @@ statement. Internally, it will call either
:cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
the C library API to create the class instance. All arguments are
optional and :cpp:func:`lammps_mpi_init` will be called automatically
if it is needed. Similarly, a possible call to
:cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
function and triggered with the optional logical argument set to
``.TRUE.``. Here is a simple example:
if it is needed. Similarly, optional calls to
:cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_kokkos_finalize`,
:cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`
are integrated into the :f:func:`close` function and triggered with the
optional logical argument set to ``.TRUE.``. Here is a simple example:
.. code-block:: fortran
@ -521,8 +522,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
This method will close down the LAMMPS instance through calling
:cpp:func:`lammps_close`. If the *finalize* argument is present and
has a value of ``.TRUE.``, then this subroutine also calls
:cpp:func:`lammps_kokkos_finalize` and
:cpp:func:`lammps_mpi_finalize`.
:cpp:func:`lammps_kokkos_finalize`, :cpp:func:`lammps_mpi_finalize`,
:cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`.
:o finalize: shut down the MPI environment of the LAMMPS
library if ``.TRUE.``.
@ -530,6 +531,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:to: :cpp:func:`lammps_close`
:to: :cpp:func:`lammps_mpi_finalize`
:to: :cpp:func:`lammps_kokkos_finalize`
:to: :cpp:func:`lammps_python_finalize`
:to: :cpp:func:`lammps_plugin_finalize`
--------
@ -2096,7 +2099,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
--------
.. f:subroutine:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
.. f:function:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
This method calls :cpp:func:`lammps_create_atoms` to create additional atoms
from a given list of coordinates and a list of atom types. Additionally,
@ -2125,6 +2128,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
will be created, not dropped, and the box dimensions will be extended.
Default is ``.FALSE.``
:otype bexpand: logical,optional
:r atoms: number of created atoms
:rtype atoms: integer(c_int)
:to: :cpp:func:`lammps_create_atoms`
.. note::
@ -2149,6 +2154,18 @@ Procedures Bound to the :f:type:`lammps` Derived Type
--------
.. f:subroutine:: create_molecule(id, jsonstr)
Add molecule template from string with JSON data
.. versionadded:: TBD
:p character(len=\*) id: desired molecule-ID
:p character(len=\*) jsonstr: string with JSON data defining the molecule template
:to: :cpp:func:`lammps_create_molecule`
--------
.. f:function:: find_pair_neighlist(style[, exact][, nsub][, reqid])
Find index of a neighbor list requested by a pair style.

2
doc/src/Howto.rst
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@ -66,6 +66,7 @@ Force fields howto
:name: force_howto
:maxdepth: 1
Howto_FFgeneral
Howto_bioFF
Howto_amoeba
Howto_tip3p
@ -92,6 +93,7 @@ Packages howto
Howto_manifold
Howto_rheo
Howto_spins
Howto_apip
Tutorials howto
===============

55
doc/src/Howto_FFgeneral.rst Normal file
View File

@ -0,0 +1,55 @@
Some general force field considerations
=======================================
A compact summary of the concepts, definitions, and properties of force
fields with explicit bonded interactions (like the ones discussed in
this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
A force field has 2 parts: the formulas that define its potential
functions and the coefficients used for a particular system. To assign
parameters it is first required to assign atom types. Those are not
only based on the elements, but also on the chemical environment due to
the atoms bound to them. This often follows the chemical concept of
*functional groups*. Example: a carbon atom bound with a single bond to
a single OH-group (alcohol) would be a different atom type than a carbon
atom bound to a methyl CH3 group (aliphatic carbon). The atom types
usually then determine the non-bonded Lennard-Jones parameters and the
parameters for bonds, angles, dihedrals, and impropers. On top of that,
partial charges have to be applied. Those are usually independent of
the atom types and are determined either for groups of atoms called
residues with some fitting procedure based on quantum mechanical
calculations, or based on some increment system that add or subtract
increments from the partial charge of an atom based on the types of
the neighboring atoms.
Force fields differ in the strategies they employ to determine the
parameters and charge distribution in how generic or specific they are
which in turn has an impact on the accuracy (compare for example
CGenFF to CHARMM and GAFF to Amber). Because of the different
strategies, it is not a good idea to use a mix of parameters from
different force field *families* (like CHARMM, Amber, or GROMOS)
and that extends to the parameters for the solvent, especially
water. The publication describing the parameterization of a force
field will describe which water model to use. Changing the water
model usually leads to overall worse results (even if it may improve
on the water itself).
In addition, one has to consider that *families* of force fields like
CHARMM, Amber, OPLS, or GROMOS have evolved over time and thus provide
different *revisions* of the force field parameters. These often
corresponds to changes in the functional form or the parameterization
strategies. This may also result in changes required for simulation
settings like the preferred cutoff or how Coulomb interactions are
computed (cutoff, smoothed/shifted cutoff, or long-range with Ewald
summation or equivalent). Unless explicitly stated in the publication
describing the force field, the Coulomb interaction cannot be chosen at
will but must match the revision of the force field. That said,
liberties may be taken during the initial equilibration of a system to
speed up the process, but not for production simulations.
----------
.. _Typelabel2:
**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).

225
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@ -0,0 +1,225 @@
Adaptive-precision interatomic potentials (APIP)
================================================
The :ref:`PKG-APIP <PKG-APIP>` enables use of adaptive-precision potentials
as described in :ref:`(Immel) <Immel2025_1>`.
In the context of this package, precision refers to the accuracy of an interatomic
potential.
Modern machine-learning (ML) potentials translate the accuracy of DFT
simulations into MD simulations, i.e., ML potentials are more accurate
compared to traditional empirical potentials.
However, this accuracy comes at a cost: there is a considerable performance
gap between the evaluation of classical and ML potentials, e.g., the force
calculation of a classical EAM potential is 100-1000 times faster compared
to the ML-based ACE method.
The evaluation time difference results in a conflict between large time and
length scales on the one hand and accuracy on the other.
This conflict is resolved by an APIP model for simulations, in which the highest precision
is required only locally but not globally.
An APIP model uses a precise but
expensive ML potential only for a subset of atoms, while a fast
potential is used for the remaining atoms.
Whether the precise or the fast potential is used is determined
by a continuous switching parameter :math:`\lambda_i` that can be defined for each
atom :math:`i`.
The switching parameter can be adjusted dynamically during a simulation or
kept constant as explained below.
The potential energy :math:`E_i` of an atom :math:`i` described by an
adaptive-precision
interatomic potential is given by :ref:`(Immel) <Immel2025_1>`
.. math::
E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
according to a fast interatomic potential,
:math:`E_i^\text{(precise)}` is the potential energy according to a precise
interatomic potential and :math:`\lambda_i\in[0,1]` is the
switching parameter that decides how the potential energies are weighted.
Adaptive-precision saves computation time when the computation of the
precise potential is not required for many atoms, i.e., when
:math:`\lambda_i=1` applies for many atoms.
The currently implemented potentials are:
.. list-table::
:header-rows: 1
* - Fast potential
- Precise potential
* - :doc:`ACE <pair_pace_apip>`
- :doc:`ACE <pair_pace_apip>`
* - :doc:`EAM <pair_eam_apip>`
-
In theory, any short-range potential can be used for an adaptive-precision
interatomic potential. How to implement a new (fast or precise)
adaptive-precision
potential is explained in :ref:`here <implementing_new_apip_styles>`.
The switching parameter :math:`\lambda_i` that combines the two potentials
can be dynamically calculated during a
simulation.
Alternatively, one can set a constant switching parameter before the start
of a simulation.
To run a simulation with an adaptive-precision potential, one needs the
following components:
.. tabs::
.. tab:: dynamic switching parameter
#. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
#. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
#. :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>` to calculate :math:`\lambda_i^\text{input}`, from which :math:`\lambda_i` is calculated.
#. :doc:`fix lambda/apip <fix_lambda_apip>` to calculate the switching parameter :math:`\lambda_i`.
#. :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>` to calculate the spatial transition zone of the switching parameter.
#. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
#. :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>` to conserve the energy when switching parameters change.
#. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
#. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
.. tab:: constant switching parameter
#. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
#. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
#. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
#. :doc:`set <set>` command to set the switching parameter :math:`\lambda_i`.
#. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
#. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
#. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
----------
Example
"""""""
.. note::
How to select the values of the parameters of an adaptive-precision
interatomic potential is discussed in detail in :ref:`(Immel) <Immel2025_1>`.
.. tabs::
.. tab:: dynamic switching parameter
Lines like these would appear in the input script:
.. code-block:: LAMMPS
atom_style apip
comm_style tiled
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix 2 all lambda/apip 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
fix 3 all lambda_thermostat/apip N_rescaling 200
fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
variable myweight atom f_4
fix 5 all balance 100 1.1 rcb weight var myweight
First, the :doc:`atom_style apip <atom_style>` and the communication style are set.
.. note::
Note, that :doc:`comm_style <comm_style>` *tiled* is required for the style *rcb* of
:doc:`fix balance <fix_balance>`, but not for APIP.
However, the flexibility offered by the balancing style *rcb*, compared to the
balancing style *shift*, is advantageous for APIP.
An adaptive-precision EAM-ACE potential, for which the switching parameter
:math:`\lambda` is calculated from the CSP, is defined via
:doc:`pair_style hybrid/overlay <pair_hybrid>`.
The fixes ensure that the switching parameter is calculated, the energy conserved,
the weight for the load balancing calculated and the load-balancing itself is done.
.. tab:: constant switching parameter
Lines like these would appear in the input script:
.. code-block:: LAMMPS
atom_style apip
comm_style tiled
pair_style hybrid/overlay eam/fs/apip pace/precise/apip
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu.yace Cu
# calculate lambda somehow
variable lambda atom ...
set group all apip/lambda v_lambda
fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
variable myweight atom f_4
fix 5 all balance 100 1.1 rcb weight var myweight
First, the :doc:`atom_style apip <atom_style>` and the communication style are set.
.. note::
Note, that :doc:`comm_style <comm_style>` *tiled* is required for the style *rcb* of
:doc:`fix balance <fix_balance>`, but not for APIP.
However, the flexibility offered by the balancing style *rcb*, compared to the
balancing style *shift*, is advantageous for APIP.
An adaptive-precision EAM-ACE potential is defined via
:doc:`pair_style hybrid/overlay <pair_hybrid>`.
The switching parameter :math:`\lambda_i` of the adaptive-precision
EAM-ACE potential is set via the :doc:`set command <set>`.
The parameter is not updated during the simulation.
Therefore, the potential is conservative.
The fixes ensure that the weight for the load balancing is calculated
and the load-balancing itself is done.
----------
.. _implementing_new_apip_styles:
Implementing new APIP pair styles
"""""""""""""""""""""""""""""""""
One can introduce adaptive-precision to an existing pair style by modifying
the original pair style.
One should calculate the force
:math:`F_i = - \nabla_i \sum_j E_j^\text{original}` for a fast potential or
:math:`F_i = - (1-\nabla_i) \sum_j E_j^\text{original}` for a precise
potential from the original potential
energy :math:`E_j^\text{original}` to see where the switching parameter
:math:`\lambda_i` needs to be introduced in the force calculation.
The switching parameter :math:`\lambda_i` is known for all atoms :math:`i`
in force calculation routine.
One needs to introduce an abortion criterion based on :math:`\lambda_i` to
ensure that all not required calculations are skipped and compute time can
be saved.
Furthermore, one needs to provide the number of calculations and measure the
computation time.
Communication within the force calculation needs to be prevented to allow
effective load-balancing.
With communication, the load balancer cannot balance few calculations of the
precise potential on one processor with many computations of the fast
potential on another processor.
All changes in the pair_style pace/apip compared to the pair_style pace
are annotated and commented.
Thus, the pair_style pace/apip can serve as an example for the implementation
of new adaptive-precision potentials.
----------
.. _Immel2025_1:
**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

38
doc/src/Howto_bioFF.rst
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@ -1,22 +1,16 @@
CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields
=======================================================
A compact summary of the concepts, definitions, and properties of
force fields with explicit bonded interactions (like the ones discussed
in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly used
in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
coefficients is done either from special sections in an input data file
via the :doc:`read_data <read_data>` command or in the input script with
commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
<bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
additional tools that can use CHARMM, AMBER, or Materials Studio
generated files to assign force field coefficients and convert their
output into LAMMPS input. LAMMPS input scripts can also be generated by
`charmm-gui.org <https://charmm-gui.org/>`_.
Here we only discuss formulas implemented in LAMMPS that correspond to
formulas commonly used in the CHARMM, AMBER, COMPASS, and DREIDING force
fields. Setting coefficients is done either from special sections in an
input data file via the :doc:`read_data <read_data>` command or in the
input script with commands like :doc:`pair_coeff <pair_coeff>` or
:doc:`bond_coeff <bond_coeff>` and so on. See the :doc:`Tools <Tools>`
doc page for additional tools that can use CHARMM, AMBER, or Materials
Studio generated files to assign force field coefficients and convert
their output into LAMMPS input. LAMMPS input scripts can also be
generated by `charmm-gui.org <https://charmm-gui.org/>`_.
CHARMM and AMBER
----------------
@ -203,9 +197,11 @@ rather than individual force constants and geometric parameters that
depend on the particular combinations of atoms involved in the bond,
angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond
term <pair_hbond_dreiding>` to describe interactions involving a
hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM
or AMBER, the DREIDING force field has not been parameterized for
considering solvents (like water).
hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM or
AMBER, the DREIDING force field has not been parameterized for
considering solvents (like water) and has no rules for assigning
(partial) charges. That will seriously limit its accuracy when used for
simulating systems where those matter.
See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
@ -272,10 +268,6 @@ compatible with a subset of OPLS interactions.
----------
.. _Typelabel2:
**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
.. _howto-MacKerell:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998). J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f

20
doc/src/Howto_spc.rst
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@ -1,5 +1,5 @@
SPC water model
===============
SPC and SPC/E water model
=========================
The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the three atoms.
@ -8,6 +8,18 @@ the two O-H bonds and the H-O-H angle rigid. A bond style of
*harmonic* and an angle style of *harmonic* or *charmm* should also be
used.
One suitable pair style with cutoff Coulomb would for instance be:
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
These commands are examples for a long-range Coulomb model:
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
* :doc:`kspace_style pppm <kspace_style>`
* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
* :doc:`kspace_style pppm/disp <kspace_style>`
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model.
@ -39,7 +51,9 @@ the SPC and SPC/E models.
Below is the code for a LAMMPS input file and a molecule file
(``spce.mol``) of SPC/E water for use with the :doc:`molecule command
<molecule>` demonstrating how to set up a small bulk water system for
SPC/E with rigid bonds.
SPC/E with rigid bonds. For simplicity and speed the example uses a
cutoff Coulomb. Most production simulations require long-range Coulomb
instead.
.. code-block:: LAMMPS

15
doc/src/Howto_tip3p.rst
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@ -5,17 +5,24 @@ The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
<howto-tip3p>` specifies a 3-site rigid water molecule with charges and
Lennard-Jones parameters assigned to each of the three atoms.
A suitable pair style with cutoff Coulomb would be:
One suitable pair style with cutoff Coulomb would for instance be:
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
or these commands for a long-range Coulomb model:
These commands are examples for a long-range Coulomb model:
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
* :doc:`kspace_style pppm <kspace_style>`
* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
* :doc:`kspace_style pppm/disp <kspace_style>`
And these pair styles are compatible with the CHARMM force field:
* :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`
* :doc:`pair_style lj/charmm/coul/long <pair_charmm>`
* :doc:`pair_style lj/charmmfsw/coul/long <pair_charmm>`
In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be
used to hold the two O-H bonds and the H-O-H angle rigid. A bond style
of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
@ -100,7 +107,9 @@ ignored.
Below is the code for a LAMMPS input file and a molecule file
(``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command
<molecule>` demonstrating how to set up a small bulk water system for
TIP3P with rigid bonds.
TIP3P with rigid bonds. For simplicity and speed the example uses a
cutoff Coulomb. Most production simulations require long-range Coulomb
instead.
.. code-block:: LAMMPS

133
doc/src/Howto_tip4p.rst
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@ -1,5 +1,5 @@
TIP4P water model
=================
TIP4P and OPC water models
==========================
The four-point TIP4P rigid water model extends the traditional
:doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
@ -9,9 +9,11 @@ the oxygen along the bisector of the HOH bond angle. A bond style of
:doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
style :doc:`zero <angle_zero>` can be used.
style :doc:`zero <angle_zero>` can be used. Very similar to the TIP4P
model is the OPC water model. It can be realized the same way as TIP4P
but has different geometry and force field parameters.
There are two ways to implement TIP4P water in LAMMPS:
There are two ways to implement TIP4P-like water in LAMMPS:
#. Use a specially written pair style that uses the :ref:`TIP3P geometry
<tip3p_molecule>` without the point M. The point M location is then
@ -21,7 +23,10 @@ There are two ways to implement TIP4P water in LAMMPS:
computationally very efficient, but the charge distribution in space
is only correct within the tip4p labeled styles. So all other
computations using charges will "see" the negative charge incorrectly
on the oxygen atom.
located on the oxygen atom unless they are specially written for using
the TIP4P geometry internally as well, e.g. :doc:`compute dipole/tip4p
<compute_dipole>`, :doc:`fix efield/tip4p <fix_efield>`, or
:doc:`kspace_style pppm/tip4p <kspace_style>`.
This can be done with the following pair styles for Coulomb with a cutoff:
@ -68,77 +73,90 @@ TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
parameters adjusted for use with a long-range Coulombic solver
(e.g. Ewald or PPPM in LAMMPS). Note that for implicit TIP4P models the
OM distance is specified in the :doc:`pair_style <pair_style>` command,
not as part of the pair coefficients.
not as part of the pair coefficients. Also parameters for the OPC
model (:ref:`Izadi <Izadi>`) are provided.
.. list-table::
:header-rows: 1
:widths: 36 19 13 15 17
:widths: 40 12 12 14 11 11
* - Parameter
- TIP4P (original)
- TIP4P/Ice
- TIP4P/2005
- TIP4P (Ewald)
- OPC
* - O mass (amu)
- 15.9994
- 15.9994
- 15.9994
- 15.9994
- 15.9994
* - H mass (amu)
- 1.008
- 1.008
- 1.008
- 1.008
- 1.008
* - O or M charge (:math:`e`)
- -1.040
- -1.1794
- -1.1128
- -1.04844
- -1.3582
* - H charge (:math:`e`)
- 0.520
- 0.5897
- 0.5564
- 0.52422
- 0.6791
* - LJ :math:`\epsilon` of OO (kcal/mole)
- 0.1550
- 0.21084
- 0.1852
- 0.16275
- 0.21280
* - LJ :math:`\sigma` of OO (:math:`\AA`)
- 3.1536
- 3.1668
- 3.1589
- 3.16435
- 3.1660
* - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
* - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
- 1.0
- 1.0
- 1.0
- 1.0
- 1.0
* - :math:`r_0` of OH bond (:math:`\AA`)
- 0.9572
- 0.9572
- 0.9572
- 0.9572
- 0.8724
* - :math:`\theta_0` of HOH angle
- 104.52\ :math:`^{\circ}`
- 104.52\ :math:`^{\circ}`
- 104.52\ :math:`^{\circ}`
- 104.52\ :math:`^{\circ}`
- 103.60\ :math:`^{\circ}`
* - OM distance (:math:`\AA`)
- 0.15
- 0.1577
- 0.1546
- 0.1250
- 0.1594
Note that the when using the TIP4P pair style, the neighbor list cutoff
Note that the when using a TIP4P pair style, the neighbor list cutoff
for Coulomb interactions is effectively extended by a distance 2 \* (OM
distance), to account for the offset distance of the fictitious charges
on O atoms in water molecules. Thus it is typically best in an
on O atoms in water molecules. Thus, it is typically best in an
efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
distance), to shrink the size of the neighbor list. This leads to
slightly larger cost for the long-range calculation, so you can test the
@ -149,7 +167,9 @@ cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
Below is the code for a LAMMPS input file using the implicit method and
the :ref:`TIP3P molecule file <tip3p_molecule>`. Because the TIP4P
charges are different from TIP3P they need to be reset (or the molecule
file changed):
file changed). For simplicity and speed the example uses a cutoff
Coulomb. Most production simulations require long-range Coulomb
instead.
.. code-block:: LAMMPS
@ -192,6 +212,94 @@ file changed):
run 20000
write_data tip4p-implicit.data nocoeff
When constructing an OPC model, we cannot use the ``tip3p.mol`` file due
to the different geometry. Below is a molecule file providing the 3
sites of an implicit OPC geometry for use with TIP4P styles. Note, that
the "Shake" and "Special" sections are missing here. Those will be
auto-generated by LAMMPS when the molecule file is loaded *after* the
simulation box has been created. These sections are required only when
the molecule file is loaded *before*.
.. _opc3p_molecule:
.. code-block::
# Water molecule. 3 point geometry for OPC model
3 atoms
2 bonds
1 angles
Coords
1 0.00000 -0.06037 0.00000
2 0.68558 0.50250 0.00000
3 -0.68558 0.50250 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -1.3582
2 0.6791
3 0.6791
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Below is a LAMMPS input file using the implicit method to implement
the OPC model using the molecule file from above and including the
PPPM long-range Coulomb solver.
.. code-block:: LAMMPS
units real
atom_style full
region box block -5 5 -5 5 -5 5
create_box 2 box bond/types 1 angle/types 1 &
extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
mass 1 15.9994
mass 2 1.008
pair_style lj/cut/tip4p/long 1 2 1 1 0.1594 12.0
pair_coeff 1 1 0.2128 3.166
pair_coeff 2 2 0.0 1.0
bond_style zero
bond_coeff 1 0.8724
angle_style zero
angle_coeff 1 103.6
kspace_style pppm/tip4p 1.0e-5
molecule water opc3p.mol # this file has the OPC geometry but is without M
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
fix rigid all shake 0.001 10 10000 b 1 a 1
minimize 0.0 0.0 1000 10000
reset_timestep 0
timestep 1.0
velocity all create 300.0 5463576
fix integrate all nvt temp 300 300 100.0
thermo_style custom step temp press etotal pe
thermo 1000
run 20000
write_data opc-implicit.data nocoeff
Below is the code for a LAMMPS input file using the explicit method and
a TIP4P molecule file. Because of using :doc:`fix rigid/small
<fix_rigid>` no bonds need to be defined and thus no extra storage needs
@ -279,3 +387,8 @@ Phys, 79, 926 (1983).
**(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
https://doi.org/10.1063/1.2121687
.. _Izadi:
**(Izadi)** Izadi, Anandakrishnan, Onufriev, J. Phys. Chem. Lett., 5, 21, 3863 (2014)
https://doi.org/10.1021/jz501780a

4
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@ -87,7 +87,9 @@ atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
so that fix rigid/small can identify rigid bodies by their molecule ID.
Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to
exclude computing intramolecular non-bonded interactions, since those
are removed by the rigid fix anyway:
are removed by the rigid fix anyway. For simplicity and speed the
example uses a cutoff Coulomb. Most production simulations require
long-range Coulomb instead.
.. code-block:: LAMMPS

4
doc/src/Install_git.rst
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@ -21,8 +21,8 @@ You can follow the LAMMPS development on 4 different git branches:
* **develop** : this branch follows the ongoing development and is
updated with every merge commit of a pull request
* **release** : this branch is updated with every "feature release";
updates are always "fast-forward" merges from *develop*
* **release** : this branch is updated with every "feature release"
and updates are always "fast-forward" merges from *develop*
* **maintenance** : this branch collects back-ported bug fixes from the
*develop* branch to the *stable* branch. It is used to update the
*stable* branch for "stable update releases".

5
doc/src/Intro_authors.rst
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@ -84,8 +84,9 @@ lammps.org". General questions about LAMMPS should be posted in the
\normalsize
Past developers include Paul Crozier and Mark Stevens, both at SNL,
and Ray Shan, now at Materials Design.
Past core developers include Paul Crozier and Mark Stevens, both at SNL,
and Ray Shan while at SNL and later at Materials Design, now at Thermo
Fisher Scientific.
----------

25
doc/src/Intro_portability.rst
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@ -28,8 +28,9 @@ Build systems
LAMMPS can be compiled from source code using a (traditional) build
system based on shell scripts, a few shell utilities (grep, sed, cat,
tr) and the GNU make program. This requires running within a Bourne
shell (``/bin/sh``). Alternatively, a build system with different back
ends can be created using CMake. CMake must be at least version 3.16.
shell (``/bin/sh`` or ``/bin/bash``). Alternatively, a build system
with different back ends can be created using CMake. CMake must be
at least version 3.16.
Operating systems
^^^^^^^^^^^^^^^^^
@ -40,11 +41,18 @@ Also, compilation and correct execution on macOS and Windows (using
Microsoft Visual C++) is checked automatically for the largest part of
the source code. Some (optional) features are not compatible with all
operating systems, either through limitations of the corresponding
LAMMPS source code or through incompatibilities of source code or
build system of required external libraries or packages.
LAMMPS source code or through incompatibilities or build system
limitations of required external libraries or packages.
Executables for Windows may be created natively using either Cygwin or
Visual Studio or with a Linux to Windows MinGW cross-compiler.
Executables for Windows may be created either natively using Cygwin,
MinGW, Intel, Clang, or Microsoft Visual C++ compilers, or with a Linux
to Windows MinGW cross-compiler. Native compilation is supported using
Microsoft Visual Studio or a terminal window (using the CMake build
system).
Executables for macOS may be created either using Xcode or GNU compilers
installed with Homebrew. In the latter case, building of LAMMPS through
Homebrew instead of a manual compile is also possible.
Additionally, FreeBSD and Solaris have been tested successfully to
run LAMMPS and produce results consistent with those on Linux.
@ -61,8 +69,9 @@ CPU architectures
^^^^^^^^^^^^^^^^^
The primary CPU architecture for running LAMMPS is 64-bit x86, but also
32-bit x86, and 64-bit ARM and PowerPC (64-bit, Little Endian) are
regularly tested.
64-bit ARM and PowerPC (64-bit, Little Endian) are currently regularly
tested. Further architectures are tested by Linux distributions that
bundle LAMMPS.
Portability compliance
^^^^^^^^^^^^^^^^^^^^^^

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@ -11,6 +11,7 @@ This section documents the following functions:
- :cpp:func:`lammps_mpi_finalize`
- :cpp:func:`lammps_kokkos_finalize`
- :cpp:func:`lammps_python_finalize`
- :cpp:func:`lammps_plugin_finalize`
- :cpp:func:`lammps_error`
--------------------
@ -119,5 +120,10 @@ calling program.
-----------------------
.. doxygenfunction:: lammps_plugin_finalize
:project: progguide
-----------------------
.. doxygenfunction:: lammps_error
:project: progguide

5
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@ -27,6 +27,7 @@ It documents the following functions:
- :cpp:func:`lammps_scatter`
- :cpp:func:`lammps_scatter_subset`
- :cpp:func:`lammps_create_atoms`
- :cpp:func:`lammps_create_molecule`
-----------------------
@ -103,4 +104,8 @@ It documents the following functions:
.. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand)
:project: progguide
-----------------------
.. doxygenfunction:: lammps_create_molecule
:project: progguide

55
doc/src/Packages_details.rst
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@ -28,6 +28,7 @@ gives those details.
* :ref:`ADIOS <PKG-ADIOS>`
* :ref:`AMOEBA <PKG-AMOEBA>`
* :ref:`APIP <PKG-APIP>`
* :ref:`ASPHERE <PKG-ASPHERE>`
* :ref:`ATC <PKG-ATC>`
* :ref:`AWPMD <PKG-AWPMD>`
@ -186,6 +187,60 @@ provided by the Ponder group in their
----------
.. _PKG-APIP:
APIP package
------------
**Contents:**
This package provides adaptive-precision interatomic potentials (APIP) as
described in:
D. Immel, R. Drautz and G. Sutmann, "Adaptive-precision potentials for
large-scale atomistic simulations", J. Chem. Phys. 162, 114119 (2025)
`link <immel2025_doi_>`_
Adaptive-precision means, that a fast interatomic potential, such as EAM,
is coupled to a precise interatomic potential, such as ACE.
This package provides the required pair_styles and fixes to run an efficient,
energy-conserving adaptive-precision simulation.
In the context of this package, precision refers to the accuracy of an interatomic
potential.
.. _immel2025_doi: https://doi.org/10.1063/5.0245877
**Authors:**
This package was written by David Immel^1,
Ralf Drautz^2 and Godehard Sutmann^1^2.
^1: Forschungszentrum Juelich, Juelich, Germany
^2: Ruhr-University Bochum, Bochum, Germany
**Install:**
The APIP package requires also the installation of ML-PACE, which has
:ref:`specific installation instructions <ml-pace>` on the
:doc:`Build extras <Build_extras>` page.
**Supporting info:**
* ``src/APIP``: filenames -> commands
* :doc:`Howto APIP <Howto_apip>`
* ``examples/PACKAGES/apip``
* :doc:`fix atom_weight/apip <fix_atom_weight_apip>`
* :doc:`fix lambda/apip <fix_lambda_apip>`
* :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`
* :doc:`pair_style eam/apip <pair_eam_apip>`
* :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`
* :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`
* :doc:`pair_style pace/apip <pair_pace_apip>`
----------
.. _PKG-ASPHERE:
ASPHERE package

5
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@ -38,6 +38,11 @@ whether an extra library is needed to build and use the package:
- :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
- amoeba
- no
* - :ref:`APIP <PKG-APIP>`
- adaptive-precision interatomic potentials
- :doc:`Howto APIP <Howto_apip>`
- ``PACKAGES/apip``
- ext
* - :ref:`ASPHERE <PKG-ASPHERE>`
- aspherical particle models
- :doc:`Howto spherical <Howto_spherical>`

20
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@ -5,18 +5,28 @@ LAMMPS has several commands which can be used to invoke Python
code directly from an input script:
* :doc:`python <python>`
* :doc:`variable python <variable>`
* :doc:`python-style variables <variable>`
* :doc:`equal-style and atom-style variables with formulas containing Python function wrappers <variable>`
* :doc:`fix python/invoke <fix_python_invoke>`
* :doc:`pair_style python <pair_python>`
The :doc:`python <python>` command which can be used to define and
execute a Python function that you write the code for. The Python
function can also be assigned to a LAMMPS python-style variable via
the :doc:`variable <variable>` command. Each time the variable is
The :doc:`python <python>` command can be used to define and execute a
Python function that you write the code for. The Python function can
also be assigned to a LAMMPS python-style variable via the
:doc:`variable <variable>` command. Each time the variable is
evaluated, either in the LAMMPS input script itself, or by another
LAMMPS command that uses the variable, this will trigger the Python
function to be invoked.
The Python function can also be referenced in the formula used to
define an :doc:`equal-style or atom-style variable <variable>`, using
the syntax for a :doc:`Python function wrapper <variable>`. This make
it easy to pass LAMMPS-related arguments to the Python function, as
well as to invoke it whenever the equal- or atom-style variable is
evaluated. For an atom-style variable it means the Python function
can be invoked once per atom, using per-atom properties as arguments
to the function.
The Python code for the function can be included directly in the input
script or in an auxiliary file. The function can have arguments which
are mapped to LAMMPS variables (also defined in the input script) and

33
doc/src/Speed_compare.rst
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@ -75,15 +75,34 @@ section below for examples where this has been done.
**Differences between the GPU and KOKKOS packages:**
* The GPU package accelerates only pair force, neighbor list, and (parts
of) PPPM calculations. The KOKKOS package attempts to run most of the
of) PPPM calculations (and runs the remaining force computations on
the CPU concurrently). The KOKKOS package attempts to run most of the
calculation on the GPU, but can transparently support non-accelerated
code (with a performance penalty due to having data transfers between
host and GPU).
* The list of which styles are accelerated by the GPU or KOKKOS package
differs with some overlap.
* The GPU package requires neighbor lists to be built on the CPU when using
hybrid pair styles, exclusion lists, or a triclinic simulation box.
* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus supports
NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is
typically resulting in equal or better performance over OpenCL.
* OpenCL in the GPU package does theoretically also support Intel CPUs or
Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
is superior.
* The GPU package benefits from running multiple MPI processes (2-8) per
GPU to parallelize the non-GPU accelerated styles. The KOKKOS package
usually not, especially when all parts of the calculation have KOKKOS
support.
* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus
supports NVIDIA, AMD, and Intel GPUs well. On NVIDIA or AMD hardware,
using native CUDA or HIP compilation, respectively, with either GPU or
KOKKOS results in equal or better performance over OpenCL.
* OpenCL in the GPU package supports NVIDIA, AMD, and Intel GPUs at the
*same time* and with the *same executable*. KOKKOS currently does not
support OpenCL.
* The GPU package supports single precision floating point, mixed
precision floating point, and double precision floating point math on
the GPU. This must be chosen at compile time. KOKKOS currently only
supports double precision floating point math. Using single or mixed
precision (recommended) results in significantly improved performance
on consumer GPUs for some loss in accuracy (which is rather small with
mixed precision). Single and mixed precision support for KOKKOS is in
development (no ETA yet).
* Some pair styles (for example :doc:`snap <pair_snap>`, :doc:`mliap
<pair_mliap>` or :doc:`reaxff <pair_reaxff>` in the KOKKOS package have
seen extensive optimizations and specializations for GPUs and CPUs.

