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Merge branch 'develop' into amoeba-gpu

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This commit is contained in:
Trung Nguyen
2022-12-14 13:16:41 -06:00
parent 959b9c220f fe7b489149
commit 8af77c690c
4848 changed files with 102983 additions and 44974 deletions
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61
.github/CODEOWNERS vendored
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@ -13,40 +13,45 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/ADIOS/* @pnorbert
src/AMOEBA/* @sjplimp
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/BPM/* @jtclemm
src/BROWNIAN/* @samueljmcameron
src/CG-DNA/* @ohenrich
src/CG-SPICA/* @yskmiyazaki
src/COLVARS/* @giacomofiorin
src/COMPRESS/* @rbberger
src/DIELECTRIC/* @ndtrung81
src/ELECTRODE/* @ludwig-ahrens
src/FEP/* @agiliopadua
src/ML-HDNNP/* @singraber
src/GPU/* @ndtrung81
src/GRANULAR/* @jtclemm @dsbolin
src/INTEL/* @wmbrownintel
src/KIM/* @ellio167
src/KOKKOS/* @stanmoore1
src/LATTE/* @cnegre
src/MANIFOLD/* @Pakketeretet2
src/MDI/* @taylor-a-barnes
src/MDI/* @taylor-a-barnes @sjplimp
src/MEAM/* @martok
src/MESONT/* @iafoss
src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde @rohskopf
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
src/ML-PACE/* @yury-lysogorskiy
src/PLUMED/* @gtribello
src/PHONON/* @lingtikong
src/PTM/* @pmla
src/OPENMP/* @akohlmey
src/PHONON/* @lingtikong
src/PLUGIN/* @akohlmey
src/PLUMED/* @gtribello
src/PTM/* @pmla
src/QMMM/* @akohlmey
src/REAXFF/* @hasanmetin @stanmoore1
src/REACTION/* @jrgissing
src/REAXFF/* @hasanmetin @stanmoore1
src/SCAFACOS/* @rhalver
src/SNAP/* @athomps
src/SPIN/* @julient31
src/TALLY/* @akohlmey
src/UEF/* @danicholson
src/VTK/* @rbberger
@ -120,27 +125,32 @@ src/dump_movie.* @akohlmey
src/exceptions.h @rbberger
src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
src/platform.* @akohlmey
src/timer.* @akohlmey
src/utils.* @akohlmey @rbberger
src/verlet.* @sjplimp @stanmoore1
src/math_eigen_impl.h @jewettaij
# tools
tools/msi2lmp/* @akohlmey
tools/coding_standard/* @akohlmey @rbberger
tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/coding_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/lammps-shell/* @akohlmey
tools/msi2lmp/* @akohlmey
tools/offline/* @rbberger
tools/singularity/* @akohlmey @rbberger
tools/swig/* @akohlmey
tools/valgrind/* @akohlmey
tools/vim/* @hammondkd
# tests
unittest/* @akohlmey @rbberger
unittest/* @akohlmey
# cmake
cmake/* @junghans @rbberger
cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
cmake/Modules/MPI4WIN.cmake @akohlmey
cmake/Modules/OpenCLLoader.cmake @akohlmey
cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/presets/*.cmake @akohlmey
@ -149,13 +159,12 @@ cmake/presets/*.cmake @akohlmey
python/* @rbberger
# fortran
fortran/* @akohlmey
fortran/* @akohlmey @hammondkd
# docs
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
doc/* @akohlmey
examples/plugin/* @akohlmey
examples/PACKAGES/pace/plugin/* @akohlmey
# for releases
src/version.h @sjplimp

7
.github/ISSUE_TEMPLATE/help_request.md vendored
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@ -1,6 +1,6 @@
---
name: Request for Help
about: "Don't post help requests here, email the lammps-users mailing list"
about: "Don't post help requests here, post in the LAMMPS forum"
title: ""
labels: invalid
assignees: ''
@ -8,8 +8,9 @@ assignees: ''
---
Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
Instead send an e-mail to the lammps-users mailing list.
Instead, you can post to the LAMMPS category in the Materials Science Community
Discourse forum at: https://matsci.org/lammps/
This issue tracker is for tracking LAMMPS development related issues only.
Thanks for your cooperation.
Thank you in advance for your cooperation.

6
.github/workflows/compile-msvc.yml vendored
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@ -26,15 +26,19 @@ jobs:
- name: Select Python version
uses: actions/setup-python@v4
with:
python-version: '3.10'
python-version: '3.11'
- name: Building LAMMPS via CMake
shell: bash
run: |
python3 -m pip install numpy
python3 -m pip install pyyaml
nuget install MSMPIsdk
nuget install MSMPIDIST
cmake -C cmake/presets/windows.cmake \
-D PKG_PYTHON=on \
-D WITH_PNG=off \
-D WITH_JPEG=off \
-S cmake -B build \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on \

4
README
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@ -16,8 +16,8 @@ National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL) version 2.
The primary author of the code is Steve Plimpton, who can be emailed
at sjplimp@sandia.gov. The LAMMPS WWW Site at www.lammps.org has
The code is maintained by the LAMMPS development team who can be emailed
at developers@lammps.org. The LAMMPS WWW Site at www.lammps.org has
more information about the code and its uses.
The LAMMPS distribution includes the following files and directories:

66
cmake/CMakeLists.txt
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@ -7,11 +7,20 @@ cmake_minimum_required(VERSION 3.10)
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
# set policy to silence warnings about ignoring ${CMAKE_REQUIRED_LIBRARIES} but use it
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
########################################
project(lammps CXX)
@ -100,7 +109,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost")
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
endif()
endif()
endif()
@ -257,6 +266,7 @@ set(STANDARD_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-POD
MOFFF
MOLECULE
MOLFILE
@ -307,6 +317,15 @@ if(PKG_ADIOS)
# script that defines the MPI::MPI_C target
enable_language(C)
find_package(ADIOS2 REQUIRED)
if(BUILD_MPI)
if(NOT ADIOS2_HAVE_MPI)
message(FATAL_ERROR "ADIOS2 must be built with MPI support when LAMMPS has MPI enabled")
endif()
else()
if(ADIOS2_HAVE_MPI)
message(FATAL_ERROR "ADIOS2 must be built without MPI support when LAMMPS has MPI disabled")
endif()
endif()
target_link_libraries(lammps PRIVATE adios2::adios2)
endif()
@ -381,9 +400,9 @@ pkg_depends(EXTRA-MOLECULE MOLECULE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
find_package(OpenMP QUIET)
if(OpenMP_FOUND)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
find_package(OpenMP COMPONENTS CXX QUIET)
if(OpenMP_CXX_FOUND)
check_omp_h_include()
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
@ -392,8 +411,8 @@ endif()
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
find_package(OpenMP COMPONENTS CXX REQUIRED)
check_omp_h_include()
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
@ -415,7 +434,7 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
@ -621,7 +640,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
endif()
endforeach()
if(PKG_ELECTRODE)
if(PKG_ELECTRODE OR PKG_ML-POD)
target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
endif()
@ -723,18 +742,17 @@ list(FIND LANGUAGES "Fortran" _index)
if(_index GREATER -1)
target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
if(LAMMPS_EXCEPTIONS)
list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
endif()
set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
set(LAMMPS_FMT_HEADERS core.h format.h)
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
set_target_properties(lammps PROPERTIES PREFIX "lib")
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
@ -743,6 +761,14 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS})
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
endif()
endforeach()
foreach(_HEADER ${LAMMPS_FMT_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER})
add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER})
add_dependencies(lammps fmt_${_HEADER})
if(BUILD_SHARED_LIBS)
install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
endif()
endforeach()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
add_library(LAMMPS::lammps ALIAS lammps)
get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
@ -850,8 +876,11 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
find_package(Python COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
file(COPY ${LAMMPS_SOURCE_DIR}/version.h DESTINATION ${CMAKE_BINARY_DIR}/python/src)
file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
endif()
endif()
@ -962,9 +991,6 @@ if(PKG_GPU)
endif()
message(STATUS "GPU precision: ${GPU_PREC}")
endif()
if(PKG_KOKKOS)
message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
endif()
if(PKG_KSPACE)
message(STATUS "<<< FFT settings >>>
-- Primary FFT lib: ${FFT}")

29
cmake/Modules/FindClangFormat.cmake
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@ -1,5 +1,10 @@
# Find clang-format
find_program(ClangFormat_EXECUTABLE NAMES clang-format
clang-format-15.0
clang-format-14.0
clang-format-13.0
clang-format-12.0
clang-format-11.0
clang-format-10.0
clang-format-9.0
clang-format-8.0
@ -14,19 +19,27 @@ if(ClangFormat_EXECUTABLE)
OUTPUT_VARIABLE clang_format_version
ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
if(clang_format_version MATCHES "^clang-format version .*")
# Arch Linux
if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
# Arch Linux output:
# clang-format version 10.0.0
# Ubuntu 18.04 LTS Output
#
# Ubuntu 18.04 LTS output:
# clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
string(REGEX REPLACE "clang-format version ([0-9.]+).*"
"\\1"
#
# Ubuntu 20.04 LTS output:
# clang-format version 10.0.0-4ubuntu1
#
# Ubuntu 22.04 LTS output:
# Ubuntu clang-format version 14.0.0-1ubuntu1
#
# Fedora 36 output:
# clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
"\\2"
ClangFormat_VERSION
"${clang_format_version}")
elseif(clang_format_version MATCHES ".*LLVM version .*")
# CentOS 7 Output
# CentOS 7 output:
# LLVM (http://llvm.org/):
# LLVM version 3.4.2
# Optimized build.