235
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@ -1,16 +1,218 @@
Measuring performance
=====================
Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.
Factors that influence performance
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The best way to do this is run the your system (actual number of
atoms) for a modest number of timesteps (say 100 steps) on several
different processor counts, including a single processor if possible.
Do this for an equilibrium version of your system, so that the
100-step timings are representative of a much longer run. There is
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
Before trying to make your simulation run faster, you should understand
how it currently performs and where the bottlenecks are. We generally
distinguish between serial performance (how fast can a single process do
the calculations?) and parallel efficiency (how much faster does a
calculation get by using more processes?). There are many factors
affecting either and below are some lists discussing some commonly
known but also some less known factors.
Factors affecting serial performance (in no specific order):
* CPU hardware: clock rate, cache sizes, CPU architecture (instructions
per clock, vectorization support, fused multiply-add support and more)
* RAM speed and number of channels that the CPU can use to access RAM
* Cooling: CPUs can change the CPU clock based on thermal load, thus the
degree of cooling can affect the speed of a CPU. Sometimes even the
temperature of neighboring compute nodes in a cluster can make a
difference.
* Compiler optimization: most of LAMMPS is written to be easy to modify
and thus compiler optimization can speed up calculations. However, too
aggressive compiler optimization can produce incorrect results or
crashes (during compilation or at runtime).
* Source code improvements: styles in the OPT, OPENMP, and INTEL package
can be faster than their base implementation due to improved data
access patterns, cache efficiency, or vectorization. Compiler optimization
is required to take full advantage of these.
* Number and kind of fixes, computes, or variables used during a simulation,
especially if they result in collective communication operations
* Pair style cutoffs and system density: calculations get slower the more
neighbors are in the neighbor list and thus for which interactions need
to be computed. Force fields with pair styles that compute interactions
between triples or quadruples of atoms or that use embedding energies or
charge equilibration will need to walk the neighbor lists multiple times.
* Neighbor list settings: tradeoff between neighbor list skin (larger
skin = more neighbors, more distances to compute before applying the
cutoff) and frequency of neighbor list builds (larger skin = fewer
neighbor list builds).
* Proximity of per-atom data in physical memory that for atoms that are
close in space improves cache efficiency (thus LAMMPS will by default
sort atoms in local storage accordingly)
* Using r-RESPA multi-timestepping or a SHAKE or RATTLE fix to constrain
bonds with higher-frequency vibrations may allow a larger (outer) timestep
and thus fewer force evaluations (usually the most time consuming step in
MD) for the same simulated time (with some tradeoff in accuracy).
Factors affecting parallel efficiency (in no specific order):
* Bandwidth and latency of communication between processes. This can vary a
lot between processes on the same CPU or physical node and processes
on different physical nodes and there vary between different
communication technologies (like Ethernet or InfiniBand or other
high-speed interconnects)
* Frequency and complexity of communication patterns required
* Number of "work units" (usually correlated with the number of atoms
and choice of force field) per MPI-process required for one time step
(if this number becomes too small, the cost of communication becomes
dominant).
* Choice of parallelization method (MPI-only, OpenMP-only, MPI+OpenMP,
MPI+GPU, MPI+GPU+OpenMP)
* Algorithmic complexity of the chosen force field (pair-wise vs. many-body
potential, Ewald vs. PPPM vs. (compensated or smoothed) cutoff-Coulomb)
* Communication cutoff: a larger cutoff results in more ghost atoms and
thus more data that needs to be communicated
* Frequency of neighbor list builds: during a neighbor list build the
domain decomposition is updated and the list of ghost atoms rebuilt
which requires multiple global communication steps
* FFT-grid settings and number of MPI processes for kspace style PPPM:
PPPM uses parallel 3d FFTs which will drop much faster in parallel
efficiency with respect to the number of MPI processes than other
parts of the force computation. Thus using MPI+OpenMP parallelization
or :doc:`run style verlet/split <run_style>` can improve parallel
efficiency by limiting the number of MPI processes used for the FFTs.
* Load (im-)balance: LAMMPS' domain decomposition assumes that atoms are
evenly distributed across the entire simulation box. If there are
areas of vacuum, this may lead to different amounts of work for
different MPI processes. Using the :doc:`processors command
<processors>` to change the spatial decomposition, or MPI+OpenMP
parallelization instead of only-MPI to have larger sub-domains, or the
(fix) balance command (without or with switching to communication style
tiled) to change the sub-domain volumes are all methods that
can help to avoid load imbalances.
Examples comparing serial performance
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Before looking at your own input deck(s), you should get some reference
data from a known input so that you know what kind of performance you
should expect from your input. For the following we therefore use the
``in.rhodo.scaled`` input file and ``data.rhodo`` data file from the
``bench`` folder. This is a system of 32000 atoms using the CHARMM force
field and long-range electrostatics running for 100 MD steps. The
performance data is printed at the end of a run and only measures the
performance during propagation and excludes the setup phase.
Running with a single MPI process on an AMD Ryzen Threadripper PRO
9985WX CPU (64 cores, 128 threads, base clock: 3.2GHz, max. clock
5.4GHz, L1/L2/L3 cache 5MB/64MB/256MB, 8 DDR5-6400 memory channels) one
gets the following performance report:
.. code-block::
Performance: 1.232 ns/day, 19.476 hours/ns, 7.131 timesteps/s, 228.197 katom-step/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
The %CPU value should be at 100% or very close. Lower values would
be an indication that there are *other* processes also using the same
CPU core and thus invalidating the performance data. The katom-step/s
value is best suited for comparisons, since it is fairly independent
from the system size. The `in.rhodo.scaled` input can be easily made
larger through replication in the three dimensions by settings variables
"x", "y", "z" to values other than 1 from the command line with the
"-var" flag. Example:
- 32000 atoms: 228.8 katom-step/s
- 64000 atoms: 231.6 katom-step/s
- 128000 atoms: 231.1 katom-step/s
- 256000 atoms: 226.4 katom-step/s
- 864000 atoms: 229.6 katom-step/s
Comparing to an AMD Ryzen 7 7840HS CPU (8 cores, 16 threads, base clock
3.8GHz, max. clock 5.1GHz, L1/L2/L3 cache 512kB/8MB/16MB, 2 DDR5-5600
memory channels), we get similar single core performance (~220
katom-step/s vs. ~230 katom-step/s) due to the similar clock and
architecture:
- 32000 atoms: 219.8 katom-step/s
- 64000 atoms: 222.5 katom-step/s
- 128000 atoms: 216.8 katom-step/s
- 256000 atoms: 221.0 katom-step/s
- 864000 atoms: 221.1 katom-step/s
Switching to an older Intel Xeon E5-2650 v4 CPU (12 cores, 12 threads,
base clock 2.2GHz, max. clock 2.9GHz, L1/L2/L3 cache (64kB/256kB/30MB, 4
DDR4-2400 memory channels) leads to a lower performance of approximately
109 katom-step/s due to differences in architecture and clock. In all
cases, when looking at multiple runs, the katom-step/s property
fluctuates by approximately 1% around the average.
From here on we are looking at the performance for the 256000 atom system only
and change several settings incrementally:
#. No compiler optimization GCC (-Og -g): 183.8 katom-step/s
#. Moderate optimization with debug info GCC (-O2 -g): 231.1 katom-step/s
#. Full compiler optimization GCC (-DNDEBUG -O3): 236.0 katom-step/s
#. Aggressive compiler optimization GCC (-O3 -ffast-math -march=native): 239.9 katom-step/s
#. Source code optimization in OPENMP package (1 thread): 266.7 katom-step/s
#. Use *fix nvt* instead of *fix npt* (compute virial only every 50 steps): 272.9 katom-step/s
#. Increase pair style cutoff by 2 :math:`\AA`: 181.2 katom-step/s
#. Use tight PPPM convergence (1.0e-6 instead of 1.0e-4): 161.9 katom-step/s
#. Use Ewald summation instead of PPPM (at 1.0e-4 convergence): 19.9 katom-step/s
The numbers show that gains from aggressive compiler optimizations are
rather small in LAMMPS, the data access optimizations in the OPENMP (and
OPT) packages are more prominent. On the other side, using more
accurate force field settings causes, not unexpectedly, a significant
slowdown (to about half the speed). Finally, using regular Ewald
summation causes a massive slowdown due to the bad algorithmic scaling
with system size.
Examples comparing parallel performance
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The parallel performance usually goes on top of the serial performance.
Using twice as many processors should increase the performance metric
by up to a factor of two. With the number of processors *N* and the
serial performance :math:`p_1` and the performance for *N* processors
:math:`p_N` we can define a *parallel efficiency* in percent as follows:
.. math::
P_{eff} = \frac{p_N}{p_1 \cdot N} \cdot 100\%
For the AMD Ryzen Threadripper PRO 9985WX CPU and the serial
simulation settings of point 6. from above, we get the following
parallel efficiency data for the 256000 atom system:
- 1 MPI task: 273.6 katom-step/s, :math:`P_{eff} = 100\%`
- 2 MPI tasks: 530.6 katom-step/s, :math:`P_{eff} = 97\%`
- 4 MPI tasks: 1.021 Matom-step/s, :math:`P_{eff} = 93\%`
- 8 MPI tasks: 1.837 Matom-step/s, :math:`P_{eff} = 84\%`
- 16 MPI tasks: 3.574 Matom-step/s, :math:`P_{eff} = 82\%`
- 32 MPI tasks: 6.479 Matom-step/s, :math:`P_{eff} = 74\%`
- 64 MPI tasks: 9.032 Matom-step/s, :math:`P_{eff} = 52\%`
- 128 MPI tasks: 12.03 Matom-step/s, :math:`P_{eff} = 34\%`
The 128 MPI tasks run uses CPU cores from hyper-threading.
For a small system with only 32000 atoms the parallel efficiency
drops off earlier when the number of work units is too small relative
to the communication overhead:
- 1 MPI task: 270.8 katom-step/s, :math:`P_{eff} = 100\%`
- 2 MPI tasks: 529.3 katom-step/s, :math:`P_{eff} = 98\%`
- 4 MPI tasks: 989.8 katom-step/s, :math:`P_{eff} = 91\%`
- 8 MPI tasks: 1.832 Matom-step/s, :math:`P_{eff} = 85\%`
- 16 MPI tasks: 3.463 Matom-step/s, :math:`P_{eff} = 80\%`
- 32 MPI tasks: 5.970 Matom-step/s, :math:`P_{eff} = 69\%`
- 64 MPI tasks: 7.477 Matom-step/s, :math:`P_{eff} = 42\%`
- 128 MPI tasks: 8.069 Matom-step/s, :math:`P_{eff} = 23\%`
Measuring performance of your input deck
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The best way to do this is run the your system (actual number of atoms)
for a modest number of timesteps (say 100 steps) on several different
processor counts, including a single processor if possible. Do this for
an equilibrium version of your system, so that the 100-step timings are
representative of a much longer run. There is typically no need to run
for 1000s of timesteps to get accurate timings; you can simply
extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. The
@ -28,12 +230,15 @@ breakdown and relative percentages. For example, trying different
options for speeding up the long-range solvers will have little impact
if they only consume 10% of the run time. If the pairwise time is
dominating, you may want to look at GPU or OMP versions of the pair
style, as discussed below. Comparing how the percentages change as
you increase the processor count gives you a sense of how different
operations within the timestep are scaling. Note that if you are
running with a Kspace solver, there is additional output on the
breakdown of the Kspace time. For PPPM, this includes the fraction
spent on FFTs, which can be communication intensive.
style, as discussed below. Comparing how the percentages change as you
increase the processor count gives you a sense of how different
operations within the timestep are scaling. If you are using PPPM as
Kspace solver, you can turn on an additional output with
:doc:`kspace_modify fftbench yes <kspace_modify>` which measures the
time spent during PPPM on the 3d FFTs, which can be communication
intensive for larger processor counts. This provides an indication
whether it is worth trying out alternatives to the default FFT settings
for additional performance.
Another important detail in the timing info are the histograms of
atoms counts and neighbor counts. If these vary widely across

102
doc/src/Tools.rst
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@ -92,6 +92,7 @@ Miscellaneous tools
* :ref:`LAMMPS coding standards <coding_standard>`
* :ref:`emacs <emacs>`
* :ref:`i-PI <ipi>`
* :ref:`JSON support <json>`
* :ref:`kate <kate>`
* :ref:`LAMMPS-GUI <lammps_gui>`
* :ref:`LAMMPS magic patterns for file(1) <magic>`
@ -364,7 +365,7 @@ These tools were provided by Aidan Thompson at Sandia
.. _fep:
fep tool
------------------
--------
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@ -379,7 +380,7 @@ See README file in the tools/fep directory.
.. _ipi:
i-PI tool
-------------------
---------
.. versionchanged:: 27June2024
@ -432,6 +433,87 @@ tools/createatoms tool's input file.
----------
.. _json:
JSON support files
------------------
.. versionadded:: 12June2025
The ``tools/json`` directory contains files and tools to support
using `JSON format <https://www.json.org/>`_ files in LAMMPS.
Currently only the :doc:`molecule command <molecule>` supports
files in JSON format directly, but this is planned to be expanded
in the future.
JSON file validation
^^^^^^^^^^^^^^^^^^^^
The JSON syntax is independent of its content, and thus the data in the
file must follow suitable conventions to be correctly parsed during
input. This can be done in a portable fashion using a `JSON schema file
<https://json-schema.org/>`_ (which is in JSON format as well) to define
those conventions. A suitable JSON validator software can then validate
JSON files against the requirements. Validating a particular JSON file
against a schema ensures that both, the syntax *and* the conventions
are followed. This is useful when writing or editing JSON files in a
text editor or when writing a pre-processing script or tool to create
JSON files for a specific purpose in LAMMPS. It **cannot** check
whether the file contents are physically meaningful, though.
One such validator tool is `check-jsonschema
<https://check-jsonschema.readthedocs.io/>`_ which is written in Python
and can be installed using the `pip Python package manager
<https://pypi.org/>`_, best in a virtual environment as shown below (for
a Bourne Shell command line):
.. code-block:: sh
python -m venv validate-json
source validate-json/bin/activate
pip install --upgrade pip
pip install check-jsonschema
To validate a specific JSON file against a provided schema (here for
a :doc:`molecule command file <molecule>` you would then run for example:
.. code-block:: sh
check-jsonschema --schemafile molecule-schema.json tip3p.json
The latest schema files are also maintained and available for download
at https://download.lammps.org/json . This enables validation of JSON
files even if the LAMMPS sources are not locally available. Example:
.. code-block:: sh
check-jsonschema --schemafile https://download.lammps.org/json/molecule-schema.json tip3p.json
JSON file format normalization
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are extensions to the strict JSON format that allow for comments
or ignore additional (dangling) commas. The ``reformat-json.cpp`` tool
will read JSON files in relaxed format, but write it out in strict format.
It is also possible to change the level of indentation from -1 (all data
one long line) to any positive integer value. The original file will be
backed up (.bak added to file name) and then overwritten.
Manual compilation (it will be automatically included in the CMake build
if building tools is requested during CMake configuration):
.. code-block:: sh
g++ -I <path/to/lammps/src> -o reformat-json reformat-json.cpp
Usage:
.. parsed-literal::
reformat-json <indent-width> <json-file-1> [<json-file-2> ...]
----------
.. _kate:
kate tool
@ -475,9 +557,13 @@ beginners to start with LAMMPS, it is also the expectation that
LAMMPS-GUI users will eventually transition to workflows that most
experienced LAMMPS users employ.
All features have been extensively exposed to keyboard shortcuts, so
that there is also appeal for experienced LAMMPS users for prototyping
and testing simulation setups.
.. image:: JPG/lammps-gui-screen.png
:align: center
:scale: 50%
Features have been extensively exposed to keyboard shortcuts, so that
there is also appeal for experienced LAMMPS users for prototyping and
testing simulation setups.
Features
^^^^^^^^
@ -502,7 +588,7 @@ Here are a few highlights of LAMMPS-GUI
- 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'
- Support for GPU, INTEL, KOKKOS/OpenMP, OPENMAP, and OPT and accelerator packages
- Support for GPU, INTEL, KOKKOS/OpenMP, OPENMP, and OPT accelerator packages
Parallelization
^^^^^^^^^^^^^^^
@ -523,8 +609,8 @@ with CMake is required.
The LAMMPS-GUI has been successfully compiled and tested on:
- Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
- Fedora Linux 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
- Fedora Linux 40 x86\_64 using GCC 14, Qt version 6.7
- Fedora Linux 41 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
- Fedora Linux 41 x86\_64 using GCC 14, Qt version 6.8
- Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
- Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.40, Qt version 6.7

6
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@ -10,7 +10,7 @@ Syntax
atom_style style args
* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
* style = *amoeba* or *angle* or *apip* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
.. parsed-literal::
@ -117,6 +117,10 @@ the Additional Information section below.
- *bond* + "angle data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers with stiffness
* - *apip*
- *atomic* + apip_lambda, apip_lambda_required, apip_lambda_input, apip_lambda_const, apip_lambda_input_ta, apip_e_fast, apip_e_precise, apip_f_const_lambda, apip_f_dyn_lambda
- :ref:`APIP <PKG-APIP>`
- adaptive-precision interatomic potentials(APIP), see :doc:`APIP howto <Howto_apip>`
* - *atomic*
- tag, type, x, v, f, image, mask
-

17
doc/src/compute_angle_local.rst
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@ -53,15 +53,17 @@ The value *eng* is the interaction energy for the angle.
The value *v_name* can be used together with the *set* keyword to
compute a user-specified function of the angle theta. The *name*
specified for the *v_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
specified for the *v_name* value is the name of an :doc:`equal-style
variable <variable>` which should evaluate a formula based on a
variable which will store the angle theta. This other variable must
be an :doc:`internal-style variable <variable>` defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The *set* keyword is used to identify the name of this
other variable associated with theta.
be an :doc:`internal-style variable <variable>` specified by the *set*
keyword. It is an internal-style variable, because this command
resets its value directly. The internal-style variable does not need
to be defined in the input script (though it can be); if it is not
defined, then the *set* option creates an :doc:`internal-style
variable <variable>` with the specified name.
Note that the value of theta for each angle which stored in the
Note that the value of theta for each angle which is stored in the
internal variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
@ -70,7 +72,6 @@ system and output the statistics in various ways:
.. code-block:: LAMMPS
variable t internal 0.0
variable cos equal cos(v_t)
variable cossq equal cos(v_t)*cos(v_t)

47
doc/src/compute_bond_local.rst
View File

@ -64,20 +64,32 @@ All these properties are computed for the pair of atoms in a bond,
whether the two atoms represent a simple diatomic molecule, or are part
of some larger molecule.
The value *dist* is the current length of the bond.
The values *dx*, *dy*, and *dz* are the xyz components of the
*distance* between the pair of atoms. This value is always the
distance from the atom of lower to the one with the higher id.
.. versionchanged:: 12Jun2025
The sign of *dx*, *dy*, *dz* is no longer determined by the atom IDs
of the bonded atoms but by their order in the bond list to be
consistent with *fx*, *fy*, and *fz*.
The value *dist* is the current length of the bond. The values *dx*,
*dy*, and *dz* are the :math:`(x,y,z)` components of the distance vector
:math:`\vec{x_i} - \vec{x_j}` between the atoms in the bond. The order
of the atoms is determined by the bond list and the respective atom-IDs
can be output with :doc:`compute property/local
<compute_property_local>`.
The value *engpot* is the potential energy for the bond,
based on the current separation of the pair of atoms in the bond.
The value *force* is the magnitude of the force acting between the
pair of atoms in the bond.
The value *force* is the magnitude of the force acting between the pair
of atoms in the bond, which is positive for a repulsive force and
negative for an attractive force.
The values *fx*, *fy*, and *fz* are the xyz components of
*force* between the pair of atoms in the bond. For bond styles that apply
non-central forces, such as :doc:`bond_style bpm/rotational
The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
the force on the first atom *i* in the bond due to the second atom *j*.
Mathematically, they are obtained by multiplying the value of *force*
from above with a unit vector created from the *dx*, *dy*, and *dz*
components of the distance vector also described above. For bond styles
that apply non-central forces, such as :doc:`bond_style bpm/rotational
<bond_bpm_rotational>`, these values only include the :math:`(x,y,z)`
components of the normal force component.
@ -118,13 +130,15 @@ moving apart.
The value *v_name* can be used together with the *set* keyword to
compute a user-specified function of the bond distance. The *name*
specified for the *v_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
variable which will store the bond distance. This other variable must
be an :doc:`internal-style variable <variable>` defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The *set* keyword is used to identify the name of this
other variable associated with theta.
specified for the *v_name* value is the name of an :doc:`equal-style
variable <variable>` which should evaluate a formula based on a
variable which stores the bond distance. This other variable must be
the :doc:`internal-style variable <variable>` specified by the *set*
keyword. It is an internal-style variable, because this command
resets its value directly. The internal-style variable does not need
to be defined in the input script (though it can be); if it is not
defined, then the *set* option creates an :doc:`internal-style
variable <variable>` with the specified name.
As an example, these commands can be added to the bench/in.rhodo
script to compute the length\ :math:`^2` of every bond in the system and
@ -132,7 +146,6 @@ output the statistics in various ways:
.. code-block:: LAMMPS
variable d internal 0.0
variable dsq equal v_d*v_d
compute 1 all property/local batom1 batom2 btype

43
doc/src/compute_dihedral_local.rst
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@ -45,30 +45,31 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of dihedral angles in the system, modified
by the group parameter as explained below.
The value *phi* (:math:`\phi`) is the dihedral angle, as defined in the diagram
on the :doc:`dihedral_style <dihedral_style>` doc page.
The value *phi* (:math:`\phi`) is the dihedral angle, as defined in
the diagram on the :doc:`dihedral_style <dihedral_style>` doc page.
The value *v_name* can be used together with the *set* keyword to compute a
user-specified function of the dihedral angle :math:`\phi`. The *name*
specified for the *v_name* value is the name of an
:doc:`equal-style variable <variable>` which should evaluate a formula based on
a variable which will store the angle :math:`\phi`. This other variable must
be an :doc:`internal-style variable <variable>` defined in the input
script; its initial numeric value can be anything. It must be an
internal-style variable, because this command resets its value
directly. The *set* keyword is used to identify the name of this
other variable associated with :math:`\phi`.
The value *v_name* can be used together with the *set* keyword to
compute a user-specified function of the dihedral angle :math:`\phi`.
The *name* specified for the *v_name* value is the name of an
:doc:`equal-style variable <variable>` which should evaluate a formula
based on a variable which will store the angle :math:`\phi`. This
other variable must be an :doc:`internal-style variable <variable>`
specified by the *set* keyword. It is an internal-style variable,
because this command resets its value directly. The internal-style
variable does not need to be defined in the input script (though it
can be); if it is not defined, then the *set* option creates an
:doc:`internal-style variable <variable>` with the specified name.
Note that the value of :math:`\phi` for each angle which stored in the internal
variable is in radians, not degrees.
Note that the value of :math:`\phi` for each angle which stored in the
internal variable is in radians, not degrees.
As an example, these commands can be added to the bench/in.rhodo
script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every dihedral
angle in the system and output the statistics in various ways:
script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every
dihedral angle in the system and output the statistics in various
ways:
.. code-block:: LAMMPS
variable p internal 0.0
variable cos equal cos(v_p)
variable cossq equal cos(v_p)*cos(v_p)
@ -100,10 +101,10 @@ no consistent ordering of the entries within the local vector or array
from one timestep to the next. The only consistency that is
guaranteed is that the ordering on a particular timestep will be the
same for local vectors or arrays generated by other compute commands.
For example, dihedral output from the
:doc:`compute property/local <compute_property_local>` command can be combined
with data from this command and output by the :doc:`dump local <dump>`
command in a consistent way.
For example, dihedral output from the :doc:`compute property/local
<compute_property_local>` command can be combined with data from this
command and output by the :doc:`dump local <dump>` command in a
consistent way.
Here is an example of how to do this:

7
doc/src/compute_msd.rst
View File

@ -49,8 +49,6 @@ proportional to the diffusion coefficient of the diffusing atoms.
The displacement of an atom is from its reference position. This is
normally the original position at the time
the compute command was issued, unless the *average* keyword is set to *yes*\ .
The value of the displacement will be
0.0 for atoms not in the specified compute group.
If the *com* option is set to *yes* then the effect of any drift in
the center-of-mass of the group of atoms is subtracted out before the
@ -111,7 +109,10 @@ distance\ :math:`^2` :doc:`units <units>`.
Restrictions
""""""""""""
Compute *msd* cannot be used with a dynamic group.
Compute *msd* cannot be used with a dynamic group and the number of
atoms in the compute group must not be changed by some fixes like,
for example, :doc:`fix deposit <fix_deposit>` or
:doc:`fix evaporate <fix_evaporate>`.
Related commands
""""""""""""""""

30
doc/src/compute_pair_local.rst
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@ -56,19 +56,33 @@ force cutoff distance for that interaction, as defined by the
:doc:`pair_style <pair_style>` and :doc:`pair_coeff <pair_coeff>`
commands.
The value *dist* is the distance between the pair of atoms.
The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the
*distance* between the pair of atoms. This value is always the
distance from the atom of higher to the one with the lower atom ID.
.. versionchanged:: 12Jun2025
The sign of *dx*, *dy*, *dz* is no longer determined by the value of
their atom-IDs but by their order in the neighbor list to be
consistent with *fx*, *fy*, and *fz*.
The value *dist* is the distance between the pair of atoms. The values
*dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the distance
vector :math:`\vec{x_i} - \vec{x_j}` between the pair of atoms. The
order of the atoms is determined by the neighbor list and the respective
atom-IDs can be output with :doc:`compute property/local
<compute_property_local>`.
The value *eng* is the interaction energy for the pair of atoms.
The value *force* is the force acting between the pair of atoms, which
is positive for a repulsive force and negative for an attractive
force. The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
*force* on atom I. For pair styles that apply non-central forces,
such as :doc:`granular pair styles <pair_gran>`, these values only include
the :math:`(x,y,z)` components of the normal force component.
force.
The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
the force vector on the first atom *i* of a pair in the neighbor list
due to the second atom *j*. Mathematically, they are obtained by
multiplying the value of *force* from above with a unit vector created
from the *dx*, *dy*, and *dz* components of the distance vector also
described above. For pair styles that apply non-central forces, such as
:doc:`granular pair styles <pair_gran>`, these values only include the
:math:`(x,y,z)` components of the normal force component.
A pair style may define additional pairwise quantities which can be
accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.

25
doc/src/compute_property_atom.rst
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@ -34,6 +34,8 @@ Syntax
i_name, d_name, i2_name[I], d2_name[I],
vfrac, s0, espin, eradius, ervel, erforce,
rho, drho, e, de, cv, buckling,
apip_lambda, apip_lambda_input, apip_e_fast,
apip_e_precise
.. parsed-literal::
@ -70,6 +72,13 @@ Syntax
*i2_name[I]* = Ith column of custom integer array with name
*d2_name[I]* = Ith column of custom floating-point array with name
.. parsed-literal::
APIP package per-atom properties:
*apip_lambda* = switching parameter
*apip_lambda_input* = input used to calculate the switching parameter
*apip_e_fast,apip_e_precise* = potential energies mixed by the adaptive-precision potential
.. parsed-literal::
PERI package per-atom properties:
@ -162,6 +171,22 @@ segment particles and define the end points of each line segment.
*corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for
triangular particles and define the corner points of each triangle.
The accessible quantities from the :doc:`APIP package <Howto_apip>` are
explained in the doc pages of this package in detail.
In short: *apip_lambda* is the switching parameter :math:`\lambda\in[0,1]`,
that is calculated from *apip_lambda_input* and that mixes the energies
of a fast (*apip_e_fast*) and a precise (*apip_e_precise*) potential
into an adaptive-precision energy.
.. note::
The energy according to the fast and the precise potential are only
computed for the subset of atoms, for which it is required, i.e.,
for an atom :math:`i` with :math:`\lambda_i=1` one does not need
:math:`E_i^\text{precise}` and with :math:`\lambda_i=0` one does
not need :math:`E_i^\text{fast}`.
In addition, the various per-atom quantities listed above for specific
packages are only accessible by this command.

27
doc/src/create_atoms.rst
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@ -396,7 +396,7 @@ correct number of particles are inserted, in a perfectly random
fashion. Which lattice sites are selected will change with the number
of processors used.
.. versionadded:: TBD
.. versionadded:: 12Jun2025
The *group* keyword adds the newly created atoms to the named
:doc:`group <group>`. If the group does not yet exist it will be
@ -416,24 +416,23 @@ atom, based on its coordinates. They apply to all styles except
*single*. The *name* specified for the *var* keyword is the name of
an :doc:`equal-style variable <variable>` that should evaluate to a
zero or non-zero value based on one or two or three variables that
will store the *x*, *y*, or *z* coordinates of an atom (one variable per
coordinate). If used, these other variables must be
:doc:`internal-style variables <variable>` defined in the input
script; their initial numeric value can be anything. They must be
internal-style variables, because this command resets their values
directly. The *set* keyword is used to identify the names of these
other variables, one variable for the *x*-coordinate of a created atom,
one for *y*, and one for *z*.
will store the *x*, *y*, or *z* coordinates of an atom (one variable
per coordinate). If used, these other variables must be specified by
the *set* keyword. They are internal-style variable, because this
command resets their values directly. The internal-style variables do
not need to be defined in the input script (though they can be); if
one (or more) is not defined, then the *set* option creates an
:doc:`internal-style variable <variable>` with the specified name.
.. figure:: img/sinusoid.jpg
:figwidth: 50%
:align: right
:target: _images/sinusoid.jpg
When an atom is created, its :math:`(x,y,z)` coordinates become the values for
any *set* variable that is defined. The *var* variable is then
evaluated. If the returned value is 0.0, the atom is not created. If
it is non-zero, the atom is created.
When an atom is about to be created, its :math:`(x,y,z)` coordinates
become the values for any *set* variable that is defined. The *var*
variable is then evaluated. If the returned value is 0.0, the atom is
not created. If it is non-zero, the atom is created.
As an example, these commands can be used in a 2d simulation, to
create a sinusoidal surface. Note that the surface is "rough" due to
@ -456,8 +455,6 @@ converts lattice spacings to distance.
region box block 0 $x 0 $y -0.5 0.5
create_box 1 box
variable xx internal 0.0
variable yy internal 0.0
variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
create_atoms 1 box var v set x xx set y yy
write_dump all atom sinusoid.lammpstrj

5
doc/src/fix.rst
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@ -201,6 +201,7 @@ accelerated styles exist.
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
* :doc:`atc <fix_atc>` - initiates a coupled MD/FE simulation
* :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
* :doc:`atom_weight/apip <fix_atom_weight_apip>` - compute atomic load of an :doc:`APIP potential <Howto_apip>` for load balancing
* :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
* :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
* :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
@ -208,6 +209,7 @@ accelerated styles exist.
* :doc:`ave/grid <fix_ave_grid>` - compute per-grid time-averaged quantities
* :doc:`ave/histo <fix_ave_histo>` - compute/output time-averaged histograms
* :doc:`ave/histo/weight <fix_ave_histo>` - weighted version of fix ave/histo
* :doc:`ave/moments <fix_ave_moments>` - compute moments of scalar quantities
* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
* :doc:`balance <fix_balance>` - perform dynamic load-balancing
@ -269,6 +271,7 @@ accelerated styles exist.
* :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol
* :doc:`indent <fix_indent>` - impose force due to an indenter
* :doc:`ipi <fix_ipi>` - enable LAMMPS to run as a client for i-PI path-integral simulations
* :doc:`lambda/apip <fix_lambda_apip>` - compute switching parameter, that controls the precision of an :doc:`APIP potential <Howto_apip>`
* :doc:`langevin <fix_langevin>` - Langevin temperature control
* :doc:`langevin/drude <fix_langevin_drude>` - Langevin temperature control of Drude oscillators
* :doc:`langevin/eff <fix_langevin_eff>` - Langevin temperature control for the electron force field model
@ -277,6 +280,7 @@ accelerated styles exist.
* :doc:`lb/momentum <fix_lb_momentum>` - :doc:`fix momentum <fix_momentum>` replacement for use with a lattice-Boltzmann fluid
* :doc:`lb/viscous <fix_lb_viscous>` - :doc:`fix viscous <fix_viscous>` replacement for use with a lattice-Boltzmann fluid
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
* :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>` - apply energy conserving correction for an :doc:`APIP potential <Howto_apip>`
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
* :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as a client for a quantum code via the MolSSI Driver Interface (MDI)
* :doc:`mdi/qmmm <fix_mdi_qmmm>` - LAMMPS operates as client for QM/MM simulation with a quantum code via the MolSSI Driver Interface (MDI)
@ -396,6 +400,7 @@ accelerated styles exist.
* :doc:`rigid/small <fix_rigid>` - constrain many small clusters of atoms to move as a rigid body with NVE integration
* :doc:`rx <fix_rx>` - solve reaction kinetic ODEs for a defined reaction set
* :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
* :doc:`set <fix_set>` - reset an atom property via an atom-style variable every N steps
* :doc:`setforce <fix_setforce>` - set the force on each atom
* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
* :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations

2
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@ -440,7 +440,7 @@ this fix uses to reset theta0 needs to generate values in radians.
----------
.. versionadded:: TBD
.. versionadded:: 12Jun2025
The *dihedral* keyword uses the specified variable to change the value of
a dihedral coefficient over time, very similar to how the *angle* keyword

143
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@ -0,0 +1,143 @@
.. index:: fix atom_weight/apip
fix atom_weight/apip command
============================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID atom_weight/apip nevery fast_potential precise_potential lambda_input lambda_zone group_lambda_input [no_rescale]
* ID, group-ID are documented in :doc:`fix <fix>` command
* atom_weight/apip = style name of this fix command
* nevery = perform load calculation every this many steps
* fast_potential = *eam* or *ace* for time measurements of the corresponding pair_style or float for constant time
* precise_potential = *ace* for a time measurement of the pair_style pace/apip or float for constant time
* lambda_input = *lambda/input* for a time measurement of pair_style lambda/input/apip or float for constant time
* lambda_zone = *lambda/zone* for a time measurement of pair_style lambda/zone/apip or float for constant time
* group_lambda_input = group-ID of the group for which lambda_input is computed
* no_rescale = do not rescale the work per processor to the measured total force-computation time
Examples
""""""""
.. code-block:: LAMMPS
fix 2 all atom_weight/apip 50 eam ace lambda/input lambda/zone all
fix 2 all atom_weight/apip 50 1e-05 0.0004 4e-06 4e-06 all
fix 2 all atom_weight/apip 50 ace ace 4e-06 4e-06 all no_rescale
Description
"""""""""""
This command approximates the load every atom causes when an
adaptive-precision interatomic potential (APIP) according to
:ref:`(Immel) <Immel2025_2>` is used.
This approximated load can be saved as atomic variable and
used as input for the dynamic load balancing via the
:doc:`fix balance <fix_balance>` command.
An adaptive-precision potential like :doc:`eam/apip <pair_eam_apip>`
and :doc:`pace/apip <pair_pace_apip>` is calculated only
for a subset of atoms.
The switching parameter that determines per atom, which potential energy is
used, can be also calculated by
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
A spatial switching zone, that ensures a smooth transition between two
different interatomic potentials, can be calculated by
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
Thus, there are up to four force-subroutines, that are computed only for a
subset of atoms and combined via the pair_style :doc:`hybrid/overlay <pair_hybrid>`.
For all four force-subroutines, the average work per atom is be measured
per processor by the corresponding pair_style.
This fix extracts these measurements of the pair styles every *nevery*
steps. The average compute times are used to calculates a per-atom vector with
the approximated atomic weight, whereas the average compute time of the four
subroutines contributes only to the load of atoms, for which the corresponding
subroutine was calculated.
If not disabled via *no_rescale*, the so calculated load is
rescaled per processor so that the total atomic compute time matches the
also measured total compute time of the whole pair_style.
This atomic weight is intended to be used
as input for :doc:`fix balance <fix_balance>`:
.. code-block:: LAMMPS
variable nevery equal 10
fix weight_atom all atom_weight/apip ${nevery} eam ace lambda/input lambda/zone all
variable myweight atom f_weight_atom
fix balance all balance ${nevery} 1.1 rcb weight var myweight
Furthermore, this fix provides the over the processors averaged compute time of the
four pair_styles, which are used to approximate the atomic weight, as vector.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options are relevant to this fix.
This fix produces a per-atom vector that contains the atomic
weight of each atom.
The per-atom vector can only be accessed on timesteps that are multiples
of *nevery*.
Furthermore, this fix computes a global vector of length 4 with
statistical information about the four different (possibly)
measured compute times per force subroutine. The four
values in the vector are as follows:
#. average compute time for one atom using the fast pair_style
#. average compute time for one atom using the precise pair_style
#. average compute time of lambda/input/apip for one atom
#. average compute time of lambda/zone/apip for one atom
The compute times are computed as average of all processors that
measured at least one computation of the corresponding style.
The vector values calculated by this fix are "intensive" and
updated whenever the per-atom vector is computed, i.e., in
timesteps that are multiples of *nevery*.
The vector and the per-atom vector 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 not invoked during
:doc:`energy minimization <minimize>`.
----------
Restrictions
""""""""""""
This fix is part of the APIP 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 balance <fix_balance>`,
:doc:`fix lambda/apip <fix_lambda_apip>`,
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
:doc:`pair_style eam/apip <pair_eam_apip>`,
:doc:`pair_style pace/apip <pair_pace_apip>`,
Default
"""""""
*no_rescale* is not used by default.
----------
.. _Immel2025_2:
**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

7
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@ -82,10 +82,9 @@ specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a compute or fix or the
evaluation of an equal-style or vector-style variable. For
vector-style variables, the specified indices can include a wildcard
character. See the :doc:`fix ave/correlate <fix_ave_correlate>` page
for details.
evaluation of an equal-style or vector-style variable. The specified
indices can include a wildcard string. See the
:doc:`fix ave/correlate <fix_ave_correlate>` page for details on that.
The *Nevery* and *Nfreq* arguments specify on what time steps the input
values will be used to calculate correlation data and the frequency

296
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@ -0,0 +1,296 @@
.. index:: fix ave/moments
fix ave/moments command
=======================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID ave/moments Nevery Nrepeat Nfreq value1 value2 ... moment1 moment2 ... keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* ave/moments = style name of this fix command
* Nevery = use input values every this many time steps
* Nrepeat = # of times to use input values for calculating averages
* Nfreq = calculate averages every this many time steps
* one or more input variables can be listed
* value = v_name
.. parsed-literal::
c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
v_name = value calculated by an equal-style variable with name
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* one or more moments to compute can be listed
* moment = *mean* or *stddev* or *variance* or *skew* or *kurtosis*, see exact definitions below.
* zero or more keyword/arg pairs may be appended
* keyword = *start* or *history*
.. parsed-literal::
*start* args = Nstart
Nstart = invoke first after this time step
*history* args = Nrecent
Nrecent = keep a history of up to Nrecent outputs
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all ave/moments 1 1000 100 v_volume mean stddev
fix 1 all ave/moments 1 200 1000 v_volume variance kurtosis history 10
Description
"""""""""""
.. versionadded:: 12Jun2025
Using one or more values as input, calculate the moments of the underlying
(population) distributions based on samples collected every few time
steps over a time step window. The definitions of the moments calculated
are given below.
The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a :doc:`compute <compute>` or
:doc:`fix <fix>` or the evaluation of an equal-style or vector-style
:doc:`variable <variable>`. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity.
If you wish to spatial- or time-average or histogram per-atom
quantities from a compute, fix, or variable, then see the :doc:`fix
ave/chunk <fix_ave_chunk>`, :doc:`fix ave/atom <fix_ave_atom>`, or
:doc:`fix ave/histo <fix_ave_histo>` commands. If you wish to sum a
per-atom quantity into a single global quantity, see the :doc:`compute
reduce <compute_reduce>` command.
Many :doc:`computes <compute>` and :doc:`fixes <fix>` produce global
quantities. See their doc pages for details. :doc:`Variables <variable>`
of style *equal* and *vector* are the only ones that can be used with
this fix. Variables of style *atom* cannot be used, since they produce
per-atom values.
The input values must all be scalars or vectors with a bracketed term
appended, indicating the :math:`I^\text{th}` value of the vector is
used.
The result of this fix can be accessed as a vector, containing the
interleaved moments of each input in order. If M moments are requested,
then the moments of input 1 will be the first M values in the vector
output by this fix. The moments of input 2 will the next M values, etc.
If there are N values, the vector length will be N*M.
----------
For input values from a compute or fix or variable, the bracketed index
I can be specified using a wildcard asterisk with the index to
effectively specify multiple values. This takes the form "\*" or "\*n"
or "m\*" or "m\*n". If :math:`N` is the size of the vector, then an
asterisk with no numeric values means all indices from 1 to :math:`N`.
A leading asterisk means all indices from 1 to n (inclusive). A
trailing asterisk means all indices from n to :math:`N` (inclusive). A
middle asterisk means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual elements of the vector
or cells of the array had been listed one by one. For examples, see the
description of this capability in :doc:`fix ave/time <fix_ave_time>`.
----------
The :math:`N_\text{every}`, :math:`N_\text{repeat}`, and
:math:`N_\text{freq}` arguments specify on what time steps the input
values will be used in order to contribute to the average. The final
statistics are generated on time steps that are a multiple of
:math:`N_\text{freq}`\ . The average is over a window of up to
:math:`N_\text{repeat}` quantities, computed in the preceding portion of
the simulation once every :math:`N_\text{every}` time steps.
.. note::
Contrary to most fix ave/* commands, it is not required that Nevery *
Nrepeat <= Nfreq. This is to allow the user to choose the time
window and number of samples contributing to the output at each
Nfreq interval.
For example, if :math:`N_\text{freq}=100` and :math:`N_\text{repeat}=5`
(and :math:`N_\text{every}=1`), then on step 100 values from time steps
96, 97, 98, 99, and 100 will be used. The fix does not compute its
inputs on steps that are not required. If :math:`N_\text{freq}=5`,
:math:`N_\text{repeat}=8` and :math:`N_\text{every}=1`, then values
will first be calculated on step 5 from steps 1-5, on step 10 from 3-10,
on step 15 from 8-15 and so on, forming a rolling average over
timesteps that span a time window larger than Nfreq.
----------
If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the compute is used. See the discussion above for how I
can be specified with a wildcard asterisk to effectively specify
multiple values.
If a value begins with "f\_", a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector
calculated by the fix is used. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.
Note that some fixes only produce their values on certain time steps,
which must be compatible with *Nevery*, else an error will result.
Users can also write code for their own fix styles and :doc:`add them to
LAMMPS <Modify>`.
If a value begins with "v\_", a variable name must follow which has been
previously defined in the input script. Only equal-style or vector-style
variables can be used, which both produce global values. Vector-style
variables require a bracketed term to specify the Ith element of the
vector calculated by the variable.
Note that variables of style *equal* and *vector* define a formula which
can reference individual atom properties or thermodynamic keywords, or
they can invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of specifying quantities to
time average.
----------
The moments are output in the order requested in the arguments following
the last input. Any number and order of moments can be specified,
although it does not make much sense to specify the same moment multiple
times. All moments are computed using a correction of the sample estimators
used to obtain unbiased cumulants :math:`k_{1..4}` (see :ref:`(Cramer)
<Cramer1>`). The correction for variance is the standard Bessel
correction. For other moments, see :ref:`(Joanes)<Joanes1>`.
For *mean*, the arithmetic mean :math:`\bar{x} = \frac{1}{n}
\sum_{i=1}^{n} x_i` is calculated.
For *variance*, the Bessel-corrected sample variance :math:`var = k_2 =
\frac{1}{n - 1} \sum_{i=1}^{n} (x_i - \bar{x})^2` is calculated.
For *stddev*, the Bessel-corrected sample standard deviation
:math:`stddev = \sqrt{k_2}` is calculated.
For *skew*, the adjusted Fisher--Pearson standardized moment :math:`G_1
= \frac{k_3}{k_2^{3/2}} = \frac{k_3}{stddev^3}` is calculated.
For *kurtosis*, the adjusted Fisher--Pearson standardized moment
:math:`G_2 = \frac{k_4}{k_2^2}` is calculated.
----------
Fix invocation and output can be modified by optional keywords.
The *start* keyword specifies that the first computation should be no
earlier than the step number given (but will still occur on a multiple
of *Nfreq*). The default is step 0. Often input values can be 0.0 at
time 0, so setting *start* to a larger value can avoid including a 0.0
in a longer series.
The *history* keyword stores the Nrecent most recent outputs on Nfreq
timesteps, so they can be accessed as global outputs of the fix. Nrecent
must be >= 1. The default is 1, meaning only the most recent output is
accessible. For example, if history 10 is specified and Nfreq = 1000,
then on timestep 20000, the Nfreq outputs from steps 20000, 19000, ...
11000 are available for access. See below for details on how to access
the history values.
For example, this will store the outputs of the previous 10 Nfreq
time steps, i.e. a window of 10000 time steps:
.. code-block:: LAMMPS
fix 1 all ave/moments 1 200 1000 v_volume mean history 10
The previous results can be accessed as values in a global array output
by this fix. Each column of the array is the vector output of the N-th
preceding Nfreq timestep. For example, assuming a single moment is
calculated, the most recent result corresponding to the third input
value would be accessed as "f_name[3][1]", "f_name[3][4]" is the 4th
most recent and so on. The current vector output is always the first
column of the array, corresponding to the most recent result.
To illustrate the utility of keeping output history, consider using
this fix in conjunction with :doc:`fix halt <fix_halt>` to stop a run
automatically if a quantity is converged to within some desired tolerance:
.. code-block:: LAMMPS
variable target equal etot
fix aveg all ave/moments 1 200 1000 v_target mean stddev history 10
variable stopcond equal "abs(f_aveg[1]-f_aveg[1][10])<f_aveg[2]"
fix fhalt all halt 1000 v_stopcond == 1
In this example, every 1000 time steps, the average and standard
deviation of the total energy over the previous 200 time steps are
calculated. If the difference between the most recent and 10-th most
recent average is lower than the most recent standard deviation, the run
is stopped.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`.
This fix produces a global vector and global array which can be accessed
by various :doc:`output commands <Howto_output>`. The values can be
accessed on any time step, but may not be current.
A global vector is produced with the # of elements = number of moments *
number of inputs. The moments are output in the order given in the fix
definition. An array is produced having # of rows = length of vector
output (with an ordering which matches the vector) and # of columns =
value of *history*. There is always at least one column.
Each element of the global vector or array can be either "intensive" or
"extensive", depending on whether the values contributing to the element
are "intensive" or "extensive". If a compute or fix provides the value
being time averaged, then the compute or fix determines whether the value
is intensive or extensive; see the page for that compute or fix for
further info. Values produced by a variable are treated as intensive.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This compute is part of the EXTRA-FIX 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 ave/time <fix_ave_time>`,
Default
"""""""
The option defaults are history = 1, start = 0.
----------
.. _Cramer1:
**(Cramer)** Cramer, Mathematical Methods of Statistics, Princeton University Press (1946).
.. _Joanes1:
**(Joanes)** Joanes, Gill, The Statistician, 47, 183--189 (1998).

100
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@ -98,52 +98,53 @@ the following dynamic equation:
\frac{dc}{dt} = -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} )
where *c* is the continuous time analog of the control variable,
*e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and
:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants
set by the corresponding
keywords described above. The discretized version of this equation is:
where *c* is the continuous time analog of the control variable, *e*
=\ *pvar*\ -\ *setpoint* is the error in the process variable, and
:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are
constants set by the corresponding keywords described above. The
discretized version of this equation is:
.. math::
c_n = c_{n-1} -\alpha \left( K_p \tau e_n + K_i \tau^2 \sum_{i=1}^n e_i + K_d (e_n - e_{n-1}) \right)
where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the time
interval between updates,
and the subscripted variables indicate the values of *c* and *e* at
successive updates.
where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the
time interval between updates, and the subscripted variables indicate
the values of *c* and *e* at successive updates.
From the first equation, it is clear that if the three gain values
:math:`K_p`, :math:`K_i`, :math:`K_d` are dimensionless constants,
then :math:`\alpha` must have
units of [unit *cvar*\ ]/[unit *pvar*\ ]/[unit time] e.g. [ eV/K/ps
]. The advantage of this unit scheme is that the value of the
constants should be invariant under a change of either the MD timestep
size or the value of *Nevery*\ . Similarly, if the LAMMPS :doc:`unit style <units>` is changed, it should only be necessary to change
the value of :math:`\alpha` to reflect this, while leaving :math:`K_p`,
:math:`K_i`, and :math:`K_d` unaltered.
then :math:`\alpha` must have units of [unit *cvar*\ ]/[unit *pvar*\
]/[unit time] e.g. [ eV/K/ps ]. The advantage of this unit scheme is
that the value of the constants should be invariant under a change of
either the MD timestep size or the value of *Nevery*\ . Similarly, if
the LAMMPS :doc:`unit style <units>` is changed, it should only be
necessary to change the value of :math:`\alpha` to reflect this, while
leaving :math:`K_p`, :math:`K_i`, and :math:`K_d` unaltered.
When choosing the values of the four constants, it is best to first
pick a value and sign for :math:`\alpha` that is consistent with the
magnitudes and signs of *pvar* and *cvar*\ . The magnitude of :math:`K_p`
should then be tested over a large positive range keeping :math:`K_i = K_d =0`.
A good value for :math:`K_p` will produce a fast response in *pvar*,
without overshooting the *setpoint*\ . For many applications, proportional
feedback is sufficient, and so :math:`K_i = K_d =0` can be used. In cases
where there is a substantial lag time in the response of *pvar* to a change
in *cvar*, this can be counteracted by increasing :math:`K_d`. In situations
magnitudes and signs of *pvar* and *cvar*\ . The magnitude of
:math:`K_p` should then be tested over a large positive range keeping
:math:`K_i = K_d =0`. A good value for :math:`K_p` will produce a
fast response in *pvar*, without overshooting the *setpoint*\ . For
many applications, proportional feedback is sufficient, and so
:math:`K_i = K_d =0` can be used. In cases where there is a
substantial lag time in the response of *pvar* to a change in *cvar*,
this can be counteracted by increasing :math:`K_d`. In situations
where *pvar* plateaus without reaching *setpoint*, this can be
counteracted by increasing :math:`K_i`. In the language of Charles Dickens,
:math:`K_p` represents the error of the present, :math:`K_i` the error of
the past, and :math:`K_d` the error yet to come.
counteracted by increasing :math:`K_i`. In the language of Charles
Dickens, :math:`K_p` represents the error of the present, :math:`K_i`
the error of the past, and :math:`K_d` the error yet to come.
Because this fix updates *cvar*, but does not initialize its value,
the initial value :math:`c_0` is that assigned by the user in the input script via
the :doc:`internal-style variable <variable>` command. This value is
used (by every other LAMMPS command that uses the variable) until this
fix performs its first update of *cvar* after *Nevery* timesteps. On
the first update, the value of the derivative term is set to zero,
because the value of :math:`e_{n-1}` is not yet defined.
the initial value :math:`c_0` is that assigned by the user in the
input script via the :doc:`internal-style variable <variable>`
command. This value is used (by every other LAMMPS command that uses
the variable) until this fix performs its first update of *cvar* after
*Nevery* timesteps. On the first update, the value of the derivative
term is set to zero, because the value of :math:`e_{n-1}` is not yet
defined.
----------
@ -154,21 +155,23 @@ must produce a global quantity, not a per-atom or local quantity.
If *pvar* begins with "c\_", a compute ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. See the individual :doc:`compute <compute>` doc page
for details. If no bracketed integer is appended, the scalar
scalar or vector. See the individual :doc:`compute <compute>` doc
page for details. If no bracketed integer is appended, the scalar
calculated by the compute is used. If a bracketed integer is
appended, the Ith value of the vector calculated by the compute is
used. Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
used. Users can also write code for their own compute styles and
:doc:`add them to LAMMPS <Modify>`.
If *pvar* begins with "f\_", a fix ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. See the individual :doc:`fix <fix>` page for
details. Note that some fixes only produce their values on certain
timesteps, which must be compatible with when fix controller
references the values, or else an error results. If no bracketed integer
is appended, the scalar calculated by the fix is used. If a bracketed
integer is appended, the Ith value of the vector calculated by the fix
is used. Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
references the values, or else an error results. If no bracketed
integer is appended, the scalar calculated by the fix is used. If a
bracketed integer is appended, the Ith value of the vector calculated
by the fix is used. Users can also write code for their own fix style
and :doc:`add them to LAMMPS <Modify>`.
If *pvar* begins with "v\_", a variable name must follow which has been
previously defined in the input script. Only equal-style variables
@ -182,19 +185,21 @@ variable.
The target value *setpoint* for the process variable must be a numeric
value, in whatever units *pvar* is defined for.
The control variable *cvar* must be the name of an :doc:`internal-style variable <variable>` previously defined in the input script. Note
that it is not specified with a "v\_" prefix, just the name of the
variable. It must be an internal-style variable, because this fix
updates its value directly. Note that other commands can use an
equal-style versus internal-style variable interchangeably.
The control variable *cvar* must be the name of an
:doc:`internal-style variable <variable>` previously defined in the
input script. Note that it is not specified with a "v\_" prefix, just
the name of the variable. It must be an internal-style variable,
because this fix updates its value directly. Note that other commands
can use an equal-style versus internal-style variable interchangeably.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Currently, no information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix.
Currently, no information about this fix is written to :doc:`binary
restart files <restart>`. None of the :doc:`fix_modify <fix_modify>`
options are relevant to this fix.
This fix produces a global vector with 3 values which can be accessed
by various :doc:`output commands <Howto_output>`. The values can be
@ -211,7 +216,8 @@ variable is in. The 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>`.
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""

3
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@ -298,7 +298,8 @@ Note that it should return the "change" in box length, not the
absolute box length. This means it should evaluate to 0.0 when
invoked on the initial timestep of the run following the definition of
fix deform. It should evaluate to a value > 0.0 to dilate the box at
future times, or a value < 0.0 to compress the box.
future times, or a value < 0.0 to compress the box. The exception
would be if the run command uses the *pre no* option.
The variable *name2* must also be an :doc:`equal-style variable
<variable>` and should calculate the rate of box length change, in

48
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View File

@ -225,22 +225,25 @@ rotated configuration of the molecule.
.. versionadded:: 21Nov2023
The *var* and *set* keywords can be used together to provide a criterion
for accepting or rejecting the addition of an individual atom, based on its
coordinates. The *name* specified for the *var* keyword is the name of an
:doc:`equal-style variable <variable>` that should evaluate to a zero or
non-zero value based on one or two or three variables that will store the
*x*, *y*, or *z* coordinates of an atom (one variable per coordinate). If
used, these other variables must be :doc:`internal-style variables
<variable>` defined in the input script; their initial numeric value can be
anything. They must be internal-style variables, because this command
resets their values directly. The *set* keyword is used to identify the
names of these other variables, one variable for the *x*-coordinate of a
created atom, one for *y*, and one for *z*. When an atom is created, its
:math:`(x,y,z)` coordinates become the values for any *set* variable that
is defined. The *var* variable is then evaluated. If the returned value
is 0.0, the atom is not created. If it is non-zero, the atom is created.
For an example of how to use these keywords, see the
The *var* and *set* keywords can be used together to provide a
criterion for accepting or rejecting the addition of an individual
atom, based on its coordinates. The *name* specified for the *var*
keyword is the name of an :doc:`equal-style variable <variable>` that
should evaluate to a zero or non-zero value based on one or two or
three variables that will store the *x*, *y*, or *z* coordinates of an
atom (one variable per coordinate). If used, these other variables
must be :doc:`internal-style variables <variable>` specified by the
*set* keyword. They must be internal-style variables, because this
command resets their values directly. The internal-style variables do
not need to be defined in the input script (though they can be); if
one (or more) is not defined, then the *set* option creates an
:doc:`internal-style variable <variable>` with the specified name.
When an atom is about to be created, its :math:`(x,y,z)` coordinates
become the values for any *set* variable that is defined. The *var*
variable is then evaluated. If the returned value is 0.0, the atom is
not created. If it is non-zero, the atom is created. For an example
of how to use the set/var keywords in a similar context, see the
:doc:`create_atoms <create_atoms>` command.
The *rate* option moves the insertion volume in the z direction (3d)
@ -304,12 +307,13 @@ units of distance or velocity.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the state of the deposition to :doc:`binary restart files <restart>`. This includes information about how many
particles have been deposited, the random number generator seed, the
next timestep for deposition, etc. See the
:doc:`read_restart <read_restart>` command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
This fix writes the state of the deposition to :doc:`binary restart
files <restart>`. This includes information about how many particles
have been deposited, the random number generator seed, the next
timestep for deposition, etc. See the :doc:`read_restart
<read_restart>` command for info on how to re-specify a fix in an
input script that reads a restart file, so that the operation of the
fix continues in an uninterrupted fashion.
.. note::

3
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View File

@ -39,10 +39,11 @@ Examples
Description
"""""""""""
.. versionadded:: 12Jun2025
Apply a Langevin thermostat as described in :ref:`(Gronbech-Jensen-2020) <Gronbech-Jensen-2020>`
to a group of atoms which models an interaction with a background
implicit solvent. As described in the papers cited below, the GJ methods
implicit solvent. As described in the papers cited below, the GJ methods
provide exact diffusion, drift, and Boltzmann sampling for linear systems for
any time step within the stability limit. The purpose of this set of methods
is therefore to significantly improve statistical accuracy at longer time steps

262
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@ -0,0 +1,262 @@
.. index:: fix lambda/apip
fix lambda/apip command
=======================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID lambda/apip thr_lo thr_hi keyword args ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* lambda/apip = style name of this fix command
* thr_lo = value below which :math:`\lambda_i^\text{input}` results in a switching parameter of 1
* thr_hi = value above which :math:`\lambda_i^\text{input}` results in a switching parameter of 0
* zero or one keyword/args pairs may be appended
* keyword = *time_averaged_zone* or *min_delta_lambda* or *lambda_non_group* or *store_atomic_stats* or *dump_atomic_history* or *group_fast* or *group_precise* or *group_ignore_lambda_input*
.. parsed-literal::
*time_averaged_zone* args = cut_lo cut_hi history_len_lambda_input history_len_lambda
cut_lo = distance at which the radial function decreases from 1
cut_hi = distance from which on the radial function is 0
history_len_lambda_input = number of time steps for which lambda_input is averaged
history_len_lambda = number of time steps for which the switching parameter is averaged
*min_delta_lambda* args = delta
delta = value below which changes of the switching parameter are neglected (>= 0)
*lambda_non_group* args = lambda_ng
lambda_ng = *precise* or *fast* or float
*precise* = assign a constant switching parameter of 0 to atoms, that are not in the group specified by group-ID
*fast* = assign a constant switching parameter of 1 to atoms, that are not in the group specified by group-ID
float = assign this constant switching parameter to atoms, that are not in the group specified by group-ID (0 <= float <= 1)
*group_fast* args = group-ID-fast
group-ID-fast = the switching parameter of 1 is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-fast
*group_precise* args = group-ID-precise
group-ID-precise = the switching parameter of 0 is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-precise
*group_ignore_lambda_input* args = group-ID-ignore-lambda-input
group-ID-ignore-lambda-input = the switching parameter of lambda_ng is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-ignore-lambda-input
*store_atomic_stats* args = none
*dump_atomic_history* args = none
Examples
""""""""
.. code-block:: LAMMPS
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
fix 2 mobile lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01 group_ignore_lambda_input immobile lambda_non_group fast
Description
"""""""""""
The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
potential according to :ref:`(Immel) <Immel2025_3>` is given by
.. math::
E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
according to a fast interatomic potential like EAM,
:math:`E_i^\text{(precise)}` is the potential energy according to a precise
interatomic potential such as ACE and :math:`\lambda_i\in[0,1]` is the
switching parameter that decides which potential energy is used.
This fix calculates the switching parameter :math:`\lambda_i` based on the
input provided from :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
The calculation of the switching parameter is described in detail in
:ref:`(Immel) <Immel2025_3>`.
This fix calculates the switching parameter for all atoms in the
:doc:`group <group>`
described by group-ID, while the value of *lambda_non_group* is used
as switching parameter for all other atoms.
First, this fix calculates per atom :math:`i` the time averaged input
:math:`\lambda^\text{input}_{\text{avg},i}` from
:math:`\lambda^\text{input}_{i}`, whereas the number of averaged timesteps
can be set via *time_averaged_zone*.
.. note::
:math:`\lambda^\text{input}_{i}` is calculated by
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`, which needs to be included
in the input script as well.
The time averaged input :math:`\lambda^\text{input}_{\text{avg},i}` is then
used to calculate the switching parameter
.. math::
\lambda_{0,i}(t) = f^\text{(cut)} \left(\frac{\lambda_{\text{avg},i}^\text{input}(t) - \lambda_\text{lo}^\text{input}}{\lambda_\text{hi}^\text{input} - \lambda_\text{lo}^\text{input}} \right)\,,
whereas the thresholds :math:`\lambda_\text{hi}^\text{input}`
and :math:`\lambda_\text{lo}^\text{input}` are set by the
values provided as *thr_lo* and *thr_hi* and :math:`f^\text{(cut)}(x)` is a cutoff function
that is 1 for :math:`x\leq 0`, decays from 1 to 0 for :math:`x\in[0,1]`, and
is 0 for :math:`x\geq 1`.
If the *group_precise* argument is used, :math:`\lambda_{0,i}=0` is used for all
atoms :math:`i` assigned to the corresponding :doc:`group <group>`.
If the *group_fast* argument is used, :math:`\lambda_{0,i}=1` is used for all
atoms :math:`i` assigned to the corresponding :doc:`group <group>`.
If an atom is in the groups *group_fast* and *group_precise*,
:math:`\lambda_{0,i}=0` is used.
If the *group_ignore_lambda_input* argument is used,
:math:`\lambda_i^\text{input}` is not computed for all atoms :math:`i` assigned
to the corresponding :doc:`group <group>`; instead, if the value is not already
set by *group_fast* or *group_precise*, the value of *lambda_non_group* is
used.
.. note::
The computation of :math:`\lambda_i^\text{input}` is not required for
atoms that are in the groups *group_fast* and *group_precise*.
Thus, one should use *group_ignore_lambda_input* and prevent the
computation of :math:`\lambda_i^\text{input}` for all atoms, for
which a constant input is used.
A spatial transition zone between the fast and the precise potential is
introduced via
.. math::
\lambda_{\text{min},i}(t) = \text{min}\left(\left\{1 - (1 -\lambda_{0,j}(t)) f^\text{(cut)}\left(\frac{r_{ij}(t)-r_{\lambda,\text{lo}}}{r_{\lambda,\text{hi}} - r_{\lambda,\text{lo}}}\right) : j \in \Omega_{\lambda,i} \right\}\right)\,,
whereas the thresholds :math:`r_{\lambda,\text{lo}}` and
:math:`r_{\lambda,\text{hi}}`
of the cutoff function are set via *time_averaged_zone* and
:math:`\Omega_{\lambda,i}` is the set of
neighboring atoms of atom :math:`i`.
.. note::
:math:`\lambda_{\text{min},i}` is calculated by
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`, which needs to be included
in the input script as well.
The switching parameter is smoothed by the calculation of the time average
.. math::
\lambda_{\text{avg},i}(t) = \frac{1}{N_{\lambda,\text{avg}}} \sum_{n=1}^{N_{\lambda,\text{avg}}} \lambda_{\text{min},i}(t - n \Delta t)\,,
whereas :math:`\Delta t` is the :doc:`timestep <timestep>` and
:math:`N_{\lambda,\text{avg}}` is the number of averaged timesteps, that
can be set via *time_averaged_zone*.
Finally, numerical fluctuations of the switching parameter are suppressed by the usage of
.. math::
\lambda_{i}(t) = \left\{
\begin{array}{ll}
\lambda_{\text{avg},i}(t) & \text{ for } \left|\lambda_{\text{avg},i}(t) - \lambda_{i}(t-\Delta t)\right|\geq \Delta\lambda_\text{min} \text{ or } \lambda_{\text{avg},i}(t)\in\{0,1\}, \\
\lambda_{i}(t-\Delta t) & \text{ otherwise}\,,
\end{array}
\right.
whereas the minimum change :math:`\Delta\lambda_\text{min}` is set by the
*min_delta_lambda* argument.
.. note::
*group_fast* affects only :math:`\lambda_{0,i}(t)`. The switching parameter
of atoms in this :doc:`group <group>` may change due to the calculation of the
spatial switching zone.
A switching parameter of 1 can be enforced by excluding the corresponding
atoms from the :doc:`group <group>` described by group-ID and using *lambda_non_group* 1
as argument.
----------
A code example for the calculation of the switching parameter for an
adaptive-precision potential is given in the following:
The adaptive-precision potential is created
by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
The input, from which the switching parameter is calculated, is provided
by :doc:`pair lambda/input/csp/apip <pair_lambda_input_apip>`.
The switching parameter is calculated by this fix, whereas the spatial
transition zone of the switching parameter is calculated by
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
.. code-block:: LAMMPS
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The saved history of the switching parameter :math:`\lambda_i`
and the saved history of
:math:`\lambda_i^\text{input}` are written to
:doc:`binary restart files <restart>` allow a smooth restart of a simulation.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
If the *store_atomic_stats* argument is used, basic statistics is provided as
per-atom array:
#. :math:`\lambda_i^\text{input}(t)`
#. :math:`\lambda_{\text{avg},i}^\text{input}(t)`
#. :math:`\lambda_{0,i}(t)`
#. :math:`\lambda_{\text{min},i}(t)`
#. :math:`\lambda_{i}(t)`
If the *dump_atomic_history* argument is used, the whole saved history
of :math:`\lambda_i^\text{input}(t)` is appended to the previously
mentioned array per atom.
The per-atom vector 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 not invoked during
:doc:`energy minimization <minimize>`.
----------
Restrictions
""""""""""""
This fix is part of the APIP 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:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
:doc:`pair_style eam/apip <pair_eam_apip>`,
:doc:`pair_style pace/apip <pair_pace_apip>`,
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
Default
"""""""
*min_delta_lambda* = 0,
*lambda_non_group* = 1,
*cut_lo* = 4.0,
*cut_hi* = 12.0,
*history_len_lambda_input* = 100,
*history_len_lambda* = 100,
*store_atomic_stats* is not used,
*dump_atomic_history* is not used,
*group_fast* is not used,
*group_precise* is not used,
*group_ignore_lambda_input* is not used
----------
.. _Immel2025_3:
**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

176
doc/src/fix_lambda_thermostat_apip.rst Normal file
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@ -0,0 +1,176 @@
.. index:: fix lambda_thermostat/apip
fix lambda_thermostat/apip command
==================================
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID lambda_thermostat/apip keyword values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* lambda_thermostat/apip = style name of this fix command
* zero or more keyword/value pairs may be appended
* keyword = *seed* or *store_atomic_forces* or *N_rescaling*
.. parsed-literal::
*seed* value = integer
integer = integer that is used as seed for the random number generator (> 0)
*store_atomic_forces* value = nevery
nevery = provide per-atom output every this many steps
*N_rescaling* value = groupsize
groupsize = rescale this many neighboring atoms (> 1)
Examples
""""""""
.. code-block:: LAMMPS
fix 2 all lambda_thermostat/apip
fix 2 all lambda_thermostat/apip N_rescaling 100
fix 2 all lambda_thermostat/apip seed 42
fix 2 all lambda_thermostat/apip seed 42 store_atomic_forces 1000
Description
"""""""""""
This command applies the local thermostat described in
:ref:`(Immel) <Immel2025_4>`
to conserve the energy when the switching parameters of an
:doc:`adaptive-precision interatomic potential <Howto_apip>` (APIP)
are updated while the gradient
of the switching parameter is neglected in the force calculation.
.. warning::
The temperature change caused by this fix is only the means to the end of
conserving the energy. Thus, this fix is not a classical thermostat, that
ensures a given temperature in the system.
All available thermostats are listed :doc:`here <Howto_thermostat>`.
The potential energy :math:`E_i` of an atom :math:`i` is given by the formula from
:ref:`(Immel) <Immel2025_4>`
.. math::
E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
according to a fast interatomic potential like EAM,
:math:`E_i^\text{(precise)}` is the potential energy according to a precise
interatomic potential such as ACE and :math:`\lambda_i\in[0,1]` is the
switching parameter that decides which potential energy is used.
This potential energy and the corresponding forces are conservative when
the switching parameter :math:`\lambda_i` is constant in time for all atoms
:math:`i`.
For a conservative force calculation and dynamic switching parameters,
the atomic force on an atom is given by
:math:`F_i = -\nabla_i \sum_j E_j` and includes the derivative of the switching
parameter :math:`\lambda_i`.
The force contribution of this gradient of the switching function can cause
large forces which are not similar to the forces of the fast or the precise
interatomic potential as discussed in :ref:`(Immel) <Immel2025_4>`.
Thus, one can neglect the gradient of the switching parameter in the force
calculation and compensate for the violation of energy conservation by
the application of the local thermostat implemented in this fix.
One can compute the violation of the energy conservation :math:`\Delta H_i`
for all atoms :math:`i` as discussed in :ref:`(Immel) <Immel2025_4>`.
To locally correct this energy violation :math:`\Delta H_i`, one
can rescale the velocity of atom :math:`i` and of neighboring atoms.
The rescaling is done relative to the center-of-mass velocity of the
group and, thus, conserves the momentum.
.. note::
This local thermostat provides the NVE ensemble rather than the NVT
ensemble as
the energy :math:`\Delta H_i` determines the rescaling factor rather than
a temperature.
Velocities :math:`v` are updated by the integrator according to
:math:`\Delta v_i = (F_i/m_i)\Delta t`, whereas `m` denotes the mass of atom
:math:`i` and :math:`\Delta t` is the time step.
One can interpret the velocity difference :math:`\Delta v` caused by the
rescaling as the application of an additional force which is given by
:math:`F^\text{lt}_i = (v^\text{unscaled}_i - v^\text{rescaled}_i) m_i
/ \Delta t` :ref:`(Immel) <Immel2025_4>`.
This additional force is computed when the *store_atomic_forces* option
is used.
The local thermostat is not appropriate for simulations at a temperature of 0K.
.. note::
The maximum decrease of the kinetic energy is achieved with a rescaling
factor of 0, i.e., the relative velocity of the group of rescaled atoms
is set to zero. One cannot decrease the energy further. Thus, the
local thermostat can fail, which is, however, reported by the returned
vector.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to
:doc:`binary restart files <restart>`. None of the
:doc:`fix_modify <fix_modify>` options are relevant to this fix.
If the *store_atomic_forces* option is used, this fix produces every
*nevery* time steps a per-atom array that contains the theoretical force
applied by the local thermostat in all three spatial dimensions in the first
three components. :math:`\Delta H_i` is the fourth component of the per-atom
array.
The per-atom array can only be accessed on timesteps that are multiples
of *nevery*.
Furthermore, this fix computes a global vector of length 6 with
information about the rescaling:
#. number of atoms whose energy changed due to the last :math:`\lambda` update
#. contribution of the potential energy to the last computed :math:`\Delta H`
#. contribution of the kinetic energy to the last computed :math:`\Delta H`
#. sum over all atoms of the absolute energy change caused by the last rescaling step
#. energy change that could not be compensated accumulated over all timesteps
#. number of atoms whose energy change could not be compensated accumulated over all timesteps
The vector and the per-atom vector 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 not invoked during
:doc:`energy minimization <minimize>`.
----------
Restrictions
""""""""""""
This fix is part of the APIP 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 lambda/apip <fix_lambda_apip>`,
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
:doc:`pair_style eam/apip <pair_eam_apip>`,
:doc:`pair_style pace/apip <pair_pace_apip>`,
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
Default
"""""""
seed = 42, N_rescaling = 200, *store_atomic_forces* is not used
----------
.. _Immel2025_4:
**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

31
doc/src/fix_qeq_rel_reaxff.rst
View File

@ -37,18 +37,18 @@ Examples
Description
"""""""""""
.. versionadded:: 19Nov2024
.. versionadded:: 2Apr2025
This fix implements the QEqR method for charge equilibration, which
differs from the QEq charge equilibration method :ref:`(Rappe and
Goddard) <Rappe4>` only in how external electric fields are accounted
for. This fix therefore raises a warning when used without :doc:`fix
efield <fix_efield>` since :doc:`fix qeq/reaxff <fix_qeq_reaxff>` should
be used without an external electric field. Charges are computed with
the QEqR method 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 method is replaced with an
effective electronegativity given by
This fix implements the QEqR method :ref:`(Lalli) <lalli2>` for charge
equilibration, which differs from the QEq charge equilibration method
:ref:`(Rappe and Goddard) <Rappe4>` only in how external electric fields
are accounted for. This fix therefore raises a warning when used without
:doc:`fix efield <fix_efield>` since :doc:`fix qeq/reaxff <fix_qeq_reaxff>`
should be used when no external electric field is present. Charges are
computed with the QEqR method 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 method is
replaced with an effective electronegativity given by
.. math::
\chi_{\mathrm{r}i} = \chi_i + \frac{\sum_{j=1}^{N} \beta(\phi_i - \phi_j) S_{ij}}
@ -61,8 +61,9 @@ external electric field and :math:`S_{ij}` is the overlap integral
between atoms :math:`i` and :math:`j`. This formulation is advantageous
over the method used by :doc:`fix qeq/reaxff <fix_qeq_reaxff>` to
account for an external electric field in that it permits periodic
boundaries in the direction of an external electric field and in that it
does not worsen long-range charge transfer seen with QEq.
boundaries in the direction of an external electric field and in
that it does not worsen long-range charge transfer seen with
QEq. See :ref:`Lalli <lalli2>` for further details.
This fix is typically used in conjunction with the ReaxFF force field
model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
@ -184,6 +185,10 @@ scale = 1.0 and maxiter = 200
----------
.. _lalli2:
**(Lalli)** Lalli and Giusti, Journal of Chemical Physics, 162, 174311 (2025).
.. _Rappe4:
**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95,

11
doc/src/fix_qtpie_reaxff.rst
View File

@ -59,8 +59,7 @@ 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>`:
electric field by using the effective electronegativity :ref:`(Lalli) <lalli>`
.. math::
\tilde{\chi}_{\mathrm{r}i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \beta(\phi_i - \phi_j)) S_{ij}}
@ -68,7 +67,8 @@ electric field by using the effective electronegativity given in
where :math:`\beta` is a scaling factor and :math:`\phi_i` and :math:`\phi_j`
are the electric potentials at the positions of atoms :math:`i` and :math:`j`
due to the external electric field.
due to the external electric field. Additional details regarding the
implementation and performance of this fix are provided in :ref:`Lalli <lalli>`.
This fix is typically used in conjunction with the ReaxFF force
field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
@ -206,10 +206,9 @@ scale = 1.0 and maxiter = 200
**(Chen)** Chen, Jiahao. Theory and applications of fluctuating-charge models.
University of Illinois at Urbana-Champaign, 2009.
.. _Gergs:
.. _lalli:
**(Gergs)** Gergs, Dirkmann and Mussenbrock.
Journal of Applied Physics 123.24 (2018).
**(Lalli)** Lalli and Giusti, Journal of Chemical Physics, 162, 174311 (2025).
.. _qeq-Aktulga2:

175
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View File

@ -0,0 +1,175 @@
.. index:: fix set
fix set command
===============
Syntax
""""""
.. code-block:: LAMMPS
fix ID group-ID set Nfreq rnflag set-args
* ID, group-ID are documented in :doc:`fix <fix>` command
* set = style name of this fix command
* Nfreq = reset per-atom properties every this many timesteps
* rnflag = 1 to reneighbor on next timestep, 0 to not
* set-args = identical to args for the :doc:`set <set>` command
Examples
""""""""
.. code-block:: LAMMPS
fix 10 all set 1 0 group all i_dump v_new
fix 10 all set 1 0 group all i_dump v_turnoff
Description
"""""""""""
.. versionadded:: 12Jun2025
Reset one or more properties of one or more atoms once every *Nfreq*
steps during a simulation.
If the *rnflag* for reneighboring is set to 1, then a reneighboring
will be triggered on the next timestep (since the fix set operation
occurs at the end of the current timestep). This is important to do
if this command changes per-atom properties that need to be
communicated to ghost atoms. If this is not the case, an *rnflag*
setting of 0 can be used; reneighboring will only be triggered on
subsequent timesteps by the usual neighbor list criteria; see the
:doc:`neigh_modify command <neigh_modify>`.
Here are two examples where an *rnflag* setting of 1 are needed. If a
custom per-atom property is changed and the :doc:`fix property/atom
<fix_property_atom>` command to create the property used the *ghost
yes* keyword. Or if per-atom charges are changed, all pair styles
which compute Coulombic interactions require charge values for ghost
atoms. In both these examples, the re-neighboring will trigger the
changes in the owned atom properties to be immediately communicated to
ghost atoms.
The arguments following *Nfreq* and *rnflag* are identical to those
allowed for the :doc:`set <set>` command, as in the examples above and
below.
Note that the group-ID setting for this command is ignored. The
syntax for the :doc:`set <set>` arguments allows selection of which
atoms have their properties reset.
This command can only be used to reset an atom property using a
per-atom variable. This option in allowed by many, but not all, of
the keyword/value pairs supported by the :doc:`set <set>` command.
The reason for this restriction is that if a per-atom variable is not
used, this command will typically not change atom properties during
the simulation.
The :doc:`set <set>` command can be used with similar syntax to this
command to reset atom properties once before or between simulations.
----------
Here is an example of input script commands which will output atoms
into a dump file only when their x-velocity crosses a threshold value
*vthresh* for the first time. Their position and x-velocity will then
be output every step for *twindow* timesteps.
.. code-block:: LAMMPS
variable vthresh equal 2 # threshold velocity
variable twindow equal 10 # dump for this many steps
#
# define custom property i_dump to store timestep threshold is crossed
#
fix 2 all property/atom i_dump
set group all i_dump -1
#
# fix set command checks for threshold crossings every step
# resets i_dump from -1 to current timestep when crossing occurs
#
variable start atom "vx > v_vthresh && i_dump == -1"
variable new atom ternary(v_start,step,i_dump)
fix 3 all set 1 0 group all i_dump v_new
#
# dump command with thresh which enforces twindow
#
dump 1 all custom 1 tmp.dump id x y vx i_dump
variable dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
dump_modify 1 thresh v_dumpflag == 1
#
# run the simulation
# final dump with all atom IDs which crossed threshold on which timestep
#
run 1000
write_dump all custom tmp.dump.final id i_dump modify thresh i_dump >= 0
The tmp.dump.final file lists which atoms crossed the velocity
threshold. This command will print the *twindow* timesteps when a
specific atom ID (104 in this case) was output in the tmp.dump file:
.. code-block:: LAMMPS
% grep "^104 " tmp.dump
If these commands are used instead of the above, then an atom can
cross the velocity threshold multiple times, and will be output for
*twindow* timesteps each time. However the write_dump command is no
longer useful.
.. code-block:: LAMMPS
variable vthresh equal 2 # threshold velocity
variable twindow equal 10 # dump for this many steps
#
# define custom property i_dump to store timestep threshold is crossed
#
fix 2 all property/atom i_dump
set group all i_dump -1
#
# fix set command checks for threshold crossings every step
# resets i_dump from -1 to current timestep when crossing occurs
#
variable start atom "vx > v_vthresh && i_dump == -1"
variable turnon atom ternary(v_start,step,i_dump)
variable stop atom "v_turnon >= 0 && (step-v_turnon) < v_twindow"
variable turnoff atom ternary(v_stop,v_turnon,-1)
fix 3 all set 1 0 group all i_dump v_turnoff
#
# dump command with thresh which enforces twindow
#
dump 1 all custom 1 tmp.dump id x y vx i_dump
variable dumpflag atom "i_dump >= 0 && (step-i_dump) < v_twindow"
dump_modify 1 thresh v_dumpflag == 1
#
# run the simulation
#
run 1000
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`set <set>`
Default
"""""""
none

12
doc/src/kspace_style.rst
View File

@ -32,6 +32,7 @@
.. index:: kspace_style msm/cg/omp
.. index:: kspace_style msm/dielectric
.. index:: kspace_style scafacos
.. index:: kspace_style zero
kspace_style command
====================
@ -43,7 +44,7 @@ Syntax
kspace_style style value
* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/disp/dipole* or *ewald/omp* or *ewald/electrode* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *pppm/electrode* or *pppm/electrode/intel* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos*
* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/disp/dipole* or *ewald/omp* or *ewald/electrode* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *pppm/electrode* or *pppm/electrode/intel* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos* or *zero*
.. parsed-literal::
@ -121,6 +122,7 @@ Syntax
*scafacos* values = method accuracy
method = fmm or p2nfft or p3m or ewald or direct
accuracy = desired relative error in forces
*zero* value = none
Examples
""""""""
@ -132,6 +134,7 @@ Examples
kspace_style msm 1.0e-4
kspace_style scafacos fmm 1.0e-4
kspace_style none
kspace_style zero
Used in input scripts:
@ -375,6 +378,13 @@ other ScaFaCoS options currently exposed to LAMMPS.
----------
.. versionadded:: 12Jun2025
The *zero* style does not do any calculations, but is compatible
with all pair styles that require some version of a kspace style.
----------
The specified *accuracy* determines the relative RMS error in per-atom
forces calculated by the long-range solver. It is set as a
dimensionless number, relative to the force that two unit point

410
doc/src/molecule.rst
View File

@ -34,7 +34,7 @@ Syntax
*ioff* value = Ioff
Ioff = offset to add to improper types
*scale* value = sfactor
sfactor = scale factor to apply to the size and mass of the molecule
sfactor = scale factor to apply to the size, mass, and dipole of the molecule
Examples
""""""""
@ -42,6 +42,7 @@ Examples
.. code-block:: LAMMPS
molecule 1 mymol.txt
molecule water tip3p.json
molecule 1 co2.txt h2o.txt
molecule CO2 co2.txt boff 3 aoff 2
molecule 1 mymol.txt offset 6 9 18 23 14
@ -65,7 +66,7 @@ templates include:
* :doc:`atom_style template <atom_style>`
The ID of a molecule template can only contain alphanumeric characters
and underscores.
and underscores, same as other IDs in LAMMPS.
A single template can contain multiple molecules, listed one per file.
Some of the commands listed above currently use only the first
@ -74,6 +75,13 @@ contains multiple molecules. The :doc:`atom_style template
<atom_style>` command allows multiple-molecule templates to define a
system with more than one templated molecule.
The molecule file can be either in a *native* format or in `JSON format
<https://www.json.org/>`_. JSON formal filenames **must** have the
extension ".json". Files with any other name will be assumed to be in
the "native" format. The details of the two formats are described
below. When referencing multiple molecule files in a single *molecule*
command, each of those files may be either format.
Each filename can be followed by optional keywords which are applied
only to the molecule in the file as used in this template. This is to
make it easy to use the same molecule file in different molecule
@ -95,40 +103,45 @@ use that attribute (e.g. no bonds).
labels will determine the actual types directly depending on the
current :doc:`labelmap <labelmap>` settings.
The *scale* keyword scales the size of the molecule. This can be
useful for modeling polydisperse granular rigid bodies. The scale
factor is applied to each of these properties in the molecule file, if
they are defined: the individual particle coordinates (Coords
section), the individual mass of each particle (Masses section), the
individual diameters of each particle (Diameters section), the total
mass of the molecule (header keyword = mass), the center-of-mass of
the molecule (header keyword = com), and the moments of inertia of the
molecule (header keyword = inertia).
The *scale* keyword scales the size of the molecule. This can be useful
for modeling polydisperse granular rigid bodies. The scale factor is
applied to each of these properties in the molecule file, if they are
defined: the individual particle coordinates (Coords or "coords"
section), the individual mass of each particle (Masses or "masses"
section), the individual diameters of each particle (Diameters or
"diameters" section), the per-atom dipoles (Dipoles or "dipoles"
section) the total mass of the molecule (header keyword = mass), the
center-of-mass of the molecule (header keyword = com), and the moments
of inertia of the molecule (header keyword = inertia).
.. note::
The molecule command can be used to define molecules with bonds,
angles, dihedrals, impropers, or special bond lists of neighbors
angles, dihedrals, impropers, and special bond lists of neighbors
within a molecular topology, so that you can later add the molecules
to your simulation, via one or more of the commands listed above.
Since this topology-related information requires that suitable storage
is reserved when LAMMPS creates the simulation box (e.g. when using
the :doc:`create_box <create_box>` command or the
:doc:`read_data <read_data>` command) suitable space has to be reserved
so you do not overflow those pre-allocated data structures when adding
molecules later. Both the :doc:`create_box <create_box>` command and
the :doc:`read_data <read_data>` command have "extra" options which
ensure space is allocated for storing topology info for molecules that
are added later.
Since this topology-related information requires that suitable
storage is reserved when LAMMPS creates the simulation box (e.g. when
using the :doc:`create_box <create_box>` command or the
:doc:`read_data <read_data>` command) suitable space has to be
reserved at that step so you do not overflow those pre-allocated data
structures when adding molecules later. Both the :doc:`create_box
<create_box>` command and the :doc:`read_data <read_data>` command
have "extra" options which ensure extra space is allocated for
storing topology info for molecules that are added later. This
feature is *not* available for the :doc:`read_restart command
<read_restart>`, thus binary restart files need to be converted
to data files first.
----------
Format of a molecule file
"""""""""""""""""""""""""
Format of a native molecule file
""""""""""""""""""""""""""""""""
The format of an individual molecule file looks similar but is
different than that of a data file read by the :doc:`read_data <read_data>`
commands. Here is a simple example for a TIP3P water molecule:
The format of an "native" individual molecule file looks similar but is
*different* from that of a data file read by the :doc:`read_data
<read_data>` commands. Here is a simple example for a TIP3P water
molecule:
.. code-block::
@ -196,7 +209,7 @@ defining a *body* particle, which requires setting the number of
.. list-table::
:header-rows: 1
:widths: 20 13 42 15
:widths: 21 12 47 20
* - Number(s)
- Keyword
@ -205,7 +218,7 @@ defining a *body* particle, which requires setting the number of
* - N
- atoms
- # of atoms N in molecule
- 0
- keyword is *required*
* - Nb
- bonds
- # of bonds Nb in molecule
@ -228,8 +241,8 @@ defining a *body* particle, which requires setting the number of
- 0
* - Ninteger Ndouble
- body
- # of integer and floating-point values in body particle
- 0
- # of integer and floating-point values in :doc:`body particle <Howto_body>`
- 0 0
* - Mtotal
- mass
- total mass of molecule
@ -669,6 +682,343 @@ the file format.
----------
Format of a JSON molecule file
""""""""""""""""""""""""""""""
.. versionadded:: 12Jun2025
The format of a JSON format individual molecule file must follow the
`JSON format <https://www.json.org/>`_, which evolved from the
JavaScript programming language as a programming-language-neutral data
interchange language. The JSON syntax is independent of its content,
and thus the data in the file must follow suitable conventions to be
correctly processed. LAMMPS provides a `JSON schema file
<https://json-schema.org/>`_ for JSON format molecule files in the
:ref:`tools/json folder <json>` to represent those conventions. Using
the schema file any JSON format molecule files can be validated. Please
note that the format requirement for JSON are very strict and the JSON
reader in LAMMPS does not accept files with extensions like comments.
Validating a particular JSON format molecule file against this schema
ensures that both, the JSON syntax requirement *and* the LAMMPS
conventions for molecule template files are followed. LAMMPS should be
able to read and parse any JSON file that passes the schema check. This
is a formal check only and thus it **cannot** check whether the file
contents are consistent or physically meaningful.
Here is a simple example for the same TIP3P water molecule from above in
JSON format and also using :doc:`type labels <labelmap>` instead of
numeric types:
.. code-block:: json
{
"application": "LAMMPS",
"format": "molecule",
"revision": 1,
"title": "Water molecule. TIP3P geometry",
"schema": "https://download.lammps.org/json/molecule-schema.json",
"units": "real",
"coords": {
"format": ["atom-id", "x", "y", "z"],
"data": [
[1, 0.00000, -0.06556, 0.00000],
[2, 0.75695, 0.52032, 0.00000],
[3, -0.75695, 0.52032, 0.00000]
]
},
"types": {
"format": ["atom-id", "type"],
"data": [
[1, "OW"],
[2, "HO1"],
[3, "HO1"]
]
},
"charges": {
"format": ["atom-id", "charge"],
"data": [
[1, -0.834],
[2, 0.417],
[3, 0.417]
]
},
"bonds": {
"format": ["bond-type", "atom1", "atom2"],
"data": [
["OW-HO1", 1, 2],
["OW-HO1", 1, 3]
]
},
"angles": {
"format": ["angle-type", "atom1", "atom2", "atom3"],
"data": [
["HO1-OW-HO1", 2, 1, 3]
]
}
}
Unlike with the native molecule file format, there are no header or body
sections, just a list of keywords with associated data. JSON format
data is read, parsed, and stored in an internal dictionary data
structure in one step and thus the order of keywords is not relevant.
Data for keywords is either provided directly following the keyword or
as a *data block*. A *data block* is a list that has to include two
keywords, "format" and "data", where the former lists keywords of the
properties that are stored in the columns of the "data" lists. The
names and order of entries in the "format" list (and thus how the data
is interpreted) are currently fixed.
Since the length of the various lists can be easily obtained from the
internal data structure, several header keywords of the "native" molecule
file are not needed. On the other hand, some additional keywords are
required to identify the conventions applied to the generic JSON file
format. The structure of the data itself mostly follows what is used
for the "native" molecule file format.
.. list-table::
:header-rows: 1
* - Keyword
- Argument(s)
- Required
- Description
* - application
- "LAMMPS"
- yes
- indicates a LAMMPS JSON file; files from other applications may be accepted in the future
* - format
- "molecule"
- yes
- indicates a molecule template file
* - revision
- an integer
- yes
- currently 1, to facility backward compatibility on changes to the conventions
* - title
- a string
- no
- information about the template which will echoed to the screen and log
* - schema
- URL as string
- no
- location of a JSON schema file for validating the molecule file format
* - units
- a string
- no
- indicates :doc:`units settings <units>` for this molecule template
* - com
- list with 3 doubles
- no
- overrides the auto-computed center-of-mass for the template
* - masstotal
- double
- no
- overrides the auto-computed total mass for the template
* - inertia
- list with 6 doubles
- no
- overrides the auto-computed moments of inertia
* - coords
- a data block
- no
- contains atom positions with the format "atom-id", "x", "y", "z" (same as Coords)
* - types
- a data block
- yes
- assigns atom types to atoms with the format "atom-id", "type" (same as Types)
* - molecule
- a data block
- no
- assigns molecule-IDs to atoms with the format "atom-id", "molecule-id" (same as Molecules)
* - fragments
- a data block
- no
- assigns atom-ids to fragment-IDs with the format "fragment-id", "atom-id-list" (same as Fragments)
* - charges
- a data block
- no
- assigns charges to atoms with the format "atom-id", "charge" (same as Charges)
* - dipoles
- a data block
- no
- assigns point dipoles to atoms with the format "atom-id", "mux", "muy", "muz" (same as Dipoles)
* - diameters
- a data block
- no
- assigns diameters to atoms with the format "atom-id", "diameter" (same as Diameters)
* - masses
- a data block
- no
- assigns per-atom masses to atoms with the format "atom-id", "mass" (same as Masses)
* - bonds
- a data block
- no
- defines bonds in the molecule template with the format "bond-type", "atom1", "atom2" (same as Bonds without bond-ID)
* - angles
- a data block
- no
- defines angles in the molecule template with the format "angle-type", "atom1", "atom2", "atom3" (same as Angles without angle-ID)
* - dihedrals
- a data block
- no
- defines dihedrals in the molecule template with the format "dihedral-type", "atom1", "atom2", "atom3", "atom4" (same as Dihedrals without dihedral-ID)
* - impropers
- a data block
- no
- defines impropers in the molecule template with the format "improper-type", "atom1", "atom2", "atom3", "atom4" (same as Impropers without improper-ID)
* - shake
- 3 JSON objects
- no
- contains the sub-sections "flags", "atoms", "bonds" described below
* - special
- 2 JSON objects
- no
- contains the sub-sections "counts" and "bonds" described below
* - body
- 2 JSON objects
- no
- contains the "integers" and "doubles" sub-sections with arrays with the same data as Body Integers and Body Doubles, respectively
The following table describes the sub-sections for the "special" entry from above:
.. list-table::
:header-rows: 1
* - Subsection
- Argument(s)
- Required
- Description
* - counts
- a data block
- yes
- contains the counts of 1-2, 1-3, and 1-4 special neighbors with the format "atom-id", "n12", "n13", "n14" (same as Special Bond Counts)
* - bonds
- a data block
- yes
- contains the lists of special neighbors to atoms with the format "atom-id", "atom-id-list" (same as Special Bonds)
The following table describes the sub-sections for the "shake" entry from above:
.. list-table::
:header-rows: 1
* - Subsection
- Argument(s)
- Required
- Description
* - flags
- a data block
- yes
- contains the counts shake flags for atoms with the format "atom-id", "flag" (same as Shake Flags)
* - atoms
- a data block
- yes
- contains the lists of shake cluster atom-ids for atoms with the format "atom-id", "atom-id-list" (same as Shake Atoms)
* - bonds
- a data block
- yes
- contains the lists of shake bond or angle types for atoms with the format "atom-id", "type-list" (same as Shake Bonds)
The "special" and "shake" sections are usually not needed, since the
data can be auto-generated as soon as the simulation box is defined.
Below is an example for what would have to be *added* to the example
JSON file above in case the molecule command needs to be issued earlier.
.. code-block:: json
"special": {
"counts": {
"format": ["atom-id", "n12", "n13", "n14"],
"data": [
[1, 2, 0, 0],
[2, 1, 1, 0],
[3, 1, 1, 0]
]
},
"bonds": {
"format": ["atom-id", "atom-id-list"],
"data": [
[1, [2, 3]],
[2, [1, 3]],
[3, [1, 2]]
]
}
},
"shake": {
"flags": {
"format": ["atom-id", "flag"],
"data": [
[1, 1],
[2, 1],
[3, 1]
]
},
"atoms": {
"format": ["atom-id", "atom-id-list"],
"data": [
[1, [1, 2, 3]],
[2, [1, 2, 3]],
[3, [1, 2, 3]]
]
},
"types": {
"format": ["atom-id", "type-list"],
"data": [
[1, ["OW-HO1", "OW-HO1", "HO1-OW-HO1"]],
[2, ["OW-HO1", "OW-HO1", "HO1-OW-HO1"]],
[3, ["OW-HO1", "OW-HO1", "HO1-OW-HO1"]]
]
}
}
Below is a minimal example of a JSON format molecule template for a body
particle for :doc:`pair style body/nparticle
<pair_body_nparticle>`. Molecule templates for body particles must
contain only one atom:
.. code-block:: json
{
"application": "LAMMPS",
"format": "molecule",
"revision": 1,
"title": "Square body for body/nparticles",
"schema": "https://download.lammps.org/json/molecule-schema.json",
"units": "real",
"coords": {
"format": ["atom-id", "x", "y", "z"],
"data": [
[1, 0.00000, 0.00000, 0.00000]
]
},
"types": {
"format": ["atom-id", "type"],
"data": [
[1, 1]
]
},
"masses": {
"format": ["atom-id", "mass"],
"data": [
[1, 1.0]
]
},
"body": {
"integers": [4],
"doubles": [
1.0, 1.0, 4.0, 0.0, 0.0, 0.0,
-0.70710678118654752440, -0.70710678118654752440, 0.0,
-0.70710678118654752440, 0.70710678118654752440, 0.0,
0.70710678118654752440, 0.70710678118654752440, 0.0,
0.70710678118654752440, -0.70710678118654752440, 0.0
]
}
}
----------
Restrictions
""""""""""""

127
doc/src/pair_eam_apip.rst Normal file
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@ -0,0 +1,127 @@
.. index:: pair_style eam/apip
.. index:: pair_style eam/fs/apip
pair_style eam/apip command
=============================
Constant precision variant: *eam*
pair_style eam/fs/apip command
================================
Constant precision variant: *eam/fs*
Syntax
""""""
.. code-block:: LAMMPS
pair_style eam/apip
pair_style eam/fs/apip
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
Description
"""""""""""
Style *eam* computes pairwise interactions for metals and metal alloys
using embedded-atom method (EAM) potentials :ref:`(Daw) <Daw2>`. The total
energy :math:`E_i` of an atom :math:`i` is given by
.. math::
E_i^\text{EAM} = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) +
\frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
where :math:`F` is the embedding energy which is a function of the atomic
electron density :math:`\rho`, :math:`\phi` is a pair potential interaction,
and :math:`\alpha` and :math:`\beta` are the element types of atoms
:math:`i` and :math:`j`. The multi-body nature of the EAM potential is a
result of the embedding energy term. Both summations in the formula are over
all neighbors :math:`j` of atom :math:`i` within the cutoff distance.
EAM is documented in detail in :doc:`pair_style eam <pair_eam>`.
The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
interatomic potential (APIP) according to :ref:`(Immel) <Immel2025_5>` is given by
.. math::
E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
whereas the switching parameter :math:`\lambda_i` is computed
dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
or set prior to a simulation via :doc:`set <set>`.
The pair style *eam/fs/apip* computes the potential energy
:math:`\lambda_i E_i^\text{EAM}` and the
corresponding force and should be combined
with a precise potential like
:doc:`pair_style pace/precise/apip <pair_pace_apip>` that computes the
potential energy :math:`(1-\lambda_i) E_i^\text{(precise)}` and the
corresponding force via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above with the individual styles. You never need to specify
a pair_coeff command with I != J arguments for the eam/apip styles.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
The eam/apip pair styles do not write their information to :doc:`binary
restart files <restart>`, since it is stored in tabulated potential
files. Thus, you need to re-specify the pair_style and pair_coeff
commands in an input script that reads a restart file.
The eam/apip pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
This pair styles are part of the APIP 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:`pair_style eam <pair_eam>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`fix lambda/apip <fix_lambda_apip>`,
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
:doc:`pair_style pace/apip <pair_pace_apip>`,
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
Default
"""""""
none
----------
.. _Immel2025_5:
**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)
.. _Daw2:
**(Daw)** Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
Daw, Baskes, Phys Rev B, 29, 6443 (1984).

8
doc/src/pair_granular.rst
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@ -421,8 +421,8 @@ by specifying different integer values for the :math:`d_{type}` input parameter.
damping option is only compatible with the normal *mdr* contact model.
Setting :math:`d_{type} = 1` is the suggested damping option. This specifies a damping
model that takes into account the contact stiffness :math:`k_{mdr}` calulated
by the normal *mdr* contact model to determine the damping coefficent:
model that takes into account the contact stiffness :math:`k_{mdr}` calculated
by the normal *mdr* contact model to determine the damping coefficient:
.. math::
@ -435,8 +435,8 @@ normal *mdr* contact model:
k_{mdr} = 2 E_{eff} a_{mdr}.
In this case, :math:`\eta_{n0}` is simply a dimensionless coefficent that scales the
the overall damping coefficent.
In this case, :math:`\eta_{n0}` is simply a dimensionless coefficient that scales the
the overall damping coefficient.
The other supported option is :math:`d_{type} = 2`, which defines a simple damping model
similar to the *velocity* option

61
doc/src/pair_hybrid.rst
View File

@ -100,6 +100,56 @@ first is assigned to intra-molecular interactions (i.e. both atoms
have the same molecule ID), the second to inter-molecular interactions
(i.e. interacting atoms have different molecule IDs).
.. admonition:: When **NOT** to use a hybrid pair style
:class: warning
Using pair style *hybrid* can be very tempting to use if you need a
**many-body potential** supporting a mix of elements for which you
cannot find a potential file that covers *all* of them. Regardless
of how this is set up, there will be *errors*. The major use case
where the error is *small*, is when the many-body sub-styles are used
on different objects (for example a slab and a liquid, a metal and a
nano-machining work piece). In that case the *mixed* terms
**should** be provided by a pair-wise additive potential (like
Lennard-Jones or Morse) to avoid unexpected behavior and reduce
errors. LAMMPS cannot easily check for this condition and thus will
accept good and bad choices alike.
Outside of this, we *strongly* recommend *against* using pair style
hybrid with many-body potentials for the following reasons:
1. When trying to combine EAM or MEAM potentials, there is a *large*
error in the embedding term, since it is computed separately for
each sub-style only.
2. When trying to combine many-body potentials like Stillinger-Weber,
Tersoff, AIREBO, Vashishta, or similar, you have to understand
that the potential of a sub-style cannot be applied in a pair-wise
fashion but will need to be applied to multiples of atoms
(e.g. a Tersoff potential of elements A and B includes the
interactions A-A, B-B, A-B, A-A-A, A-A-B, A-B-B, A-B-A, B-A-A,
B-A-B, B-B-A, B-B-B; AIREBO also considers all quadruples of
atom elements).
3. When one of the sub-styles uses charge-equilibration (= QEq; like
in ReaxFF or COMB) you have inconsistent QEq behavior because
either you try to apply QEq to *all* atoms but then you are
missing the QEq parameters for the non-QEq pair style (and it
would be inconsistent to apply QEq for pair styles that are not
parameterized for QEq) or else you would have either no charges or
fixed charges interacting with the QEq which also leads to
inconsistent behavior between two sub-styles. When attempting to
use multiple ReaxFF instances to combine different potential
files, you might be able to work around the QEq limitations, but
point 2. still applies.
We understand that it is frustrating to not be able to run simulations
due to lack of available potential files, but that does not justify
combining potentials in a broken way via pair style hybrid. This is
not what the hybrid pair styles are designed for.
----------
Here are two examples of hybrid simulations. The *hybrid* style could
be used for a simulation of a metal droplet on a LJ surface. The metal
atoms interact with each other via an *eam* potential, the surface atoms
@ -374,12 +424,11 @@ selected sub-style.
----------
.. note::
Several of the potentials defined via the pair_style command in
LAMMPS are really many-body potentials, such as Tersoff, AIREBO, MEAM,
ReaxFF, etc. The way to think about using these potentials in a
hybrid setting is as follows.
Even though the command name "pair_style" would suggest that these are
pair-wise interactions, several of the potentials defined via the
pair_style command in LAMMPS are really many-body potentials, such as
Tersoff, AIREBO, MEAM, ReaxFF, etc. The way to think about using these
potentials in a hybrid setting is as follows.
A subset of atom types is assigned to the many-body potential with a
single :doc:`pair_coeff <pair_coeff>` command, using "\* \*" to include

151
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@ -0,0 +1,151 @@
.. index:: pair_style lambda/input/apip
.. index:: pair_style lambda/input/csp/apip
pair_style lambda/input/apip command
====================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style lambda/input/apip cutoff
* lambda/input/apip = style name of this pair style
* cutoff = global cutoff (distance units)
pair_style lambda/input/csp/apip command
========================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style lambda/input/csp/apip lattice keyword args
* lambda/input/csp/apip = style name of this pair style
* lattice = *fcc* or *bcc* or integer
.. parsed-literal::
*fcc* = use 12 nearest neighbors to calculate the CSP like in a perfect fcc lattice
*bcc* = use 8 nearest neighbors to calculate the CSP like in a perfect bcc lattice
integer = use N nearest neighbors to calculate the CSP
* zero or more keyword/args pairs may be appended
* keyword = *cutoff* or *N_buffer*
.. parsed-literal::
*cutoff* args = cutoff
cutoff = distance in which neighboring atoms are considered (> 0)
*N_buffer* args = N_buffer
N_buffer = number of additional neighbors, which are included in the j-j+N/2 calculation
Examples
""""""""
.. code-block:: LAMMPS
pair_style lambda/input/csp/apip fcc
pair_style lambda/input/csp/apip fcc cutoff 5.0
pair_style lambda/input/csp/apip bcc cutoff 5.0 N_buffer 2
pair_style lambda/input/csp/apip 14
Description
"""""""""""
This pair_styles calculates :math:`\lambda_i^\text{input}(t)`, which
is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
The pair_style lambda_input sets :math:`\lambda_i^\text{input}(t) = 0`.
The pair_style lambda_input/csp calculates
:math:`\lambda_i^\text{input}(t) = \text{CSP}_i(t)`.
The centro-symmetry parameter (CSP) :ref:`(Kelchner) <Kelchner_2>` is described
in :doc:`compute centro/atom <compute_centro_atom>`.
The lattice argument is described in
:doc:`compute centro/atom <compute_centro_atom>` and determines
the number of neighboring atoms that are used to compute the CSP.
The *N_buffer* argument allows to include more neighboring atoms in
the calculation of the contributions from the pair j,j+N/2 to the CSP as
discussed in :ref:`(Immel) <Immel2025_6>`.
The computation of :math:`\lambda_i^\text{input}(t)` is done by this
pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
takes time and this pair_style can be included in the load-balancing via
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
A code example for the calculation of the switching parameter for an adaptive-
precision potential is given in the following:
The adaptive-precision potential is created
by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
The input, from which the switching parameter is calculated, is provided
by this pair_style.
The switching parameter is calculated by :doc:`fix lambda/apip <fix_lambda_apip>`,
whereas the spatial
transition zone of the switching parameter is calculated by
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
.. code-block:: LAMMPS
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The cutoff distance for this pair style can be mixed. The default mix
value is *geometric*\ . See the "pair_modify" command for details.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style writes no information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
to be specified in an input script that reads a restart file.
This pair style does not support the use of the *inner*, *middle*,
and *outer* keywords of the :doc:`run_style respa <run_style>` command.
----------
Restrictions
""""""""""""
This fix is part of the APIP 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:`compute centro/atom <compute_centro_atom>`,
:doc:`fix lambda/apip <fix_lambda_apip>`,
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
:doc:`pair_style eam/apip <pair_eam_apip>`,
:doc:`pair_style pace/apip <pair_pace_apip>`,
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
Default
"""""""
N_buffer=0, cutoff=5.0
----------
.. _Kelchner_2:
**(Kelchner)** Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
.. _Immel2025_6:
**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

106
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@ -0,0 +1,106 @@
.. index:: pair_style lambda/zone/apip
pair_style lambda/zone/apip command
===================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style lambda/zone/apip cutoff
* lambda/zone/apip = style name of this pair style
* cutoff = global cutoff (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style lambda/zone/apip 12.0
Description
"""""""""""
This pair_style calculates :math:`\lambda_{\text{min},i}`, which
is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
The meaning of :math:`\lambda_{\text{min},i}` is documented in
:doc:`fix lambda/apip <fix_lambda_apip>`, as this pair_style is for use with
:doc:`fix lambda/apip <fix_lambda_apip>` only.
This pair_style requires only the global cutoff as argument.
The remaining quantities, that are required to calculate
:math:`\lambda_{\text{min},i}` are extracted from
:doc:`fix lambda/apip <fix_lambda_apip>` and, thus,
do not need to be passed to this pair_style as arguments.
.. warning::
The cutoff given as argument to this pair style is only relevant for the
neighbor list creation. The radii, which define :math:`r_{\lambda,\text{hi}}` and :math:`r_{\lambda,\text{lo}}` are defined by :doc:`fix lambda/apip <fix_lambda_apip>`.
The computation of :math:`\lambda_{\text{min},i}` is done by this
pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
takes time and this pair_style can be included in the load-balancing via
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
A code example for the calculation of the switching parameter for an
adaptive-precision interatomic potential (APIP) is given in the following:
The adaptive-precision potential is created
by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
The input, from which the switching parameter is calculated, is provided
by :doc:`pair lambda/input/csp/apip <pair_lambda_input_apip>`.
The switching parameter is calculated by :doc:`fix lambda/apip <fix_lambda_apip>`,
whereas the spatial transition zone of the switching parameter is calculated
by this pair style.
.. code-block:: LAMMPS
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The cutoff distance for this pair style can be mixed. The default mix
value is *geometric*\ . See the "pair_modify" command for details.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style writes no information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
to be specified in an input script that reads a restart file.
This pair style does not support the use of the *inner*, *middle*,
and *outer* keywords of the :doc:`run_style respa <run_style>` command.
----------
Restrictions
""""""""""""
This fix is part of the APIP 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 lambda/apip <fix_lambda_apip>`,
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
:doc:`pair_style eam/apip <pair_eam_apip>`,
:doc:`pair_style pace/apip <pair_pace_apip>`,
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
Default
"""""""
none

2
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View File

@ -27,7 +27,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 12Jun2025
Pair style *lj/pirani* computes pairwise interactions from an Improved
Lennard-Jones (ILJ) potential according to :ref:`(Pirani) <Pirani>`.

23
doc/src/pair_lj_smooth.rst
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@ -48,13 +48,19 @@ At the inner cutoff the force and its first derivative
will match the non-smoothed LJ formula. At the outer cutoff the force
and its first derivative will be 0.0. The inner cutoff cannot be 0.0.
Explicit expressions for the coefficients C1, C2, C3, C4, as well as the
energy discontinuity at the cutoff can be found here :ref:`(Leoni_1) <Leoni_1>`
and here :ref:`(Leoni_2) <Leoni_2>`
.. note::
this force smoothing causes the energy to be discontinuous both
in its values and first derivative. This can lead to poor energy
conservation and may require the use of a thermostat. Plot the energy
and force resulting from this formula via the
:doc:`pair_write <pair_write>` command to see the effect.
conservation and may require the use of a thermostat. The energy
value discontinuity can be eliminated by shifting the potential
energy to be zero at the outer cutoff using the pair_modify shift
option. With or without shifting, you can plot the resulting energy
and force via the :doc:`pair_write <pair_write>` command to see the effect.
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -122,3 +128,14 @@ Default
"""""""
none
----------
.. _Leoni_1:
**(Leoni_1)** F. Leoni et al., Phys Rev Lett, 134, 128201 (2025).
.. _Leoni_2:
**(Leoni_2)** F. Leoni et al., Phys Rev Lett, 134, Supplementary Material (2025).

147
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@ -0,0 +1,147 @@
.. index:: pair_style pace/apip
.. index:: pair_style pace/fast/apip
.. index:: pair_style pace/precise/apip
pair_style pace/apip command
============================
pair_style pace/fast/apip command
=================================
pair_style pace/precise/apip command
====================================
Constant precision variant: *pace*
Syntax
""""""
.. code-block:: LAMMPS
pair_style pace/apip ... keyword values ...
pair_style pace/fast/apip ... keyword values ...
pair_style pace/precise/apip ... keyword values ...
* one or more keyword/value pairs may be appended
.. parsed-literal::
keyword = keywords of :doc:`pair pace <pair_pace>`
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay pace/fast/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * pace/fast/apip Cu_fast.yace Cu
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
Description
"""""""""""
Pair style :doc:`pace <pair_pace>` computes interactions using the Atomic
Cluster Expansion (ACE), which is a general expansion of the atomic energy in
multi-body basis functions :ref:`(Drautz19) <Drautz2019_2>`. The *pace*
pair style provides an efficient implementation that is described in
this paper :ref:`(Lysogorskiy21) <Lysogorskiy20211_2>`.
The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
interatomic potential (APIP) according to
:ref:`(Immel25) <Immel2025_7>` is given by
.. math::
E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
whereas the switching parameter :math:`\lambda_i` is computed
dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
or set prior to a simulation via :doc:`set <set>`.
The pair style *pace/precise/apip* computes the potential energy
:math:`(1-\lambda_i) E_i^\text{(pace)}` and the
corresponding force and should be combined
with a fast potential that computes the potential energy
:math:`\lambda_i E_i^\text{(fast)}` and the corresponding force
via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
The pair style *pace/fast/apip* computes the potential energy
:math:`\lambda_i E_i^\text{(pace)}` and the
corresponding force and should be combined
with a precise potential that computes the potential energy
:math:`(1-\lambda_i) E_i^\text{(precise)}` and the corresponding force
via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
The pair_styles *pace/fast/apip* and *pace/precise/apip*
commands may be followed by the optional keywords of
:doc:`pair_style pace <pair_pace>`, which are described
:doc:`here <pair_pace>`.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.
This pair styles does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair styles does not write its information to :doc:`binary restart
files <restart>`, since it is stored in potential files. Thus, you need
to re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
This pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
----------
Restrictions
""""""""""""
This pair styles are part of the APIP 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:`pair_style pace <pair_pace>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`fix lambda/apip <fix_lambda_apip>`,
:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`,
:doc:`pair_style eam/apip <pair_eam_apip>`,
:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
Default
"""""""
See :doc:`pair_style pace <pair_pace>`.
----------
.. _Drautz2019_2:
**(Drautz19)** Drautz, Phys Rev B, 99, 014104 (2019).
.. _Lysogorskiy20211_2:
**(Lysogorskiy21)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
.. _Immel2025_7:
**(Immel25)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

8
doc/src/pair_style.rst
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@ -188,7 +188,9 @@ accelerated styles exist.
* :doc:`eam/cd <pair_eam>` - concentration-dependent EAM
* :doc:`eam/cd/old <pair_eam>` - older two-site model for concentration-dependent EAM
* :doc:`eam/fs <pair_eam>` - Finnis-Sinclair EAM
* :doc:`eam/fs/apip <pair_eam_apip>` - :doc:`adaptive precision <Howto_apip>` version of FS EAM, used as fast potential
* :doc:`eam/he <pair_eam>` - Finnis-Sinclair EAM modified for Helium in metals
* :doc:`eam/apip <pair_eam_apip>` - :doc:`adaptive-precision <Howto_apip>` version of EAM, used as fast potential
* :doc:`edip <pair_edip>` - three-body EDIP potential
* :doc:`edip/multi <pair_edip>` - multi-element EDIP potential
* :doc:`edpd <pair_mesodpd>` - eDPD particle interactions
@ -217,6 +219,9 @@ accelerated styles exist.
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
* :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis
* :doc:`lambda/input/apip <pair_lambda_input_apip>` - constant as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
* :doc:`lambda/input/csp/apip <pair_lambda_input_apip>` - CSP as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
* :doc:`lambda/zone/apip <pair_lambda_zone_apip>` - transition zone of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
* :doc:`lcbop <pair_lcbop>` - long-range bond-order potential (LCBOP)
* :doc:`lebedeva/z <pair_lebedeva_z>` - Lebedeva interlayer potential for graphene with normals along z-axis
* :doc:`lennard/mdf <pair_mdf>` - LJ potential in A/B form with a taper function
@ -330,6 +335,9 @@ accelerated styles exist.
* :doc:`oxrna2/xstk <pair_oxrna2>` -
* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
* :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
* :doc:`pace/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
* :doc:`pace/fast/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as fast potential
* :doc:`pace/precise/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
* :doc:`pedone <pair_pedone>` - Pedone (PMMCS) potential (non-Coulomb part)
* :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
* :doc:`peri/eps <pair_peri>` - Peridynamic EPS potential

40
doc/src/plugin.rst
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@ -10,16 +10,17 @@ Syntax
plugin command args
* command = *load* or *unload* or *list* or *clear*
* command = *load* or *unload* or *list* or *clear* or *restore*
* args = list of arguments for a particular plugin command
.. parsed-literal::
*load* file = load plugin(s) from shared object in *file*
*unload* style name = unload plugin *name* of style *style*
*style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *compute* or *fix* or *region* or *command*
*style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *compute* or *fix* or *region* or *command* or *run* or *min*
*list* = print a list of currently loaded plugins
*clear* = unload all currently loaded plugins
*restore* = restore all loaded plugins
Examples
""""""""
@ -31,6 +32,7 @@ Examples
plugin unload command hello
plugin list
plugin clear
plugin restore
Description
"""""""""""
@ -40,22 +42,46 @@ commands into a LAMMPS binary from so-called dynamic shared object (DSO)
files. This enables to add new functionality to an existing LAMMPS
binary without having to recompile and link the entire executable.
.. admonition:: Plugins are a global, per-executable property
:class: Hint
Unlike most settings in LAMMPS, plugins are a per-executable global
property. Loading a plugin means that it is not only available for
the current LAMMPS instance but for all *future* LAMMPS instances.
After a :doc:`clear <clear>` command, all currently loaded plugins
will be restored and do not need to be loaded again.
When using the library interface or the Python or Fortran module
to create multiple concurrent LAMMPS instances, all plugins should
be loaded by the first created LAMMPS instance as all future instances
will inherit them. To import plugins that were loaded by a different
LAMMPS instance, use the *restore* command.
The *load* command will load and initialize all plugins contained in the
plugin DSO with the given filename. A message with information the
plugin style and name and more will be printed. Individual DSO files
may contain multiple plugins. More details about how to write and
plugin DSO with the given filename. A message with information about
the plugin style and name and more will be printed. Individual DSO
files may contain multiple plugins. If a plugin is already loaded
it will be skipped. More details about how to write and
compile the plugin DSO is given in programmer's guide part of the manual
under :doc:`Developer_plugins`.
The *unload* command will remove the given style or the given name from
the list of available styles. If the plugin style is currently in use,
that style instance will be deleted.
that style instance will be deleted and replaced by the default setting
for that style.
The *list* command will print a list of the loaded plugins and their
styles and names.
The *clear* command will unload all currently loaded plugins.
.. versionadded:: 12Jun2025
The *restore* command will restore all currently loaded plugins.
This allows to "import" plugins into a different LAMMPS instance.
.. admonition:: Automatic loading of plugins
:class: note
@ -79,7 +105,7 @@ If plugins access functions or classes from a package,
LAMMPS must have been compiled with that package included.
Plugins are dependent on the LAMMPS binary interface (ABI)
and particularly the MPI library used. So they are not guaranteed
and particularly the MPI library used. So they are not guaranteed
to work when the plugin was compiled with a different MPI library
or different compilation settings or a different LAMMPS version.
There are no checks, so if there is a mismatch the plugin object

637
doc/src/python.rst
View File

@ -10,7 +10,7 @@ Syntax
python mode keyword args ...
* mode = *source* or name of Python function
* mode = *source* or *name* of Python function
if mode is *source*:
@ -18,35 +18,39 @@ Syntax
keyword = *here* or name of a *Python file*
*here* arg = inline
inline = one or more lines of Python code which defines func
inline = one or more lines of Python code which will be executed immediately
must be a single argument, typically enclosed between triple quotes
*Python file* = name of a file with Python code which will be executed immediately
* if *mode* is the name of a Python function, one or more keywords with/without arguments must be appended
* if *mode* is *name* of a Python function:
.. parsed-literal::
one or more keywords with/without arguments must be appended
keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists*
*invoke* arg = none = invoke the previously defined Python function
*invoke* arg = logreturn (optional)
invoke the previously-defined Python function
if logreturn is specified, print the return value of the invoked function to the screen and logfile
*input* args = N i1 i2 ... iN
N = # of inputs to function
i1,...,iN = value, SELF, or LAMMPS variable name
value = integer number, floating point number, or string
SELF = reference to LAMMPS itself which can be accessed by Python function
variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
SELF = reference to LAMMPS itself which can then be accessed by Python function
variable = v_name, where name = name of a LAMMPS variable, e.g. v_abc
internal variable = iv_name, where name = name of a LAMMPS internal-style variable, e.g. iv_xyz
*return* arg = varReturn
varReturn = v_name = LAMMPS variable name which the return value of the Python function will be assigned to
*format* arg = fstring with M characters
M = N if no return value, where N = # of inputs
M = N+1 if there is a return value
fstring = each character (i,f,s,p) corresponds in order to an input or return value
'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
fstring = each character (i,f,s,p) corresponds (in order) to an input or return value
'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
*length* arg = Nlen
Nlen = max length of string returned from Python function
*file* arg = filename
filename = file of Python code, which defines func
filename = file of Python code, which defines the Python function
*here* arg = inline
inline = one or more lines of Python code which defines func
inline = one or more lines of Python code which defines the Python function
must be a single argument, typically enclosed between triple quotes
*exists* arg = none = Python code has been loaded by previous python command
@ -56,7 +60,7 @@ Examples
.. code-block:: LAMMPS
python pForce input 2 v_x 20.0 return v_f format fff file force.py
python pForce invoke
python pForce invoke logreturn
python factorial input 1 myN return v_fac format ii here """
def factorial(n):
@ -87,75 +91,149 @@ Examples
Description
"""""""""""
The *python* command allows interfacing LAMMPS with an embedded Python
interpreter and enables either executing arbitrary python code in that
interpreter, registering a Python function for future execution (as a
python style variable, from a fix interfaced with python, or for direct
invocation), or invoking such a previously registered function.
The *python* command interfaces LAMMPS with an embedded Python
interpreter and enables executing arbitrary python code in that
interpreter. This can be done immediately, by using *mode* = *source*.
Or execution can be deferred, by registering a Python function for later
execution, by using *mode* = *name* of a Python function.
Arguments, including LAMMPS variables, can be passed to the function
from the LAMMPS input script and a value returned by the Python function
assigned to a LAMMPS variable. The Python code for the function can be included
directly in the input script or in a separate Python file. The function
can be standard Python code or it can make "callbacks" to LAMMPS through
its library interface to query or set internal values within LAMMPS.
This is a powerful mechanism for performing complex operations in a
LAMMPS input script that are not possible with the simple input script
and variable syntax which LAMMPS defines. Thus your input script can
operate more like a true programming language.
Later execution can be triggered in one of two ways. One is to use the
python command again with its *invoke* keyword. The other is to trigger
the evaluation of a python-style, equal-style, vector-style, or
atom-style variable. A python-style variable invokes its associated
Python function; its return value becomes the value of the python-style
variable. Equal-, vector-, and atom-style variables can use a Python
function wrapper in their formulas which encodes the python-style
variable name, and specifies arguments (which themselves can be numeric
formulas) to pass to the Python function associated with the
python-style variable.
As explained on the :doc:`variable <variable>` doc page, the definition
of a python-style variable associates a Python function name with the
variable. Its specification must match the *mode* argument of the
*python* command for the Python function name. For example these two
commands would be consistent:
.. code-block:: LAMMPS
variable foo python myMultiply
python myMultiply return v_foo format f file funcs.py
The two commands can appear in either order in the input script so long
as both are specified before the Python function is invoked for the
first time.
Note that python-style, equal-style, vector-style, and atom-style
variables can be used in many different ways within LAMMPS. They can be
evaluated directly in an input script, effectively replacing the
variable with its value. Or they can be passed to various commands as
arguments, so that the variable is evaluated multiple times during a
simulation run. See the :doc:`variable <variable>` command doc page for
more details on variable styles which enable Python function evaluation.
The Python code for a Python function can be included directly in the
input script or in a separate Python file. The function can be standard
Python code or it can make "callbacks" to LAMMPS through its library
interface to query or set internal values within LAMMPS. This is a
powerful mechanism for performing complex operations in a LAMMPS input
script that are not possible with the simple input script and variable
syntax which LAMMPS defines. Thus your input script can operate more
like a true programming language.
Use of this command requires building LAMMPS with the PYTHON package
which links to the Python library so that the Python interpreter is
embedded in LAMMPS. More details about this process are given below.
There are two ways to invoke a Python function once it has been
registered. One is using the *invoke* keyword. The other is to assign
the function to a :doc:`python-style variable <variable>` defined in
your input script. Whenever the variable is evaluated, it will execute
the Python function to assign a value to the variable. Note that
variables can be evaluated in many different ways within LAMMPS. They
can be substituted with their result directly in an input script, or
they can be passed to various commands as arguments, so that the
variable is evaluated during a simulation run.
A broader overview of how Python can be used with LAMMPS is given in the
:doc:`Use Python with LAMMPS <Python_head>` section of the
documentation. There also is an ``examples/python`` directory which
documentation. There is also an ``examples/python`` directory which
illustrates use of the python command.
----------
The first argument of the *python* command is either the *source*
keyword or the name of a Python function. This defines the mode
of the python command.
The first argument to the *python* command is the *mode* setting, which
is either *source* or the *name* of a Python function.
.. versionchanged:: 22Dec2022
If the *source* keyword is used, it is followed by either a file name or
the *here* keyword. No other keywords can be used. The *here* keyword
is followed by a string with python commands, either on a single line
enclosed in quotes, or as multiple lines enclosed in triple quotes.
These Python commands will be passed to the python interpreter and
executed immediately without registering a Python function for future
execution. The code will be loaded into and run in the "main" module of
the Python interpreter. This allows running arbitrary Python code at
any time while processing the LAMMPS input file. This can be used to
pre-load Python modules, initialize global variables, define functions
or classes, or perform operations using the python programming language.
The Python code will be executed in parallel on all MPI processes. No
arguments can be passed.
If *source* is used, it is followed by either the *here* keyword or a
file name containing Python code. The *here* keyword is followed by a
single *inline* argument which is a string containing one or more python
commands. The string can either be on the same line as the *python*
command, enclosed in quotes, or it can be multiple lines enclosed in
triple quotes.
In all other cases, the first argument is the name of a Python function
that will be registered with LAMMPS for future execution. The function
may already be defined (see *exists* keyword) or must be defined using
the *file* or *here* keywords as explained below.
In either case, the in-line code or the file contents are passed to the
python interpreter and executed immediately. The code will be loaded
into and run in the "main" module of the Python interpreter. This
allows running arbitrary Python code at any time while processing the
LAMMPS input file. This can be used to pre-load Python modules,
initialize global variables, define functions or classes, or perform
operations using the Python programming language. The Python code will
be executed in parallel on all the MPI processes being used to run
LAMMPS. Note that no arguments can be passed to the executed Python
code.
If the *invoke* keyword is used, no other keywords can be used, and a
If the *mode* setting is the *name* of a Python function, then it will
be registered with LAMMPS for future execution (or can already be
defined, see the *exists* keyword). One or more keywords must follow
the *mode* function name. One of the keywords must be *invoke*, *file*,
*here*, or *exists*, which specifies what Python code to load into the
Python interpreter. Note that only one of those 4 keywords is allowed
since their operations are mutually exclusive.
----------
If the *invoke* keyword is used, no other keywords can be used. A
previous *python* command must have registered the Python function
referenced by this command. This invokes the Python function with the
previously defined arguments and the return value is processed as
explained below. You can invoke the function as many times as you wish
in your input script.
referenced by this command, which can then be invoked multiple times in
an input script via the *invoke* keyword. Each invocation passes
current values for arguments to the Python function. A return value of
the Python function will be ignored unless the Python function is linked
to a :doc:`python style variable <variable>` with the *return* keyword.
This return value can be logged to the screen and logfile by adding the
optional *logreturn* argument to the *invoke* keyword. In that case a
message with the name of the python command and the return value is
printed. Note that return values of python functions are otherwise
*only* accessible when the function is invoked indirectly by evaluating
its associated :doc:`python style variable <variable>`, as described
below.
The *file* keyword gives the name of a file containing Python code,
which should end with a ".py" suffix. The code will be immediately
loaded into and run in the "main" module of the Python interpreter. The
Python code will be executed in parallel on all MPI processes. Note
that Python code which contains a function definition does NOT "execute"
the function when it is run; it simply defines the function so that it
can be invoked later.
The *here* keyword does the same thing, except that the Python code
follows as a single argument to the *here* keyword. This can be done
using triple quotes as delimiters, as in the examples above and below.
This allows Python code to be listed verbatim in your input script, with
proper indentation, blank lines, and comments, as desired. See the
:doc:`Commands parse <Commands_parse>` doc page, for an explanation of
how triple quotes can be used as part of input script syntax.
The *exists* keyword takes no argument. It simply means that Python
code containing the needed Python function has already been loaded into
the LAMMPS Python interpreter, for example by previous *python source*
command or in a file that was loaded previously with the *file*
keyword. This allows use of a single file of Python code which contains
multiple functions, any of which can be used in the same (or different)
input scripts (see below).
Note that the Python code that is loaded and run by the *file* or *here*
keyword must contain a function with the specified function *name*. To
operate properly when the function is later invoked, the code for the
function must match the *input* and *return* and *format* keywords
specified by the python command. Otherwise Python will generate an
error.
----------
The other keywords which can be used with the *python* command are
*input*, *return*, *format*, and *length*.
The *input* keyword defines how many arguments *N* the Python function
expects. If it takes no arguments, then the *input* keyword should not
@ -169,35 +247,63 @@ itself using the :doc:`LAMMPS Python module <Python_module>`. This
enables the function to call back to LAMMPS through its library
interface as explained below. This allows the Python function to query
or set values internal to LAMMPS which can affect the subsequent
execution of the input script. A LAMMPS variable can also be used as an
argument, specified as v_name, where "name" is the name of the variable.
Any style of LAMMPS variable returning a scalar or a string can be used,
as defined by the :doc:`variable <variable>` command. The *format*
keyword must be used to set the type of data that is passed to Python.
Each time the Python function is invoked, the LAMMPS variable is
evaluated and its value is passed to the Python function.
execution of the input script.
A LAMMPS variable can also be used as an *input* argument, specified as
v_name, where "name" is the name of the variable defined in the input
script. Any style of LAMMPS variable returning a scalar or a string can
be used, as defined by the :doc:`variable <variable>` command. The
style of variable must be consistent with the *format* keyword
specification for the type of data that is passed to Python. Each time
the Python function is invoked, the LAMMPS variable is evaluated and its
value is passed as an argument to the Python function. Note that a
python-style variable can be used as an argument, which means that the a
Python function can use arguments which invoke other Python functions.
A LAMMPS internal-style variable can also be used as an *input*
argument, specified as iv_name, where "name" is the name of the
internal-style variable. The internal-style variable does not have to
be defined in the input script (though it can be); if it is not defined,
this command creates an :doc:`internal-style variable <variable>` with
the specified name.
An internal-style variable must be used when an equal-style,
vector-style, or atom-style variable triggers the invocation of the
Python function defined by this command, by including a Python function
wrapper with arguments in its formula. Each of the arguments must be
specified as an internal-style variable via the *input* keyword.
In brief, the syntax for a Python function wrapper in a variable formula
is ``py_varname(arg1,arg2,...argN)``, where "varname" is the name of a
python-style variable associated with a Python function defined by this
command. One or more arguments to the function wrapper can themselves
be sub-formulas which the variable command will evaluate and pass as
arguments to the Python function. This is done by assigning the numeric
result for each argument to an internal-style variable; thus the *input*
keyword must specify the arguments as internal-style variables and their
format (see below) as "f" for floating point. This is because LAMMPS
variable formulas are calculated with floating point arithmetic (any
integer values are converted to floating point). Note that the Python
function can also have additional inputs, also specified by the *input*
keyword, which are NOT arguments in the Python function wrapper. See
the example below for the ``mixedargs`` Python function.
See the :doc:`variable <variable>` command doc page for full details on
formula syntax including for Python function wrappers. Examples using
Python function wrappers are shown below. Note that as explained above
with python-style variables, Python function wrappers can be nested; a
sub-formula for an argument can contain its own Python function wrapper
which invokes another Python function.
The *return* keyword is only needed if the Python function returns a
value. The specified *varReturn* must be of the form v_name, where
"name" is the name of a python-style LAMMPS variable, defined by the
value. The specified *varReturn* is of the form v_name, where "name" is
the name of a python-style LAMMPS variable, defined by the
:doc:`variable <variable>` command. The Python function can return a
numeric or string value, as specified by the *format* keyword.
As explained on the :doc:`variable <variable>` doc page, the definition
of a python-style variable associates a Python function name with the
variable. This must match the *Python function name* first argument of
the *python* command. For example these two commands would be
consistent:
.. code-block:: LAMMPS
variable foo python myMultiply
python myMultiply return v_foo format f file funcs.py
The two commands can appear in either order in the input script so
long as both are specified before the Python function is invoked for
the first time. Afterwards, the variable 'foo' is associated with
the Python function 'myMultiply'.
numeric or string value, as specified by the *format* keyword. This
return value is *only* accessible when its associated python-style
variable is evaluated. When the *invoke* keyword is used, the return
value of the python function is ignored unless the optional *logreturn*
argument is specified.
The *format* keyword must be used if the *input* or *return* keywords
are used. It defines an *fstring* with M characters, where M = sum of
@ -214,47 +320,16 @@ but only if the output of the Python function is flagged as a numeric
value ("i" or "f") via the *format* keyword.
If the *return* keyword is used and the *format* keyword specifies the
output as a string, then the default maximum length of that string is
63 characters (64-1 for the string terminator). If you want to return
a longer string, the *length* keyword can be specified with its *Nlen*
value set to a larger number (the code allocates space for Nlen+1 to
include the string terminator). If the Python function generates a
output as a string, then the default maximum length of that string is 63
characters (64-1 for the string terminator). If you want to return a
longer string, the *length* keyword can be specified with its *Nlen*
value set to a larger number. LAMMPS will then allocate Nlen+1 space to
include the string terminator. If the Python function generates a
string longer than the default 63 or the specified *Nlen*, it will be
truncated.
----------
Either the *file*, *here*, or *exists* keyword must be used, but only
one of them. These keywords specify what Python code to load into the
Python interpreter. The *file* keyword gives the name of a file
containing Python code, which should end with a ".py" suffix. The code
will be immediately loaded into and run in the "main" module of the
Python interpreter. The Python code will be executed in parallel on all
MPI processes. Note that Python code which contains a function
definition does not "execute" the function when it is run; it simply
defines the function so that it can be invoked later.
The *here* keyword does the same thing, except that the Python code
follows as a single argument to the *here* keyword. This can be done
using triple quotes as delimiters, as in the examples above. This
allows Python code to be listed verbatim in your input script, with
proper indentation, blank lines, and comments, as desired. See the
:doc:`Commands parse <Commands_parse>` doc page, for an explanation of
how triple quotes can be used as part of input script syntax.
The *exists* keyword takes no argument. It means that Python code
containing the required Python function with the given name has already
been executed, for example by a *python source* command or in the same
file that was used previously with the *file* keyword.
Note that the Python code that is loaded and run must contain a function
with the specified function name. To operate properly when later
invoked, the function code must match the *input* and *return* and
*format* keywords specified by the python command. Otherwise Python
will generate an error.
----------
This section describes how Python code can be written to work with
LAMMPS.
@ -275,16 +350,16 @@ keyword once to load several functions, and the *exists* keyword
thereafter in subsequent python commands to register the other functions
that were previously loaded with LAMMPS.
A Python function you define (or more generally, the code you load)
can import other Python modules or classes, it can make calls to other
A Python function you define (or more generally, the code you load) can
import other Python modules or classes, it can make calls to other
system functions or functions you define, and it can access or modify
global variables (in the "main" module) which will persist between
successive function calls. The latter can be useful, for example, to
prevent a function from being invoke multiple times per timestep by
different commands in a LAMMPS input script that access the returned
python-style variable associated with the function. For example,
consider this function loaded with two global variables defined
outside the function:
consider this function loaded with two global variables defined outside
the function:
.. code-block:: python
@ -308,32 +383,33 @@ previous value is simply returned, without re-computing it. The
"global" statement inside the Python function allows it to overwrite the
global variables from within the local context of the function.
Note that if you load Python code multiple times (via multiple python
commands), you can overwrite previously loaded variables and functions
if you are not careful. E.g. if the code above were loaded twice, the
global variables would be re-initialized, which might not be what you
want. Likewise, if a function with the same name exists in two chunks
of Python code you load, the function loaded second will override the
function loaded first.
Also note that if you load Python code multiple times (via multiple
python commands), you can overwrite previously loaded variables and
functions if you are not careful. E.g. if the code above were loaded
twice, the global variables would be re-initialized, which might not be
what you want. Likewise, if a function with the same name exists in two
chunks of Python code you load, the function loaded second will override
the function loaded first.
It's important to realize that if you are running LAMMPS in parallel,
each MPI task will load the Python interpreter and execute a local
copy of the Python function(s) you define. There is no connection
between the Python interpreters running on different processors.
This implies three important things.
each MPI task will load the Python interpreter and execute a local copy
of the Python function(s) you define. There is no connection between
the Python interpreters running on different processors. This implies
three important things.
First, if you put a print or other statement creating output to the
screen in your Python function, you will see P copies of the output,
when running on P processors. If the prints occur at (nearly) the same
time, the P copies of the output may be mixed together. When loading
the LAMMPS Python module into the embedded Python interpreter, it is
possible to pass the pointer to the current LAMMPS class instance and
via the Python interface to the LAMMPS library interface, it is possible
to determine the MPI rank of the current process and thus adapt the
Python code so that output will only appear on MPI rank 0. The
following LAMMPS input demonstrates how this could be done. The text
'Hello, LAMMPS!' should be printed only once, even when running LAMMPS
in parallel.
time, the P copies of the output may be mixed together.
It is possible to avoid this issue, by passing the pointer to the
current LAMMPS class instance to the Python function via the {input}
SELF argument described above. The Python function can then use the
Python interface to the LAMMPS library interface, and determine the MPI
rank of the current process. The Python code can then ensure output
will only appear on MPI rank 0. The following LAMMPS input demonstrates
how this could be done. The text 'Hello, LAMPS!' should be printed only
once, even when running LAMMPS in parallel.
.. code-block:: LAMMPS
@ -348,27 +424,26 @@ in parallel.
python python_hello invoke
If your Python code loads Python modules that are not pre-loaded by the
Python library, then it will load the module from disk. This may be a
bottleneck if 1000s of processors try to load a module at the same time.
On some large supercomputers, loading of modules from disk by Python may
be disabled. In this case you would need to pre-build a Python library
that has the required modules pre-loaded and link LAMMPS with that
library.
Second, if your Python code loads Python modules that are not pre-loaded
by the Python library, then it will load the module from disk. This may
be a bottleneck if 1000s of processors try to load a module at the same
time. On some large supercomputers, loading of modules from disk by
Python may be disabled. In this case you would need to pre-build a
Python library that has the required modules pre-loaded and link LAMMPS
with that library.
Third, if your Python code calls back to LAMMPS (discussed in the
next section) and causes LAMMPS to perform an MPI operation requires
global communication (e.g. via MPI_Allreduce), such as computing the
global temperature of the system, then you must ensure all your Python
Third, if your Python code calls back to LAMMPS (discussed in the next
section) and causes LAMMPS to perform an MPI operation requires global
communication (e.g. via MPI_Allreduce), such as computing the global
temperature of the system, then you must ensure all your Python
functions (running independently on different processors) call back to
LAMMPS. Otherwise the code may hang.
----------
Your Python function can "call back" to LAMMPS through its
library interface, if you use the SELF input to pass Python
a pointer to LAMMPS. The mechanism for doing this in your
Python function is as follows:
As mentioned above, a Python function can "call back" to LAMMPS through
its library interface, if the SELF input is used to pass Python a
pointer to LAMMPS. The mechanism for doing this is as follows:
.. code-block:: python
@ -393,15 +468,15 @@ appeared in your input script. In this case, LAMMPS should output
Hello from inside Python
to the screen and log file. Note that since the LAMMPS print command
itself takes a string in quotes as its argument, the Python string
must be delimited with a different style of quotes.
itself takes a string in quotes as its argument, the Python string must
be delimited with a different style of quotes.
The :doc:`Python_head` page describes the syntax
for how Python wraps the various functions included in the LAMMPS
library interface.
The :doc:`Python_head` page describes the syntax for how Python wraps
the various functions included in the LAMMPS library interface.
A more interesting example is in the ``examples/python/in.python`` script
which loads and runs the following function from ``examples/python/funcs.py``:
A more interesting example is in the ``examples/python/in.python``
script which loads and runs the following function from
``examples/python/funcs.py``:
.. code-block:: python
@ -416,7 +491,7 @@ which loads and runs the following function from ``examples/python/funcs.py``:
lmp.set_variable("cut",cut) # set a variable in LAMMPS
lmp.command("pair_style lj/cut ${cut}") # LAMMPS command
#lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
#lmp.command("pair_style lj/cut %d" % cut) # alternate form of LAMMPS command
lmp.command("pair_coeff * * 1.0 1.0") # ditto
lmp.command("run 10") # ditto
@ -432,51 +507,160 @@ with these input script commands:
python loop invoke
This has the effect of looping over a series of 10 short runs (10
timesteps each) where the pair style cutoff is increased from a value
of 1.0 in distance units, in increments of 0.1. The looping stops
when the per-atom potential energy falls below a threshold of -4.0 in
energy units. More generally, Python can be used to implement a loop
with complex logic, much more so than can be created using the LAMMPS
timesteps each) where the pair style cutoff is increased from a value of
1.0 in distance units, in increments of 0.1. The looping stops when the
per-atom potential energy falls below a threshold of -4.0 in energy
units. More generally, Python can be used to implement a loop with
complex logic, much more so than can be created using the LAMMPS
:doc:`jump <jump>` and :doc:`if <if>` commands.
Several LAMMPS library functions are called from the loop function.
Get_natoms() returns the number of atoms in the simulation, so that it
can be used to normalize the potential energy that is returned by
extract_compute() for the "thermo_pe" compute that is defined by
default for LAMMPS thermodynamic output. Set_variable() sets the
value of a string variable defined in LAMMPS. This library function
is a useful way for a Python function to return multiple values to
LAMMPS, more than the single value that can be passed back via a
return statement. This cutoff value in the "cut" variable is then
substituted (by LAMMPS) in the pair_style command that is executed
next. Alternatively, the "LAMMPS command option" line could be used
in place of the 2 preceding lines, to have Python insert the value
into the LAMMPS command string.
extract_compute() for the "thermo_pe" compute that is defined by default
for LAMMPS thermodynamic output. Set_variable() sets the value of a
string variable defined in LAMMPS. This library function is a useful
way for a Python function to return multiple values to LAMMPS, more than
the single value that can be passed back via a return statement. This
cutoff value in the "cut" variable is then substituted (by LAMMPS) in
the pair_style command that is executed next. Alternatively, the
"alternate form of LAMMPS command" line could be used in place of the 2
preceding lines, to have Python insert the value into the LAMMPS command
string.
.. note::
When using the callback mechanism just described, recognize that
there are some operations you should not attempt because LAMMPS cannot
execute them correctly. If the Python function is invoked between
runs in the LAMMPS input script, then it should be OK to invoke any
LAMMPS input script command via the library interface command() or
file() functions, so long as the command would work if it were
executed in the LAMMPS input script directly at the same point.
there are some operations you should not attempt because LAMMPS
cannot execute them correctly. If the Python function is invoked
between runs in the LAMMPS input script, then it should be OK to
invoke any LAMMPS input script command via the library interface
command() or file() functions, so long as the command would work if
it were executed in the LAMMPS input script directly at the same
point.
However, a Python function can also be invoked during a run, whenever
an associated LAMMPS variable it is assigned to is evaluated. If the
variable is an input argument to another LAMMPS command (e.g. :doc:`fix setforce <fix_setforce>`), then the Python function will be invoked
inside the class for that command, in one of its methods that is
invoked in the middle of a timestep. You cannot execute arbitrary
input script commands from the Python function (again, via the
command() or file() functions) at that point in the run and expect it
to work. Other library functions such as those that invoke computes
or other variables may have hidden side effects as well. In these
cases, LAMMPS has no simple way to check that something illogical is
being attempted.
The same applies to Python functions called during a simulation run at
each time step using :doc:`fix python/invoke <fix_python_invoke>`.
----------
As noted above, a Python function can be invoked during a run, whenever
an associated python-style variable it is assigned to is evaluated.
If the variable is an input argument to another LAMMPS command
(e.g. :doc:`fix setforce <fix_setforce>`), then the Python function will
be invoked inside the class for that command, possibly in one of its
methods that is invoked in the middle of a timestep. You cannot execute
arbitrary input script commands from the Python function (again, via the
command() or file() functions) at that point in the run and expect it to
work. Other library functions such as those that invoke computes or
other variables may have hidden side effects as well. In these cases,
LAMMPS has no simple way to check that something illogical is being
attempted.
The same constraints apply to Python functions called during a
simulation run at each time step using the :doc:`fix python/invoke
<fix_python_invoke>` command.
----------
As noted above, a Python function can also be invoked within the formula
for an equal-style, vector-style, or atom-style variable. This means
the Python function will be invoked whenever that variable is invoked.
In the case of a vector-style variable, the Python function can be
invoked once per element of the global vector. In the case of an
atom-style variable, the Python function can be invoked once per atom.
Here are three simple examples using equal-, vector-, and atom-style
variables to trigger execution of a Python function:
.. code-block:: LAMMPS
variable foo python truncate
python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x):
return int(x)
"""
variable ptrunc equal py_foo(press)
print "TRUNCATED pressure = ${ptrunc}"
The Python ``truncate`` function simply converts a floating-point value
to an integer value. When the LAMMPS print command evaluates the
equal-style ``ptrunc`` variable, the current thermodynamic pressure is
passed to the Python function. The truncated value is output to the
screen and logfile by the print command. Note that the *input* keyword
for the *python* command, specifies an internal-style variable named
"arg" as iv_arg which is required to invoke the Python function from a
Python function wrapper.
The last 2 lines can be replaced by these to define a vector-style
variable which invokes the same Python ``truncate`` function:
.. code-block:: LAMMPS
compute ke all temp
variable ke vector c_ke
variable ketrunc vector py_foo(v_ke)
thermo_style custom step temp epair v_ketrunc[*6]
The vector-style variable ``ketrunc`` invokes the Python ``truncate``
function on each of the 6 components of the global kinetic energy tensor
calculated by the :doc:`compute ke <compute_ke>` command. The 6
truncated values will be printed with thermo output to the screen and
log file.
Or the last 2 lines of the equal-style variable example can be replaced
by these to define atom-style variables which invoke the same Python
``truncate`` function:
.. code-block:: LAMMPS
variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z)
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
When the dump command invokes the 3 atom-style variables, their
arguments x,y,z to the Python function wrapper are the current per-atom
coordinates of each atom. The Python ``truncate`` function is thus
invoked 3 times for each atom, and the truncated coordinate values for
each atom are written to the dump file.
Note that when using a Python function wrapper in a variable, arguments
can be passed to the Python function either from the variable formula or
by *input* keyword to the :doc:`python command <python>`. For example,
consider these (made up) commands:
.. code-block:: LAMMPS
variable foo python mixedargs
python mixedargs return v_foo input 6 7.5 v_myValue iv_arg1 iv_argy iv_argz v_flag &
format fffffsf here """
def mixedargs(a,b,x,y,z,flag):
...
return result
"""
variable flag string optionABC
variable myValue equal "2.0*temp*c_pe"
compute pe all pe
compute peatom all pe/atom
variable field atom py_foo(x+3.0,sqrt(y),(z-zlo)*c_peatom)
They define a Python ``mixedargs`` function with 6 arguments. Three of
them are internal-style variables, which the variable formula calculates
as numeric values for each atom and passes to the function. In this
example, these arguments are themselves small formulas containing the
x,y,z coordinates of each atom as well as a per-atom compute (c_peratom)
and thermodynamic keyword (zlo).
The other three arguments ``(7.5,v_myValue,v_flag)`` are defined by the
*python* command. The first and last are constant values ("7.5" and the
``optionABC`` string). The second argument (``myValue``) is the result
of an equal-style variable formula which accesses the system temperature
and potential energy.
The "result" returned by each invocation of the Python ``mixedargs``
function becomes the per-atom value in the atom-style "field" variable,
which could be output to a dump file or used elsewhere in the input
script.
----------
@ -485,12 +669,11 @@ interactively or by using Python to launch a Python script stored in a
file, and your code has an error, you will typically see informative
error messages. That is not the case when you run Python code from
LAMMPS using an embedded Python interpreter. The code will typically
fail silently. LAMMPS will catch some errors but cannot tell you
where in the Python code the problem occurred. For example, if the
Python code cannot be loaded and run because it has syntax or other
logic errors, you may get an error from Python pointing to the
offending line, or you may get one of these generic errors from
LAMMPS:
fail silently. LAMMPS will catch some errors but cannot tell you where
in the Python code the problem occurred. For example, if the Python
code cannot be loaded and run because it has syntax or other logic
errors, you may get an error from Python pointing to the offending line,
or you may get one of these generic errors from LAMMPS:
.. parsed-literal::
@ -504,16 +687,16 @@ you will typically get this generic error from LAMMPS:
Python function evaluation failed
Here are three suggestions for debugging your Python code while
running it under LAMMPS.
Here are three suggestions for debugging your Python code while running
it under LAMMPS.
First, don't run it under LAMMPS, at least to start with! Debug it
using plain Python. Load and invoke your function, pass it arguments,
check return values, etc.
Second, add Python print statements to the function to check how far
it gets and intermediate values it calculates. See the discussion
above about printing from Python when running in parallel.
Second, add Python print statements to the function to check how far it
gets and intermediate values it calculates. See the discussion above
about printing from Python when running in parallel.
Third, use Python exception handling. For example, say this statement
in your Python function is failing, because you have not initialized the
@ -523,8 +706,7 @@ variable foo:
foo += 1
If you put one (or more) statements inside a "try" statement,
like this:
If you put one (or more) statements inside a "try" statement, like this:
.. code-block:: python
@ -563,13 +745,15 @@ If you use Python code which calls back to LAMMPS, via the SELF input
argument explained above, there is an extra step required when building
LAMMPS. LAMMPS must also be built as a shared library and your Python
function must be able to load the :doc:`"lammps" Python module
<Python_module>` that wraps the LAMMPS library interface. These are the
same steps required to use Python by itself to wrap LAMMPS. Details on
these steps are explained on the :doc:`Python <Python_head>` doc page.
Note that it is important that the stand-alone LAMMPS executable and the
LAMMPS shared library be consistent (built from the same source code
files) in order for this to work. If the two have been built at
different times using different source files, problems may occur.
<Python_module>` that wraps the LAMMPS library interface.
These are the same steps required to use Python by itself to wrap
LAMMPS. Details on these steps are explained on the :doc:`Python
<Python_head>` doc page. Note that it is important that the stand-alone
LAMMPS executable and the LAMMPS shared library be consistent (built
from the same source code files) in order for this to work. If the two
have been built at different times using different source files,
problems may occur.
Another limitation of calling back to Python from the LAMMPS module
using the *python* command in a LAMMPS input is that both, the Python
@ -583,7 +767,8 @@ global variables will become invisible.
Related commands
""""""""""""""""
:doc:`shell <shell>`, :doc:`variable <variable>`, :doc:`fix python/invoke <fix_python_invoke>`
:doc:`shell <shell>`, :doc:`variable <variable>`,
:doc:`fix python/invoke <fix_python_invoke>`
Default
"""""""

3
doc/src/read_dump.rst
View File

@ -16,12 +16,13 @@ Syntax
.. parsed-literal::
field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz*
field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz* or *apip_lambda*
*x*,\ *y*,\ *z* = atom coordinates
*vx*,\ *vy*,\ *vz* = velocity components
*q* = charge
*ix*,\ *iy*,\ *iz* = image flags in each dimension
*fx*,\ *fy*,\ *fz* = force components
*apip_lambda* = switching parameter of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
* zero or more keyword/value pairs may be appended
* keyword = *nfile* or *box* or *timestep* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*

18
doc/src/run.rst
View File

@ -103,14 +103,16 @@ must be done.
.. note::
If your input script changes the system between 2 runs, then the
initial setup must be performed to ensure the change is recognized by
all parts of the code that are affected. Examples are adding a
:doc:`fix <fix>` or :doc:`dump <dump>` or :doc:`compute <compute>`, changing
a :doc:`neighbor <neigh_modify>` list parameter, or writing restart file
which can migrate atoms between processors. LAMMPS has no easy way to
check if this has happened, but it is an error to use the *pre no*
option in this case.
If your input script "changes" the system between 2 runs, then the
initial setup typically needs to be performed to ensure the change
is recognized by all parts of the code that are affected. Examples
are adding a :doc:`fix <fix>` or :doc:`dump <dump>` or
:doc:`compute <compute>`, changing a :doc:`neighbor <neigh_modify>`
list parameter, using the :doc:`set <set>` command, or writing a
restart file via the :doc:`write_restart <write_restart>` command,
which can migrate atoms between processors. LAMMPS has no easy way
to check if this has happened, but it is an error to use the *pre
no* option in these cases.
If *post* is specified as "no", the full timing summary is skipped;
only a one-line summary timing is printed.

800
doc/src/set.rst
View File

@ -22,21 +22,114 @@ Syntax
for style = *region*, ID = a region ID
* one or more keyword/value pairs may be appended
* keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
*dipole* or *dipole/random* or *quat* or *spin/atom* or *spin/atom/random* or
*spin/electron* or *radius/electron* or
*quat* or *quat/random* or *diameter* or *shape* or *length* or *tri* or
*theta* or *theta/random* or *angmom* or *omega* or
*mass* or *density* or *density/disc* or *temperature* or
*volume* or *image* or *bond* or *angle* or *dihedral* or
*improper* or *sph/e* or *sph/cv* or *sph/rho* or
*smd/contact/radius* or *smd/mass/density* or *dpd/theta* or
*edpd/temp* or *edpd/cv* or *cc* or *epsilon* or
*i_name* or *d_name* or *i2_name* or *d2_name*
* keyword = *angle* or *angmom* or *apip/lambda* or *bond* or *cc* or *charge*
or *density* or *density/disc* or *diameter* or *dihedral* or *dipole*
or *dipole/random* or *dpd/theta* or *edpd/cv* or *edpd/temp* or
*epsilon* or *image* or *improper* or *length* or *mass* or *mol* or
*omega* or *quat* or *quat/random* or *radius/electron* or *shape* or
*smd/contact/radius* or *smd/mass/density* or *sph/cv* or *sph/e* or
*sph/rho* or *spin/atom* or *spin/atom/random* or *spin/electron* or
*temperature* or *theta* or *theta/random* or *tri* or *type* or
*type/fraction* or *type/ratio* or *type/subset* or *volume* or *vx*
or *vy* or *vz* or *x* or *y* or *z* or *i_name* or *d_name* or
*i2_name* or *d2_name*
.. parsed-literal::
*angle* value = numeric angle type or angle type label, for all angles between selected atoms
*angmom* values = Lx Ly Lz
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
any of Lx,Ly,Lz can be an atom-style variable (see below)
*apip/lambda* value = fast or precise or float
fast = switching parameter of fast potential (1)
precise = switching parameter of fast potential (0)
float = constant float or atom-style variable (between 0 and 1)
*bond* value = numeric bond type or bond type label, for all bonds between selected atoms
*cc* values = index cc
index = index of a chemical species (1 to Nspecies)
cc = chemical concentration of tDPD particles for a species (mole/volume units)
cc can be an atom-style variable (see below)
*charge* value = atomic charge (charge units)
value can be an atom-style variable (see below)
*density* value = particle density for a sphere or ellipsoid (mass/distance\^3 units), or for a triangle (mass/distance\^2 units) or line (mass/distance units) particle
value can be an atom-style variable (see below)
*density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
value can be an atom-style variable (see below)
*diameter* value = diameter of spherical particle (distance units)
value can be an atom-style variable (see below)
*dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
*dipole* values = x y z
x,y,z = orientation of dipole moment vector
any of x,y,z can be an atom-style variable (see below)
*dipole/random* values = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
*dpd/theta* value = internal temperature of DPD particles (temperature units)
value can be an atom-style variable (see below)
value can be NULL which sets internal temp of each particle to KE temp
*edpd/cv* value = volumetric heat capacity of eDPD particles (energy/temperature/volume units)
value can be an atom-style variable (see below)
*edpd/temp* value = temperature of eDPD particles (temperature units)
value can be an atom-style variable (see below)
*epsilon* value = dielectric constant of the medium where the atoms reside
value can be an atom-style variable (see below)
*image* values = nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
any of nx,ny,nz can be an atom-style variable (see below)
*improper* value = numeric improper type or improper type label, for all impropers between selected atoms
*length* value = len
len = length of line segment (distance units)
len can be an atom-style variable (see below)
*mass* value = per-atom mass (mass units)
value can be an atom-style variable (see below)
*mol* value = molecule ID
the moleclue ID can be an atom-style variable (see below)
*omega* values = Wx Wy Wz
Wx,Wy,Wz = components of angular velocity vector (radians/time units)
any of Wx,Wy,Wz can be an atom-style variable (see below)
*quat* values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle (degrees)
any of a,b,c,theta values can be an atom-style variable (see below)
*quat/random* value = seed
seed = random # seed (positive integer) for quaternion orientations
*radius/electron* value = eradius
eradius = electron radius (or fixed-core radius) (distance units)
value can be an atom-style variable (see below)
*shape* values = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
any of Sx,Sy,Sz can be an atom-style variable (see below)
*smd/contact/radius* value = radius for short range interactions, i.e. contact and friction
value can be an atom-style variable (see below)
*smd/mass/density* value = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
*sph/cv* value = heat capacity of SPH particles (need units)
value can be an atom-style variable (see below)
*sph/e* value = energy of SPH particles (need units)
value can be an atom-style variable (see below)
*sph/rho* value = density of SPH particles (need units)
value can be an atom-style variable (see below)
*spin/atom* values = g x y z
g = magnitude of magnetic spin vector (in Bohr magneton's unit)
x,y,z = orientation of magnetic spin vector
any of x,y,z can be an atom-style variable (see below)
*spin/atom/random* values = seed Dlen
seed = random # seed (positive integer) for magnetic spin orientations
Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
*spin/electron* value = espin
espin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
value can be an atom-style variable (see below)
*temperature* value = temperature for finite-size particles (temperature units)
value can be an atom-style variable (see below)
*theta* value = angle (degrees)
angle = orientation of line segment with respect to x-axis
value can be an atom-style variable (see below)
*theta/random* value = seed
seed = random # seed (positive integer) for line segment orienations
*tri* value = side
side = side length of equilateral triangle (distance units)
value can be an atom-style variable (see below)
*type* value = numeric atom type or type label
value can be an atom-style variable (see below)
*type/fraction* values = type fraction seed
@ -51,104 +144,22 @@ Syntax
type = numeric atom type or type label
Nsubset = exact number of selected atoms to set to new atom type
seed = random # seed (positive integer)
*mol* value = molecule ID
value can be an atom-style variable (see below)
*x*,\ *y*,\ *z* value = atom coordinate (distance units)
*volume* value = particle volume for Peridynamic particle (distance\^3 units)
value can be an atom-style variable (see below)
*vx*,\ *vy*,\ *vz* value = atom velocity (velocity units)
value can be an atom-style variable (see below)
*charge* value = atomic charge (charge units)
*x*,\ *y*,\ *z* value = atom coordinate (distance units)
value can be an atom-style variable (see below)
*dipole* values = x y z
x,y,z = orientation of dipole moment vector
any of x,y,z can be an atom-style variable (see below)
*dipole/random* value = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
*spin/atom* values = g x y z
g = magnitude of magnetic spin vector (in Bohr magneton's unit)
x,y,z = orientation of magnetic spin vector
any of x,y,z can be an atom-style variable (see below)
*spin/atom/random* value = seed Dlen
seed = random # seed (positive integer) for magnetic spin orientations
Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
*radius/electron* values = eradius
eradius = electron radius (or fixed-core radius) (distance units)
*spin/electron* value = espin
espin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
*quat* values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle (degrees)
any of a,b,c,theta can be an atom-style variable (see below)
*quat/random* value = seed
seed = random # seed (positive integer) for quaternion orientations
*diameter* value = diameter of spherical particle (distance units)
value can be an atom-style variable (see below)
*shape* value = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
*length* value = len
len = length of line segment (distance units)
len can be an atom-style variable (see below)
*tri* value = side
side = side length of equilateral triangle (distance units)
side can be an atom-style variable (see below)
*theta* value = angle (degrees)
angle = orientation of line segment with respect to x-axis
angle can be an atom-style variable (see below)
*theta/random* value = seed
seed = random # seed (positive integer) for line segment orienations
*angmom* values = Lx Ly Lz
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
any of Lx,Ly,Lz can be an atom-style variable (see below)
*omega* values = Wx Wy Wz
Wx,Wy,Wz = components of angular velocity vector (radians/time units)
any of wx,wy,wz can be an atom-style variable (see below)
*mass* value = per-atom mass (mass units)
value can be an atom-style variable (see below)
*density* value = particle density for a sphere or ellipsoid (mass/distance\^3 units), or for a triangle (mass/distance\^2 units) or line (mass/distance units) particle
value can be an atom-style variable (see below)
*density/disc* value = particle density for a 2d disc or ellipse (mass/distance\^2 units)
value can be an atom-style variable (see below)
*temperature* value = temperature for finite-size particles (temperature units)
value can be an atom-style variable (see below)
*volume* value = particle volume for Peridynamic particle (distance\^3 units)
value can be an atom-style variable (see below)
*image* nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
any of nx,ny,nz can be an atom-style variable (see below)
*bond* value = numeric bond type or bond type label, for all bonds between selected atoms
*angle* value = numeric angle type or angle type label, for all angles between selected atoms
*dihedral* value = numeric dihedral type or dihedral type label, for all dihedrals between selected atoms
*improper* value = numeric improper type or improper type label, for all impropers between selected atoms
*rheo/rho* value = density of RHEO particles (mass/distance\^3)
*rheo/status* value = status or phase of RHEO particles (unitless)
*sph/e* value = energy of SPH particles (need units)
value can be an atom-style variable (see below)
*sph/cv* value = heat capacity of SPH particles (need units)
value can be an atom-style variable (see below)
*sph/rho* value = density of SPH particles (need units)
value can be an atom-style variable (see below)
*smd/contact/radius* = radius for short range interactions, i.e. contact and friction
value can be an atom-style variable (see below)
*smd/mass/density* = set particle mass based on volume by providing a mass density
value can be an atom-style variable (see below)
*dpd/theta* value = internal temperature of DPD particles (temperature units)
value can be an atom-style variable (see below)
value can be NULL which sets internal temp of each particle to KE temp
*edpd/temp* value = temperature of eDPD particles (temperature units)
value can be an atom-style variable (see below)
*edpd/cv* value = volumetric heat capacity of eDPD particles (energy/temperature/volume units)
value can be an atom-style variable (see below)
*cc* values = index cc
index = index of a chemical species (1 to Nspecies)
cc = chemical concentration of tDPD particles for a species (mole/volume units)
*epsilon* value = dielectric constant of the medium where the atoms reside
*i_name* value = custom integer vector with name
value can be an atom-style variable (see below)
*d_name* value = custom floating-point vector with name
*i2_name* value = column of a custom integer array with name
value can be an atom-style variable (see below)
*i2_name* value = custom integer array with name
column specified as i2_name[N] where N is 1 to Ncol
*d2_name* value = column of a custom floating-point array with name
value can be an atom-style variable (see below)
*d2_name* value = custom floating-point array with name
column specified as d2_name[N] where N is 1 to Ncol
value can be an atom-style variable (see below)
Examples
""""""""
@ -177,22 +188,26 @@ Description
Set one or more properties of one or more atoms. Since atom
properties are initially assigned by the :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>` or :doc:`create_atoms <create_atoms>`
commands, this command changes those assignments. This can be useful
for overriding the default values assigned by the
:doc:`create_atoms <create_atoms>` command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions,
:doc:`read_restart <read_restart>` or :doc:`create_atoms
<create_atoms>` commands, this command changes those assignments.
This can be useful for overriding the default values assigned by the
:doc:`create_atoms <create_atoms>` command (e.g. charge = 0.0). It
can be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can
be used to change the labeling of atoms by atom type or molecule ID
when they are output in :doc:`dump <dump>` files. It can also be useful
for debugging purposes; i.e. positioning an atom at a precise location
to compute subsequent forces or energy.
when they are output in :doc:`dump <dump>` files. It can also be
useful for debugging purposes; i.e. positioning an atom at a precise
location to compute subsequent forces or energy.
Note that the *style* and *ID* arguments determine which atoms have
their properties reset. The remaining keywords specify which
properties to reset and what the new values are. Some strings like
*type* or *mol* can be used as a style and/or a keyword.
The :doc:`fix set <fix_set>` command can be used with similar syntax
to this command to reset atom properties once every *N* steps during a
simulation using via atom-style variables.
----------
This section describes how to select which atoms to change
@ -211,8 +226,8 @@ can be specified, e.g. "C". The style *mol* selects all the atoms in
a range of molecule IDs.
In each of the range cases, the range can be specified as a single
numeric value, or a wildcard asterisk can be used to specify a range
of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
numeric value, or with a wildcard asterisk to specify a range of
values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
example, for the style *type*, if N = the number of atom types, then
an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
@ -222,25 +237,25 @@ means all types from m to n (inclusive). For all the styles except
The style *group* selects all the atoms in the specified group. The
style *region* selects all the atoms in the specified geometric
region. See the :doc:`group <group>` and :doc:`region <region>` commands
for details of how to specify a group or region.
region. See the :doc:`group <group>` and :doc:`region <region>`
commands for details of how to specify a group or region.
----------
This section describes the keyword options for which properties to
The next section describes the keyword options for which properties to
change, for the selected atoms.
Note that except where explicitly prohibited below, all of the
keywords allow an :doc:`atom-style or atomfile-style variable
<variable>` to be used as the specified value(s). If the value is a
variable, it should be specified as v_name, where name is the
variable name. In this case, the variable will be evaluated, and its
resulting per-atom value used to determine the value assigned to each
selected atom. Note that the per-atom value from the variable will be
ignored for atoms that are not selected via the *style* and *ID*
settings explained above. A simple way to use per-atom values from
the variable to reset a property for all atoms is to use style *atom*
with *ID* = "\*"; this selects all atom IDs.
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated, and its resulting
per-atom value used to determine the value assigned to each selected
atom. Note that the per-atom value from the variable will be ignored
for atoms that are not selected via the *style* and *ID* settings
explained above. A simple way to use per-atom values from the
variable to reset a property for all atoms is to use style *atom* with
*ID* = "\*"; this selects all atom IDs.
Atom-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command
@ -256,52 +271,110 @@ from a file.
.. note::
Atom-style and atomfile-style variables return floating point
per-atom values. If the values are assigned to an integer variable,
such as the molecule ID, then the floating point value is truncated to
its integer portion, e.g. a value of 2.6 would become 2.
per-atom values. If the values are assigned to an integer
variable, such as the molecule ID, then the floating point value is
truncated to its integer portion, e.g. a value of 2.6 would
become 2.
----------
.. versionchanged:: 28Mar2023
Support for type labels was added for setting atom, bond, angle,
dihedral, and improper types
Support for type labels was added for setting angle types
Keyword *type* sets the atom type for all selected atoms. A specified
value can be either a numeric atom type or an atom type label. When
using a numeric type, the specified value must be from 1 to ntypes,
where ntypes was set by the :doc:`create_box <create_box>` command or
the *atom types* field in the header of the data file read by the
:doc:`read_data <read_data>` command. When using a type label it must
have been defined previously. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
Keyword *angle* sets the angle type of all angles of selected atoms to
the specified value. The value can be a numeric type from 1 to
nangletypes. Or it can be a angle type label. See the :doc:`Howto
type labels <Howto_type_labels>` doc page for the allowed syntax of
type labels and a general discussion of how type labels can be used.
All atoms in a particular angle must be selected atoms in order for
the change to be made. The value of nangletypes was set by the *angle
types* field in the header of the data file read by the
:doc:`read_data <read_data>` command. This keyword does NOT allow use
of an atom-style variable.
Keyword *type/fraction* sets the atom type for a fraction of the selected
atoms. The actual number of atoms changed is not guaranteed
to be exactly the specified fraction (0 <= *fraction* <= 1), but
should be statistically close. Random numbers are used in such a way
that a particular atom is changed or not changed, regardless of how
many processors are being used. This keyword does not allow use of an
atom-style variable.
Keyword *angmom* sets the angular momentum of selected atoms. The
particles must be ellipsoids as defined by the :doc:`atom_style
ellipsoid <atom_style>` command or triangles as defined by the
:doc:`atom_style tri <atom_style>` command. The angular momentum
vector of the particles is set to the 3 specified components.
Keywords *type/ratio* and *type/subset* also set the atom type for a
fraction of the selected atoms. The actual number of atoms changed
will be exactly the requested number. For *type/ratio* the specified
fraction (0 <= *fraction* <= 1) determines the number. For
*type/subset*, the specified *Nsubset* is the number. An iterative
algorithm is used which ensures the correct number of atoms are
selected, in a perfectly random fashion. Which atoms are selected
will change with the number of processors used. These keywords do not
allow use of an atom-style variable.
.. versionchanged:: 28Mar2023
Keyword *mol* sets the molecule ID for all selected atoms. The
:doc:`atom style <atom_style>` being used must support the use of
molecule IDs.
Support for type labels was added for setting bond types
Keywords *x*, *y*, *z*, and *charge* set the coordinates or
charge of all selected atoms. For *charge*, the :doc:`atom style
<atom_style>` being used must support the use of atomic
charge. Keywords *vx*, *vy*, and *vz* set the velocities of all
selected atoms.
Keyword *bond* sets the bond type of all bonds of selected atoms to
the specified value. The value can be a numeric type from 1 to
nbondtypes. Or it can be a bond type label. See the :doc:`Howto type
labels <Howto_type_labels>` doc page for the allowed syntax of type
labels and a general discussion of how type labels can be used. All
atoms in a particular bond must be selected atoms in order for the
change to be made. The value of nbondtypes was set by the *bond
types* field in the header of the data file read by the
:doc:`read_data <read_data>` command. This keyword does NOT allow use
of an atom-style variable.
Keyword *cc* sets the chemical concentration of a tDPD particle for a
specified species as defined by the DPD-MESO package. Currently, only
:doc:`atom_style tdpd <atom_style>` defines particles with this
attribute. An integer for "index" selects a chemical species (1 to
Nspecies) where Nspecies is set by the atom_style command. The value
for the chemical concentration must be >= 0.0.
Keyword *charge* set the charge of all selected atoms. The :doc:`atom
style <atom_style>` being used must support the use of atomic charge.
Keyword *density* or *density/disc* also sets the mass of all selected
particles, but in a different way. The particles must have a per-atom
mass attribute, as defined by the :doc:`atom_style <atom_style>`
command. If the atom has a radius attribute (see :doc:`atom_style
sphere <atom_style>`) and its radius is non-zero, its mass is set from
the density and particle volume for 3d systems (the input density is
assumed to be in mass/distance\^3 units). For 2d, the default is for
LAMMPS to model particles with a radius attribute as spheres.
However, if the *density/disc* keyword is used, then they can be
modeled as 2d discs (circles). Their mass is set from the density and
particle area (the input density is assumed to be in mass/distance\^2
units).
If the atom has a shape attribute (see :doc:`atom_style ellipsoid
<atom_style>`) and its 3 shape parameters are non-zero, then its mass
is set from the density and particle volume (the input density is
assumed to be in mass/distance\^3 units). The *density/disc* keyword
has no effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
If the atom has a length attribute (see :doc:`atom_style line
<atom_style>`) and its length is non-zero, then its mass is set from
the density and line segment length (the input density is assumed to
be in mass/distance units). If the atom has an area attribute (see
:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
mass is set from the density and triangle area (the input density is
assumed to be in mass/distance\^2 units).
If none of these cases are valid, then the mass is set to the density
value directly (the input density is assumed to be in mass units).
Keyword *diameter* sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the :doc:`atom_style sphere
<atom_style>` command. The diameter of a particle can be set to 0.0,
which means they will be treated as point particles. Note that this
command does not adjust the particle mass, even if it was defined with
a density, e.g. via the :doc:`read_data <read_data>` command.
.. versionchanged:: 28Mar2023
Support for type labels was added for setting dihedral types
Keyword *dihedral* sets the dihedral type of all dihedrals of selected
atoms to the specified value. The value can be a numeric type from 1
to ndihedraltypes. Or it can be a dihedral type label. See the
:doc:`Howto type labels <Howto_type_labels>` doc page for the allowed
syntax of type labels and a general discussion of how type labels can
be used. All atoms in a particular dihedral must be selected atoms in
order for the change to be made. The value of ndihedraltypes was set
by the *dihedral types* field in the header of the data file read by
the :doc:`read_data <read_data>` command. This keyword does NOT allow
use of an atom-style variable.
Keyword *dipole* uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
@ -313,40 +386,106 @@ moment vectors for the selected atoms and sets the magnitude of each
to the specified *Dlen* value. For 2d systems, the z component of the
orientation is set to 0.0. Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used. This keyword does not allow use of an
many processors are being used. This keyword does NOT allow use of an
atom-style variable.
.. versionchanged:: 15Sep2022
Keyword *dpd/theta* sets the internal temperature of a DPD particle as
defined by the DPD-REACT package. If the specified value is a number
it must be >= 0.0. If the specified value is NULL, then the kinetic
temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2
m v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal
temperature is set to Tkin. If the specified value is an atom-style
variable, then the variable is evaluated for each particle. If a
value >= 0.0, the internal temperature is set to that value. If it is
< 0.0, the computation of Tkin is performed and the internal
temperature is set to that value.
Keyword *spin/atom* uses the specified g value to set the magnitude of the
magnetic spin vectors, and the x,y,z values as components of a vector
to set as the orientation of the magnetic spin vectors of the selected
atoms. This keyword was previously called *spin*.
Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
heat capacity of an eDPD particle as defined by the DPD-MESO package.
Currently, only :doc:`atom_style edpd <atom_style>` defines particles
with these attributes. The values for the temperature and heat
capacity must be positive.
.. versionchanged:: 15Sep2022
Keyword *epsilon* sets the dielectric constant of a particle to be
that of the medium where the particle resides as defined by the
DIELECTRIC package. Currently, only :doc:`atom_style dielectric
<atom_style>` defines particles with this attribute. The value for the
dielectric constant must be >= 0.0. Note that the set command with
this keyword will rescale the particle charge accordingly so that the
real charge (e.g., as read from a data file) stays intact. To change
the real charges, one needs to use the set command with the *charge*
keyword. Care must be taken to ensure that the real and scaled charges
and the dielectric constants are consistent.
Keyword *spin/atom/random* randomizes the orientation of the magnetic spin
vectors for the selected atoms and sets the magnitude of each to the
specified *Dlen* value. This keyword was previously called *spin/random*.
Keyword *image* sets which image of the simulation box the atom is
considered to be in. An image of 0 means it is inside the box as
defined. A value of 2 means add 2 box lengths to get the true value.
A value of -1 means subtract 1 box length to get the true value.
LAMMPS updates these flags as atoms cross periodic boundaries during
the simulation. The flags can be output with atom snapshots via the
:doc:`dump <dump>` command. If a value of NULL is specified for any
of nx,ny,nz, then the current image value for that dimension is
unchanged. For non-periodic dimensions only a value of 0 can be
specified. This command can be useful after a system has been
equilibrated and atoms have diffused one or more box lengths in
various directions. This command can then reset the image values for
atoms so that they are effectively inside the simulation box, e.g if a
diffusion coefficient is about to be measured via the :doc:`compute
msd <compute_msd>` command. Care should be taken not to reset the
image flags of two atoms in a bond to the same value if the bond
straddles a periodic boundary (rather they should be different by +/-
1). This will not affect the dynamics of a simulation, but may mess
up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
.. versionadded:: 15Sep2022
.. versionchanged:: 28Mar2023
Keyword *radius/electron* uses the specified value to set the radius of
electrons or fixed cores.
Support for type labels was added for setting improper types
.. versionadded:: 15Sep2022
Keyword *improper* sets the improper type of all impropers of selected
atoms to the specified value. The value can be a numeric type from 1
to nimpropertypes. Or it can be a improper type label. See the
:doc:`Howto type labels <Howto_type_labels>` doc page for the allowed
syntax of type labels and a general discussion of how type labels can
be used. All atoms in a particular improper must be selected atoms in
order for the change to be made. The value of nimpropertypes was set
by the *improper types* field in the header of the data file read by
the :doc:`read_data <read_data>` command. This keyword does NOT allow
use of an atom-style variable.
Keyword *spin/electron* sets the spin of an electron (+/- 1) or indicates
nuclei (=0), fixed-cores (=2), or pseudo-cores (= 3).
Keyword *length* sets the length of selected atoms. The particles
must be line segments as defined by the :doc:`atom_style line
<atom_style>` command. If the specified value is non-zero the line
segment is (re)set to a length = the specified value, centered around
the particle position, with an orientation along the x-axis. If the
specified value is 0.0, the particle will become a point particle.
Note that this command does not adjust the particle mass, even if it
was defined with a density, e.g. via the :doc:`read_data <read_data>`
command.
Keyword *mass* sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the
:doc:`atom_style <atom_style>` command. See the "mass" command for
how to set mass values on a per-type basis.
Keyword *mol* sets the molecule ID for all selected atoms. The
:doc:`atom style <atom_style>` being used must support the use of
molecule IDs.
Keyword *omega* sets the angular velocity of selected atoms. The
particles must be spheres as defined by the :doc:`atom_style sphere
<atom_style>` command. The angular velocity vector of the particles
is set to the 3 specified components.
Keyword *quat* uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. The
particles must define a quaternion for their orientation
(e.g. ellipsoids, triangles, body particles) as defined by the
:doc:`atom_style <atom_style>` command. Note that particles defined by
:doc:`atom_style ellipsoid <atom_style>` have 3 shape parameters. The 3
values must be non-zero for each particle set by this command. They
are used to specify the aspect ratios of an ellipsoidal particle,
:doc:`atom_style <atom_style>` command. Note that particles defined
by :doc:`atom_style ellipsoid <atom_style>` have 3 shape parameters.
The 3 values must be non-zero for each particle set by this command.
They are used to specify the aspect ratios of an ellipsoidal particle,
which is oriented by default with its x-axis along the simulation
box's x-axis, and similarly for y and z. If this body is rotated (via
the right-hand rule) by an angle theta around a unit rotation vector
@ -360,51 +499,77 @@ ignored, since a rotation vector of (0,0,1) is the only valid choice.
Keyword *quat/random* randomizes the orientation of the quaternion for
the selected atoms. The particles must define a quaternion for their
orientation (e.g. ellipsoids, triangles, body particles) as defined by
the :doc:`atom_style <atom_style>` command. Random numbers are used in
such a way that the orientation of a particular atom is the same,
the :doc:`atom_style <atom_style>` command. Random numbers are used
in such a way that the orientation of a particular atom is the same,
regardless of how many processors are being used. For 2d systems,
only orientations in the xy plane are generated. As with keyword
*quat*, for ellipsoidal particles, the 3 shape values must be non-zero
for each particle set by this command. This keyword does not allow
for each particle set by this command. This keyword does NOT allow
use of an atom-style variable.
Keyword *diameter* sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the :doc:`atom_style sphere
<atom_style>` command. The diameter of a particle can be set to 0.0,
which means they will be treated as point particles. Note that this
command does not adjust the particle mass, even if it was defined with
a density, e.g. via the :doc:`read_data <read_data>` command.
.. versionadded:: 15Sep2022
Keyword *radius/electron* uses the specified value to set the radius
of electrons or fixed cores.
Keyword *shape* sets the size and shape of the selected atoms. The
particles must be ellipsoids as defined by the :doc:`atom_style
ellipsoid <atom_style>` command. The *Sx*, *Sy*, *Sz* settings
are the 3 diameters of the ellipsoid in each direction. All 3 can be
set to the same value, which means the ellipsoid is effectively a
sphere. They can also all be set to 0.0 which means the particle will
be treated as a point particle. Note that this command does not
adjust the particle mass, even if it was defined with a density,
e.g. via the :doc:`read_data <read_data>` command.
ellipsoid <atom_style>` command. The *Sx*, *Sy*, *Sz* settings are
the 3 diameters of the ellipsoid in each direction. All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
They can also all be set to 0.0 which means the particle will be
treated as a point particle. Note that this command does not adjust
the particle mass, even if it was defined with a density, e.g. via the
:doc:`read_data <read_data>` command.
Keyword *length* sets the length of selected atoms. The particles
must be line segments as defined by the :doc:`atom_style line
<atom_style>` command. If the specified value is non-zero the line
segment is (re)set to a length = the specified value, centered around
the particle position, with an orientation along the x-axis. If the
specified value is 0.0, the particle will become a point particle.
Note that this command does not adjust the particle mass, even if it
was defined with a density, e.g. via the :doc:`read_data <read_data>`
command.
Keyword *smd/contact/radius* only applies to simulations with the
Smooth Mach Dynamics package MACHDYN. Itsets an interaction radius
for computing short-range interactions, e.g. repulsive forces to
prevent different individual physical bodies from penetrating each
other. Note that the SPH smoothing kernel diameter used for computing
long range, nonlocal interactions, is set using the *diameter*
keyword.
Keyword *tri* sets the size of selected atoms. The particles must be
triangles as defined by the :doc:`atom_style tri <atom_style>` command.
If the specified value is non-zero the triangle is (re)set to be an
equilateral triangle in the xy plane with side length = the specified
value, with a centroid at the particle position, with its base
parallel to the x axis, and the y-axis running from the center of the
base to the top point of the triangle. If the specified value is 0.0,
the particle will become a point particle. Note that this command
does not adjust the particle mass, even if it was defined with a
density, e.g. via the :doc:`read_data <read_data>` command.
Keyword *smd/mass/density* sets the mass of all selected particles,
but it is only applicable to the Smooth Mach Dynamics package MACHDYN.
It assumes that the particle volume has already been correctly set and
calculates particle mass from the provided mass density value.
Keywords *sph/cv*, *sph/e*, and *sph/rho* set the heat capacity,
energy, and density of smoothed particle hydrodynamics (SPH)
particles. See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to
using SPH in LAMMPS.
.. note::
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.
.. versionchanged:: 15Sep2022
Keyword *spin/atom* uses the specified g value to set the magnitude of
the magnetic spin vectors, and the x,y,z values as components of a
vector to set as the orientation of the magnetic spin vectors of the
selected atoms. This keyword was previously called *spin*.
.. versionchanged:: 15Sep2022
Keyword *spin/atom/random* randomizes the orientation of the magnetic
spin vectors for the selected atoms and sets the magnitude of each to
the specified *Dlen* value. This keyword does NOT allow use of an
atom-style variable. This keyword was previously called
*spin/random*.
.. versionadded:: 15Sep2022
Keyword *spin/electron* sets the spin of an electron (+/- 1) or
indicates nuclei (=0), fixed-cores (=2), or pseudo-cores (= 3).
Keyword *temperature* sets the temperature of a finite-size particle.
Currently, only the GRANULAR package supports this attribute. The
temperature must be added using an instance of :doc:`fix property/atom
<fix_property_atom>` The values for the temperature must be positive.
Keyword *theta* sets the orientation of selected atoms. The particles
must be line segments as defined by the :doc:`atom_style line
@ -413,169 +578,78 @@ orientation angle of the line segments with respect to the x axis.
Keyword *theta/random* randomizes the orientation of theta for the
selected atoms. The particles must be line segments as defined by the
:doc:`atom_style line <atom_style>` command. Random numbers are used in
such a way that the orientation of a particular atom is the same,
:doc:`atom_style line <atom_style>` command. Random numbers are used
in such a way that the orientation of a particular atom is the same,
regardless of how many processors are being used. This keyword does
not allow use of an atom-style variable.
NOT allow use of an atom-style variable.
Keyword *angmom* sets the angular momentum of selected atoms. The
particles must be ellipsoids as defined by the :doc:`atom_style
ellipsoid <atom_style>` command or triangles as defined by the
:doc:`atom_style tri <atom_style>` command. The angular momentum
vector of the particles is set to the 3 specified components.
Keyword *tri* sets the size of selected atoms. The particles must be
triangles as defined by the :doc:`atom_style tri <atom_style>`
command. If the specified value is non-zero the triangle is (re)set
to be an equilateral triangle in the xy plane with side length = the
specified value, with a centroid at the particle position, with its
base parallel to the x axis, and the y-axis running from the center of
the base to the top point of the triangle. If the specified value is
0.0, the particle will become a point particle. Note that this
command does not adjust the particle mass, even if it was defined with
a density, e.g. via the :doc:`read_data <read_data>` command.
Keyword *omega* sets the angular velocity of selected atoms. The
particles must be spheres as defined by the :doc:`atom_style sphere
<atom_style>` command. The angular velocity vector of the particles is
set to the 3 specified components.
.. versionchanged:: 28Mar2023
Keyword *mass* sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the :doc:`atom_style
<atom_style>` command. See the "mass" command for how to set mass
values on a per-type basis.
Support for type labels was added for setting atom types
Keyword *density* or *density/disc* also sets the mass of all selected
particles, but in a different way. The particles must have a per-atom
mass attribute, as defined by the :doc:`atom_style <atom_style>`
command. If the atom has a radius attribute (see :doc:`atom_style
sphere <atom_style>`) and its radius is non-zero, its mass is set from
the density and particle volume for 3d systems (the input density is
assumed to be in mass/distance\^3 units). For 2d, the default is for
LAMMPS to model particles with a radius attribute as spheres. However,
if the *density/disc* keyword is used, then they can be modeled as 2d
discs (circles). Their mass is set from the density and particle area
(the input density is assumed to be in mass/distance\^2 units).
If the atom has a shape attribute (see :doc:`atom_style ellipsoid
<atom_style>`) and its 3 shape parameters are non-zero, then its mass is
set from the density and particle volume (the input density is assumed
to be in mass/distance\^3 units). The *density/disc* keyword has no
effect; it does not (yet) treat 3d ellipsoids as 2d ellipses.
If the atom has a length attribute (see :doc:`atom_style line
<atom_style>`) and its length is non-zero, then its mass is set from the
density and line segment length (the input density is assumed to be in
mass/distance units). If the atom has an area attribute (see
:doc:`atom_style tri <atom_style>`) and its area is non-zero, then its
mass is set from the density and triangle area (the input density is
assumed to be in mass/distance\^2 units).
If none of these cases are valid, then the mass is set to the density
value directly (the input density is assumed to be in mass units).
Keyword *temperature* sets the temperature of a finite-size particle.
Currently, only the GRANULAR package supports this attribute. The
temperature must be added using an instance of
:doc:`fix property/atom <fix_property_atom>` The values for the
temperature must be positive.
Keyword *volume* sets the volume of all selected particles. Currently,
only the :doc:`atom_style peri <atom_style>` command defines particles
with a volume attribute. Note that this command does not adjust the
particle mass.
Keyword *image* sets which image of the simulation box the atom is
considered to be in. An image of 0 means it is inside the box as
defined. A value of 2 means add 2 box lengths to get the true value. A
value of -1 means subtract 1 box length to get the true value. LAMMPS
updates these flags as atoms cross periodic boundaries during the
simulation. The flags can be output with atom snapshots via the
:doc:`dump <dump>` command. If a value of NULL is specified for any of
nx,ny,nz, then the current image value for that dimension is unchanged.
For non-periodic dimensions only a value of 0 can be specified. This
command can be useful after a system has been equilibrated and atoms
have diffused one or more box lengths in various directions. This
command can then reset the image values for atoms so that they are
effectively inside the simulation box, e.g if a diffusion coefficient is
about to be measured via the :doc:`compute msd <compute_msd>` command.
Care should be taken not to reset the image flags of two atoms in a bond
to the same value if the bond straddles a periodic boundary (rather they
should be different by +/- 1). This will not affect the dynamics of a
simulation, but may mess up analysis of the trajectories if a LAMMPS
diagnostic or your own analysis relies on the image flags to unwrap a
molecule which straddles the periodic box.
Keywords *bond*, *angle*, *dihedral*, and *improper*, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value. The value can be a numeric type from 1 to
nbondtypes (nangletypes, etc). Or it can be a type label (bond type
label, angle type label, etc). See the :doc:`Howto type labels
Keyword *type* sets the atom type for all selected atoms. A specified
value can be either a numeric atom type or an atom type label. When
using a numeric type, the specified value must be from 1 to ntypes,
where ntypes was set by the :doc:`create_box <create_box>` command or
the *atom types* field in the header of the data file read by the
:doc:`read_data <read_data>` command. When using a type label it must
have been defined previously. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used. All atoms in
a particular bond (angle, etc) must be selected atoms in order for the
change to be made. The value of nbondtypes (nangletypes, etc) was set
by the *bond types* (\ *angle types*, etc) field in the header of the
data file read by the :doc:`read_data <read_data>` command. These
keywords do not allow use of an atom-style variable.
and a general discussion of how type labels can be used.
Keywords *rheo/rho* and *rheo/status* set the density and the status of
rheo particles. In particular, one can only set the phase in the status
as described by the :doc:`RHEO howto page <Howto_rheo>`.
Keyword *type/fraction* sets the atom type for a fraction of the
selected atoms. The actual number of atoms changed is not guaranteed
to be exactly the specified fraction (0 <= *fraction* <= 1), but
should be statistically close. Random numbers are used in such a way
that a particular atom is changed or not changed, regardless of how
many processors are being used. This keyword does NOT allow use of an
atom-style variable.
Keywords *sph/e*, *sph/cv*, and *sph/rho* set the energy, heat capacity,
and density of smoothed particle hydrodynamics (SPH) particles. See
`this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
Keywords *type/ratio* and *type/subset* also set the atom type for a
fraction of the selected atoms. The actual number of atoms changed
will be exactly the requested number. For *type/ratio* the specified
fraction (0 <= *fraction* <= 1) determines the number. For
*type/subset*, the specified *Nsubset* is the number. An iterative
algorithm is used which ensures the correct number of atoms are
selected, in a perfectly random fashion. Which atoms are selected
will change with the number of processors used. These keywords do not
allow use of an atom-style variable.
.. note::
Keyword *volume* sets the volume of all selected particles.
Currently, only the :doc:`atom_style peri <atom_style>` command
defines particles with a volume attribute. Note that this command
does not adjust the particle mass.
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.
Keywords *vx*, *vy*, and *vz* set the velocities of all selected
atoms.
Keyword *smd/mass/density* sets the mass of all selected particles, but
it is only applicable to the Smooth Mach Dynamics package MACHDYN. It
assumes that the particle volume has already been correctly set and
calculates particle mass from the provided mass density value.
Keywords *x*, *y*, *z* set the coordinates of all selected atoms.
Keyword *smd/contact/radius* only applies to simulations with the Smooth
Mach Dynamics package MACHDYN. Itsets an interaction radius for
computing short-range interactions, e.g. repulsive forces to prevent
different individual physical bodies from penetrating each other. Note
that the SPH smoothing kernel diameter used for computing long range,
nonlocal interactions, is set using the *diameter* keyword.
Keyword *dpd/theta* sets the internal temperature of a DPD particle as
defined by the DPD-REACT package. If the specified value is a number it
must be >= 0.0. If the specified value is NULL, then the kinetic
temperature Tkin of each particle is computed as 3/2 k Tkin = KE = 1/2 m
v\^2 = 1/2 m (vx\*vx+vy\*vy+vz\*vz). Each particle's internal
temperature is set to Tkin. If the specified value is an atom-style
variable, then the variable is evaluated for each particle. If a value
>= 0.0, the internal temperature is set to that value. If it is < 0.0,
the computation of Tkin is performed and the internal temperature is set
to that value.
Keywords *edpd/temp* and *edpd/cv* set the temperature and volumetric
heat capacity of an eDPD particle as defined by the DPD-MESO package.
Currently, only :doc:`atom_style edpd <atom_style>` defines particles
with these attributes. The values for the temperature and heat capacity
must be positive.
Keyword *cc* sets the chemical concentration of a tDPD particle for a
specified species as defined by the DPD-MESO package. Currently, only
:doc:`atom_style tdpd <atom_style>` defines particles with this
attribute. An integer for "index" selects a chemical species (1 to
Nspecies) where Nspecies is set by the atom_style command. The value for
the chemical concentration must be >= 0.0.
Keyword *epsilon* sets the dielectric constant of a particle, precisely
of the medium where the particle resides as defined by the DIELECTRIC
package. Currently, only :doc:`atom_style dielectric <atom_style>`
defines particles with this attribute. The value for the dielectric
constant must be >= 0.0. Note that the set command with this keyword
will rescale the particle charge accordingly so that the real charge
(e.g., as read from a data file) stays intact. To change the real
charges, one needs to use the set command with the *charge*
keyword. Care must be taken to ensure that the real and scaled charges,
and dielectric constants are consistent.
Keyword *apip/lambda* sets the switching parameter of an
adaptive-precision interatomic potential (:doc:`APIP <Howto_apip>`).
The precise potential is used for an atom when its switching parameter
:math:`\lambda` is 0. The fast potential is used for an atom when its
switching parameter :math:`\lambda` is 1. Both potentials are partially
used for :math:`\lambda\in(0,1)`.
Keywords *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
per-atom integer and floating-point vectors or arrays that have been
added via the :doc:`fix property/atom <fix_property_atom>` command.
When that command is used specific names are given to each attribute
which are the "name" portion of these keywords. For arrays *i2_name*
and *d2_name*, the column of the array must also be included following
the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
and *d2_name*, the column of the array to set must also be included
following the name in brackets: e.g. d2_xyz[2] or i2_mySpin[3].
Restrictions
""""""""""""
@ -584,7 +658,7 @@ You cannot set an atom attribute (e.g. *mol* or *q* or *volume*\ ) if
the :doc:`atom_style <atom_style>` does not have that attribute.
This command requires inter-processor communication to coordinate the
setting of bond types (angle types, etc). This means that your system
setting of bond types (angle types, etc). This means that the system
must be ready to perform a simulation before using one of these
keywords (force fields set, atom mass set, etc). This is not
necessary for other keywords.
@ -599,7 +673,7 @@ Related commands
""""""""""""""""
:doc:`create_box <create_box>`, :doc:`create_atoms <create_atoms>`,
:doc:`read_data <read_data>`
:doc:`read_data <read_data>`, :doc:`fix set <fix_set>`
Default
"""""""

190
doc/src/variable.rst
View File

@ -45,7 +45,8 @@ Syntax
*universe* args = one or more strings
*world* args = one string for each partition of processors
*equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords, math operations, built-in functions, atom values and vectors, compute/fix/variable references
*equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords,
math operations, built-in functions, atom values and vectors, compute/fix/variable references
numbers = 0.0, 100, -5.4, 2.8e-4, etc
constants = PI, version, on, off, true, false, yes, no
thermo keywords = vol, ke, press, etc from :doc:`thermo_style <thermo_style>`
@ -67,8 +68,13 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()
feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x),
gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name),
extract_setting(name), label2type(kind,label),
is_typelabel(kind,label), is_timeout()
feature functions = is_available(category,feature), is_active(category,feature),
is_defined(category,id)
python function wrapper = py_varname(x,y,z,...)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d2_name[i][j]
@ -127,18 +133,21 @@ command), or used as input to an averaging fix (see the :doc:`fix
ave/time <fix_ave_time>` command). Variables of style *vector* store
a formula which produces a vector of such values which can be used as
input to various averaging fixes, or elements of which can be part of
thermodynamic output. Variables of style *atom* store a formula which
when evaluated produces one numeric value per atom which can be output
to a dump file (see the :doc:`dump custom <dump>` command) or used as
input to an averaging fix (see the :doc:`fix ave/chunk
<fix_ave_chunk>` and :doc:`fix ave/atom <fix_ave_atom>` commands).
Variables of style *atomfile* can be used anywhere in an input script
that atom-style variables are used; they get their per-atom values
from a file rather than from a formula. Variables of style *python*
can be hooked to Python functions using code you provide, so that the
variable gets its value from the evaluation of the Python code.
Variables of style *internal* are used by a few commands which set
their value directly.
thermodynamic output.
Variables of style *atom* store a formula which when evaluated
produces one numeric value per atom which can be output to a dump file
(see the :doc:`dump custom <dump>` command) or used as input to an
averaging fix (see the :doc:`fix ave/chunk <fix_ave_chunk>` and
:doc:`fix ave/atom <fix_ave_atom>` commands). Variables of style
*atomfile* can be used anywhere in an input script that atom-style
variables are used; they get their per-atom values from a file rather
than from a formula.
Variables of style *python* can be hooked to Python functions using
Python code you provide, so that the variable gets its value from the
evaluation of the Python code. Variables of style *internal* are used
by a few commands which set their value directly.
.. note::
@ -166,15 +175,16 @@ simulation.
.. note::
When an input script line is encountered that defines a variable
of style *equal* or *vector* or *atom* or *python* that contains a
formula or Python code, the formula is NOT immediately evaluated. It
will be evaluated every time when the variable is **used** instead. If
you simply want to evaluate a formula in place you can use as
so-called. See the section below about "Immediate Evaluation of
Variables" for more details on the topic. This is also true of a
*format* style variable since it evaluates another variable when it is
invoked.
When an input script line is encountered that defines a variable of
style *equal* or *vector* or *atom* or *python* that contains a
formula or links to Python code, the formula or Python code is NOT
immediately evaluated. Instead, it is evaluated each time the
variable is **used**. If you simply want to evaluate a formula in
place you can use a so-called immediate variable. as described in
the preceding note. Or see the section below about "Immediate
Evaluation of Variables" for more details on the topic. This is
also true of a *format* style variable since it evaluates another
variable when it is invoked.
Variables of style *equal* and *vector* and *atom* can be used as
inputs to various other commands which evaluate their formulas as
@ -183,12 +193,12 @@ this context, variables of style *timer* or *internal* or *python* can
be used in place of an equal-style variable, with the following two
caveats.
First, internal-style variables can be used except by commands that
set the value stored by the internal variable. When the LAMMPS
command evaluates the internal-style variable, it will use the value
set (internally) by another command. Second, python-style variables
can be used so long as the associated Python function, as defined by
the :doc:`python <python>` command, returns a numeric value. When the
First, internal-style variables require their values be set by code
elsewhere in LAMMPS. When a LAMMPS input script or command evaluates
an internal-style variable, it must have a current value set
(internally) via that mechanism. Second, python-style variables can
be used so long as the associated Python function, as defined by the
:doc:`python <python>` command, returns a numeric value. When the
LAMMPS command evaluates the python-style variable, the Python
function will be executed.
@ -388,13 +398,24 @@ using the :doc:`command-line switch -var <Run_options>`.
For the *internal* style a numeric value is provided. This value will
be assigned to the variable until a LAMMPS command sets it to a new
value. There are currently only two LAMMPS commands that require
*internal* variables as inputs, because they reset them:
:doc:`create_atoms <create_atoms>` and :doc:`fix controller
<fix_controller>`. As mentioned above, an internal-style variable can
be used in place of an equal-style variable anywhere else in an input
script, e.g. as an argument to another command that allows for
equal-style variables.
value.
Note however, that most commands which use internal-style variables do
not require them to be defined in the input script. They create one or
more internal-style variables if they do not already exist. Examples
are these commands:
* :doc:`create_atoms <create_atoms>`
* :doc:`fix deposit <fix_deposit>`
* :doc:`compute bond/local <compute_bond_local>`
* :doc:`compute angle/local <compute_angle_local>`
* :doc:`compute dihedral/local <compute_dihedral_local>`
* :doc:`python <python>` command in conjunction with Python function wrappers used in equal- and atom-style variable formulas
A command which does require an internal-style variable to be defined in
the input script is the :doc:`fix controller <fix_controller>` command,
because another (arbitrary) command typically also references the
variable.
----------
@ -439,6 +460,15 @@ python-style variable can be used in place of an equal-style variable
anywhere in an input script, e.g. as an argument to another command
that allows for equal-style variables.
A python-style variable can also be used within the formula for an
equal-style or atom-style formula in a Python function wrapper, as
explained below for variable formulas. In this context, the usage
syntax is py_varname(arg1,arg2,...), where varname is the name of the
python-style variable. When a Python wrapper function is used in an
atom-style formula, it can be invoked once per atom using arguments
specific to each atom. The resulting values in the atom-style
variable can thus be calculated by Python code.
----------
For the *string* style, a single string is assigned to the variable.
@ -528,9 +558,9 @@ is a valid (though strange) variable formula:
Specifically, a formula can contain numbers, constants, thermo
keywords, math operators, math functions, group functions, region
functions, special functions, feature functions, atom values, atom
vectors, custom atom properties, compute references, fix references, and references to other
variables.
functions, special functions, feature functions, Python function
wrappers, atom values, atom vectors, custom atom properties, compute
references, fix references, and references to other variables.
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Number | 0.2, 100, 1.0e20, -15.4, etc |
@ -551,6 +581,8 @@ variables.
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Feature functions | is_available(category,feature), is_active(category,feature), is_defined(category,id) |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Python func wrapper | py_varname(x,y,z,...) |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom vectors | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q |
@ -1161,6 +1193,84 @@ variable name.
----------
Python Function wrapper
------------------------
A Python function wrapper enables the formula for an equal-style or
atom-style variable to invoke functions coded in Python. In the case
of an equal-style variable, the Python-coded function will be invoked
once. In the case of an atom-style variable, it can be invoked once
per atom, if one or more of its arguments include a per-atom quantity,
e.g. the position of an atom. As illustrated below, the reason to use
a Python function wrapper is to make it easy to pass LAMMPS-related
arguments to the Python-coded function associated with a python-style
variable.
The syntax for defining a Python function wrapper is
.. code-block:: LAMMPS
py_varname(arg1,arg2,...argN)
where *varname* is the name of a python-style variable which couples
to a Python-coded function. The function will be passed the zero or
more arguments listed in parentheses: *arg1*, *arg2*, ... *argN*. As
with Math Functions, each argument can itself be an arbitrarily
complex formula.
A Python function wrapper can be used in the following manner by an
input script:
.. code-block:: LAMMPS
variable foo python truncate
python truncate return v_foo input 1 v_arg format fi here """
def truncate(x):
return int(x)
"""
variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z)
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
The first two commands define a python-style variable *foo* and couple
it to the Python-coded function *truncate()* which takes a single
floating point argument, and returns its truncated integer value. In
this case, the Python code for truncate() is included in the *python*
command; it could also be contained in a file. See the :doc:`python
<python>` command doc page for details.
The next three commands define atom-style variables *xtrunc*,
*ytrunc*, and *ztrunc*. Each of them include the same Python function
wrapper in their formula, with a different argument. The atom-style
variable *xtrunc* will invoke the python-style variable *foo*, which
will in turn invoke the Python-coded *truncate()* method. Because
*xtrunc* is an atom-style variable, and the argument *x* in the Python
function wrapper is a per-atom quantity (the x-coord of each atom),
each processor will invoke the *truncate()* method once per atom, for
the atoms it owns.
When invoked for the Ith atom, the value of the *arg* internal-style
variable, defined by the *python* command, is set to the x-coord of
the Ith atom. The call via python-style variable *foo* to the Python
*truncate()* function passes the value of the *arg* variable as the
function's first (and only) argument. Likewise, the return value of
the Python function is stored by the python-style variable *foo* and
used in the *xtrunc* atom-style variable formula for the Ith atom.
The resulting per-atom vector for *xtrunc* will thus contain the
truncated x-coord of every atom in the system. The dump command
includes the truncated xyz coords for each atom in its output.
See the :doc:`python <python>` command for more details on options the
*python* command can specify as well as examples of more complex Python
functions which can be wrapped in this manner. In particular, the
Python function can take a variety of arguments, some generated by the
*python* command, and others by the arguments of the Python function
wrapper.
----------
Atom Values and Vectors
-----------------------

2
doc/utils/requirements.txt
View File

@ -2,6 +2,7 @@ Sphinx >= 5.3.0, <8.3.0
sphinxcontrib-spelling
sphinxcontrib-jquery
sphinx-design
sphinx-toolbox
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx-tabs>=3.4.1
breathe
@ -10,3 +11,4 @@ six
pyyaml
linkchecker
ipython
numpy

12
doc/utils/sphinx-config/conf.py.in
View File

@ -50,6 +50,7 @@ extensions = [
'sphinx.ext.mathjax',
'sphinx.ext.imgmath',
'sphinx.ext.autodoc',
'sphinx_toolbox.collapse',
'lammps_theme',
'sphinxcontrib.jquery',
'sphinxfortran.fortran_domain',
@ -370,6 +371,17 @@ latex_elements = {
{%
\hypersetup{pageanchor=false}% avoid duplicate destination warnings
\begin{titlepage}%
\sffamily\Large
The LAMMPS developers are thinking about dropping the PDF format version of
the LAMMPS manual. This would allow us to focus on the HTML version, use
HTML-only features, and skip checking if the documentation source files,
especially the embedded mathematical expressions, are compatible with \LaTeX{} output.
Please let us know how you feel about this change by sending an email to
\texttt{developers@lammps.org} stating whether you agree or disagree with
removing support for the PDF format version of the manual and optionally
provide arguments for your preference.
\clearpage
\sffamily\bfseries
\begingroup % for PDF information dictionary
\def\endgraf{ }\def\and{\& }%

42
doc/utils/sphinx-config/false_positives.txt
View File

@ -33,6 +33,7 @@ activationfunctions
acylindricity
addforce
Addington
addstep
addtorque
adf
Adhikari
@ -82,6 +83,7 @@ Alessandro
Alexey
ali
aliceblue
aliphatic
Allera
Allinger
allocatable
@ -103,6 +105,7 @@ Amit
amsmath
amu
Amzallag
Anandakrishnan
analytical
Anders
Andric
@ -110,6 +113,7 @@ Andrienko
Andzelm
Ang
anglegrad
anglelist
angleoffset
angletangrad
angmom
@ -132,6 +136,8 @@ anton
Antonelli
anysize
api
apip
APIP
apolar
Apoorva
Appl
@ -227,6 +233,7 @@ Bagi
Bagnold
Baig
Bajaj
bak
Bal
balancer
Balankura
@ -347,6 +354,7 @@ Bomont
BondAngle
BondBond
bondchk
bondlist
bondmax
bondscreened
bondscreenedspin
@ -395,6 +403,7 @@ Broglie
brownian
brownw
Broyden
Bruenger
Bruskin
Brusselle
Bryantsev
@ -524,6 +533,7 @@ civ
CKD
ckk
Clang
clearstep
clearstore
Cleary
Clebsch
@ -626,6 +636,7 @@ cp
cpp
cpu
cradius
Cramer
createatoms
createAtoms
CreateIDs
@ -647,6 +658,7 @@ CSiC
csld
cslib
CSlib
csp
cstdio
cstdlib
cstring
@ -666,6 +678,7 @@ cuFFT
CuH
Cui
Cummins
cumulants
Cundall
cundall
Curk
@ -819,6 +832,7 @@ diffusively
diffusivities
diffusivity
dihedral
dihedrallist
dihedrals
Dihedrals
dihydride
@ -1169,6 +1183,7 @@ Fermionic
Ferrand
fexternal
Fexternal
ffast
ffield
ffl
fflush
@ -1324,7 +1339,6 @@ Geocomputing
georg
Georg
Geotechnica
Gergs
germain
Germann
Germano
@ -1352,6 +1366,7 @@ Gillan
Gingold
Gissinger
github
Giusti
GJ
gjf
gjwagne
@ -1374,6 +1389,7 @@ gmres
gname
gneb
GNEB
Godehard
Goerigk
Goga
Goldfarb
@ -1609,8 +1625,10 @@ Imageint
Imagemagick
imagename
imd
Immel
Impey
impl
improperlist
impropers
Impropers
imulator
@ -1727,6 +1745,7 @@ Iyz
iz
izcm
ized
Izadi
Izrailev
Izumi
Izvekov
@ -1763,6 +1782,7 @@ jik
JIK
jku
jN
Joanes
Joannopoulos
Jochim
Jonsson
@ -1807,6 +1827,7 @@ Karniadakis
Karplus
Karttunen
kate
katom
Katsnelson
Katsura
Kaufmann
@ -1855,6 +1876,7 @@ Kloss
Kloza
kmax
Kmax
kMC
KMP
kmu
Knizhnik
@ -1919,6 +1941,7 @@ Lachet
Lackmann
Ladd
lagrangian
Lalli
lambdai
LambdaLanczos
Lambrecht
@ -1981,6 +2004,7 @@ lennard
Lennard
Lenosky
Lenz
Leoni
Lett
Leuven
Leven
@ -2182,6 +2206,7 @@ Materias
mathbf
mathjax
matlab
Matom
Matous
matplotlib
Matsubara
@ -2479,6 +2504,7 @@ namespaces
nan
NaN
Nandor
nanglelist
nangles
Nangletype
nangletypes
@ -2515,6 +2541,7 @@ nbodies
nbody
Nbody
nbond
nbondlist
nbonds
nbondtype
Nbondtype
@ -2536,6 +2563,7 @@ ncount
nd
ndactrung
ndescriptors
ndihedrallist
ndihedrals
Ndihedraltype
ndihedraltypes
@ -2593,6 +2621,7 @@ NiAlH
Nicklas
Niklasson
Nikolskiy
nimproperlist
nimpropers
Nimpropertype
nimpropertypes
@ -2687,6 +2716,7 @@ Nprocs
npt
nr
Nr
Nrecent
Nrecompute
Nrepeat
nreset
@ -2765,6 +2795,7 @@ ocl
octahedral
octants
Odegard
Og
Ohara
O'Hearn
ohenrich
@ -2797,6 +2828,7 @@ oneMKL
oneway
onlysalt
ons
Onufriev
OO
Oord
opencl
@ -3105,6 +3137,7 @@ Pxy
pxz
py
Py
pyargs
pydir
pylammps
PyLammps
@ -3345,6 +3378,7 @@ Rmin
RMS
rmsd
rnage
rnflag
rng
rNEMD
ro
@ -3400,6 +3434,7 @@ ry
Ryckaert
Rycroft
Rydbergs
Ryzen
rz
Rz
Sabry
@ -3819,6 +3854,8 @@ Thiaville
Thibaudeau
Thijsse
Thirumalai
thr
Threadripper
threebody
thrid
ThunderX
@ -4044,6 +4081,7 @@ Vaiwala
valent
Valeriu
valgrind
validator
Valone
valuev
Valuev
@ -4053,6 +4091,7 @@ Vanduyfhuys
varargs
varavg
variational
varname
Varshalovich
Varshney
vashishta
@ -4121,6 +4160,7 @@ volpress
volumetric
von
Voro
voro
Vorobyov
voronoi
Voronoi

5
examples/COUPLE/plugin/CMakeLists.txt
View File

@ -27,10 +27,7 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
find_package(MPI REQUIRED)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI REQUIRED COMPONENTS C)
##########################

2
examples/COUPLE/plugin/liblammpsplugin.c
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@ -79,6 +79,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(mpi_finalize);
ADDSYM(kokkos_finalize);
ADDSYM(python_finalize);
ADDSYM(plugin_finalize);
ADDSYM(error);
ADDSYM(expand);
@ -140,6 +141,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(scatter_subset);
ADDSYM(create_atoms);
ADDSYM(create_molecule);
ADDSYM(find_pair_neighlist);
ADDSYM(find_fix_neighlist);

2
examples/COUPLE/plugin/liblammpsplugin.h
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@ -134,6 +134,7 @@ struct _liblammpsplugin {
void (*mpi_finalize)();
void (*kokkos_finalize)();
void (*python_finalize)();
void (*plugin_finalize)();
void (*error)(void *, int, const char *);
char *(*expand)(void *, const char *);
@ -206,6 +207,7 @@ struct _liblammpsplugin {
int (*create_atoms)(void *, int, const int64_t *, const int *, const double *, const double *,
const int64_t *, int);
#endif
int (*create_molecule)(void *, const char *, const char *);
int (*find_pair_neighlist)(void *, const char *, int, int, int);
int (*find_fix_neighlist)(void *, const char *, int);

2
examples/COUPLE/simple/CMakeLists.txt
View File

@ -25,10 +25,10 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
find_package(MPI QUIET)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET COMPONENTS C CXX)
##########################

34
examples/PACKAGES/apip/Cu-1.yace Normal file
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@ -0,0 +1,34 @@
NOTE: This is a simple potential for the example. Production usage without testing is not recommended. Provided by Yury Lysogorskiy (ICAMS, RUB, Germany).
elements: [Cu]
E0: [0]
deltaSplineBins: 0.001
embeddings:
0: {ndensity: 2, FS_parameters: [1, 1, 1, 0.5], npoti: FinnisSinclairShiftedScaled, rho_core_cutoff: 100000, drho_core_cutoff: 250}
bonds:
[0, 0]: {nradmax: 2, lmax: 2, nradbasemax: 15, radbasename: ChebPow, radparameters: [2], radcoefficients: [[[0.99440439385969503, -0.085048653403583918, -0.23248632054717755, -0.22732701549371864, 0.026354948476648921, 0.21853318667456997, 0.05745747498169812, -0.19717925712228765, -0.11474256770370879, 0.12738668745839368, 0.053777769435472259, -0.11094768379576209, 0.072620812391582482, -0.058715761632824881, 0.030359986427775303], [0.96259704765772924, -0.10129488003029259, -0.10345557604916655, -0.020393848425879282, 0.076671442494272601, 0.10318554794001746, 0.0555341702761026, 0.00083194423680727696, -0.018184436957498409, -0.021866885826555403, -0.020179969116479776, 0.021880011516616484, 0.053112509345249602, -0.083707026393616657, 0.020611714544479017], [1.001530579978529, -0.030080648426358471, -0.13318582671063051, -0.24371635685809706, -0.22760541127468878, -0.041144767051648642, 0.18080289144697201, 0.24543156067198274, 0.11014559411659355, -0.069512010077804498, -0.1172049950938457, -0.027509386703874331, 0.056985864219913585, 0.037536629112081353, -0.044222474537374087]], [[0.25716120576634355, 1.7485527550537943, 0.91889737965719875, 0.50902244208852199, -0.15895537149482841, -0.48109723575282892, -0.17843605933015286, 0.39450608859531944, 0.59293909285591195, 0.18268386912819001, -0.34706543720907351, -0.3210061634328315, 0.21678650779400246, 0.39500148786376449, -0.31820913370341625], [0.0079213202761679105, 1.0212489038630681, 0.011530454475879359, -0.049445152058907642, -0.15268524878755677, -0.2319378608755131, -0.20612580998548105, -0.067027395211212315, 0.08241096034972574, 0.11288597065081186, 0.01355948960244063, -0.074722461388416803, -0.022724332047049267, 0.088871664887057056, 0.031667459613258314], [-0.0069872405356639312, 0.9939655327342134, 0.035044055182587928, 0.099765277857093104, 0.11687607289674087, 0.030241996404391416, -0.12367698594314165, -0.22480900218170197, -0.17727517861619441, -0.015144941558075584, 0.11375495728241894, 0.090680932947050971, -0.041190210394591399, -0.10085768296286811, 0.055789864104988186]]], prehc: 0, lambdahc: 0, rcut: 3.8999999999999999, dcut: 0.01, rcut_in: 0, dcut_in: 0, inner_cutoff_type: density}
functions:
0:
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [0.26072556900842869, -0.03073189825062177]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [0.64429175483702295, -0.1630534353246999]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [3], ls: [0], ms_combs: [0], ctildes: [0.51856313423563594, -0.4259316875879266]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [4], ls: [0], ms_combs: [0], ctildes: [-0.078113533662468398, -0.70352070540668643]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [5], ls: [0], ms_combs: [0], ctildes: [-0.45633111544093646, -0.7859368117550467]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [6], ls: [0], ms_combs: [0], ctildes: [-0.19608401600520556, -0.59151667874441172]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [7], ls: [0], ms_combs: [0], ctildes: [0.30580228338697285, -0.29248216980800118]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [8], ls: [0], ms_combs: [0], ctildes: [0.40167461008815436, -0.15647925731818518]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [9], ls: [0], ms_combs: [0], ctildes: [0.053519057558225343, -0.25900906688118652]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [10], ls: [0], ms_combs: [0], ctildes: [-0.20446546815457517, -0.40019216010057629]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [11], ls: [0], ms_combs: [0], ctildes: [-0.070020661105060208, -0.33441939205411986]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [12], ls: [0], ms_combs: [0], ctildes: [0.15734064575001952, -0.055233119903794807]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [13], ls: [0], ms_combs: [0], ctildes: [0.10021406559793103, 0.18641744536767416]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [14], ls: [0], ms_combs: [0], ctildes: [-0.14066730990975543, 0.14711096149210373]}
- {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [15], ls: [0], ms_combs: [0], ctildes: [0.031100766650549283, -0.13720067925313634]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [1, 1], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0984212008195524, 0.49756623164565855]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.2591109116320176, 0.21348077494861176, -0.5182218232640351, -0.4269615498972234]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.015905361441871636, 0.023783303055646809, -0.031810722883743273, -0.047566606111293624, 0.031810722883743286, 0.047566606111293638]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [2, 1], ls: [0, 0], ms_combs: [0, 0], ctildes: [0.63958612617724186, 1.6623415103929948]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [2, 1], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.14199022782503917, 0.0069900458821809735, -0.28398045565007829, -0.013980091764361944]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [2, 1], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.028732470496968317, -0.037173039560267927, -0.05746494099393664, 0.074346079120535868, 0.057464940993936654, -0.074346079120535882]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [2, 2], ls: [0, 0], ms_combs: [0, 0], ctildes: [0.056442895466964321, 0.0054387873274233034]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.025326283180140272, -0.19511149476156769, -0.050652566360280531, 0.39022298952313533]}
- {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.012754475331985416, -0.058934602152610385, -0.025508950663970836, 0.11786920430522078, 0.025508950663970843, -0.11786920430522081]}

6006
examples/PACKAGES/apip/Cu_300K_Immel_2023.eam.fs Normal file
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11
examples/PACKAGES/apip/README Normal file
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@ -0,0 +1,11 @@
The APIP package is based on the paper:
David Immel, Ralf Drautz, Godehard Sutmann; Adaptive-precision potentials for large-scale atomistic simulations. J. Chem. Phys. 14 March 2025; 162 (11): 114119. https://doi.org/10.1063/5.0245877
The pair_style pace/apip requires the installation of lib/pace of the ML-PACE package.
The installation of lib/pace is described in src/ML-PACE/README .
Examples of how to use an adaptive-precision potential are provided in examples/PACKAGES/apip .
in.vacancy contains a small example that can be used to visualize the transition region and get a visual impression of the selected parameters.
in.surface.balance in a more realistic example, in which a surface is simulated and the benefit of fix apip_atom_weight and fix balance for adaptive-precision interatomic potentials is demonstrated.

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