2
cmake/Modules/FindCythonize.cmake
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@ -22,7 +22,7 @@ endif()
if(Python_EXECUTABLE)
get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
find_program(Cythonize_EXECUTABLE
NAMES cythonize3 cythonize cythonize.bat
NAMES cythonize-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR} cythonize3 cythonize cythonize.bat
HINTS ${_python_path})
endif()

19
cmake/Modules/FindZMQ.cmake
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@ -1,19 +0,0 @@
find_path(ZMQ_INCLUDE_DIR zmq.h)
find_library(ZMQ_LIBRARY NAMES zmq)
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
# Copy the results to the output variables and target.
if(ZMQ_FOUND)
set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
if(NOT TARGET ZMQ::ZMQ)
add_library(ZMQ::ZMQ UNKNOWN IMPORTED)
set_target_properties(ZMQ::ZMQ PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${ZMQ_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}")
endif()
endif()

103
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -112,45 +112,76 @@ 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 custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${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)
# 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)
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)
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")
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${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")
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")
else()
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)

15
cmake/Modules/LAMMPSUtils.cmake
View File

@ -24,6 +24,21 @@ function(validate_option name values)
endif()
endfunction(validate_option)
# helper function to check for usable omp.h header
function(check_omp_h_include)
find_package(OpenMP COMPONENTS CXX QUIET)
if(OpenMP_CXX_FOUND)
set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
check_include_file_cxx(omp.h _have_omp_h)
else()
set(_have_omp_h FALSE)
endif()
set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE)
endfunction()
# helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable)
file(GLOB _dirs ${path})

107
cmake/Modules/MPI4WIN.cmake
View File

@ -1,39 +1,74 @@
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${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)
# 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)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${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")
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${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")
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")

17
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -15,8 +15,9 @@ if(Kokkos_ENABLE_OPENMP)
if(NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
else()
if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
# NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
endif()
endif()
endif()
@ -47,8 +48,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "0ec97fc0c356dd65bd2487defe81a7bf" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "84991eca9f066383abe119a5bc7a11c4" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
ExternalProject_Add(kokkos_build
@ -72,7 +73,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.6.01 REQUIRED CONFIG)
find_package(Kokkos 3.7.00 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()
@ -138,6 +139,12 @@ if(PKG_KSPACE)
endif()
endif()
if(PKG_ML-IAP)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp)
endif()
if(PKG_PHONON)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)

27
cmake/Modules/Packages/MDI.cmake
View File

@ -49,6 +49,14 @@ if(DOWNLOAD_MDI)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# python plugins are not supported and thus must be always off on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
unset(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_CROSSCOMPILING)
set(CMAKE_INSTALL_LIBDIR lib)
endif()
endif()
# download/ build MDI library
# always build static library with -fpic
@ -57,8 +65,9 @@ if(DOWNLOAD_MDI)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
CMAKE_ARGS
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@ -70,23 +79,23 @@ if(DOWNLOAD_MDI)
-Dplugins=ON
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
ExternalProject_get_property(mdi_build PREFIX)
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
file(MAKE_DIRECTORY ${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi)
file(MAKE_DIRECTORY ${PREFIX}/include/mdi)
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
)
IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
)
set(MDI_DEP_LIBS "")
# if compiling with python plugins we need

11
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -2,7 +2,13 @@
set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
if(PKG_PYTHON)
find_package(Cythonize QUIET)
if(Cythonize_FOUND)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
find_package(Python COMPONENTS NumPy QUIET)
else()
# assume we have NumPy
set(Python_NumPy_FOUND ON)
endif()
if(Cythonize_FOUND AND Python_NumPy_FOUND)
set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
endif()
endif()
@ -11,6 +17,9 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
find_package(Python COMPONENTS NumPy REQUIRED)
endif()
if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif()

20
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,6 +1,6 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.10.15.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "848ad6a6cc79fa82745927001fb1c9b5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
@ -15,23 +15,9 @@ execute_process(
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
# enforce building libyaml-cpp as static library and turn off optional features
set(YAML_BUILD_SHARED_LIBS OFF)
set(YAML_CPP_BUILD_CONTRIB OFF)
set(YAML_CPP_BUILD_TOOLS OFF)
add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
target_link_libraries(pace PRIVATE yaml-cpp-pace)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
endif()

4
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -58,12 +58,12 @@ if(DOWNLOAD_QUIP)
BUILD_COMMAND env QUIP_ARCH=lammps make libquip
INSTALL_COMMAND ""
BUILD_IN_SOURCE YES
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}
)
ExternalProject_get_property(quip_build SOURCE_DIR)
add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
set_target_properties(LAMMPS::QUIP PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
add_dependencies(LAMMPS::QUIP quip_build)

20
cmake/Modules/Packages/PLUMED.cmake
View File

@ -47,15 +47,15 @@ if(DOWNLOAD_PLUMED)
endif()
message(STATUS "PLUMED download requested - we will build our own")
if(PLUMED_MODE STREQUAL "STATIC")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
@ -78,12 +78,12 @@ if(DOWNLOAD_PLUMED)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
@ -96,7 +96,7 @@ else()
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")

9
cmake/Modules/Packages/VTK.cmake
View File

@ -1,4 +1,9 @@
find_package(VTK REQUIRED NO_MODULE)
include(${VTK_USE_FILE})
target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
if (VTK_MAJOR_VERSION VERSION_LESS 9.0)
include(${VTK_USE_FILE})
target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
vtk_module_autoinit(TARGETS lammps MODULES VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
endif()

1
cmake/presets/all_off.cmake
View File

@ -56,6 +56,7 @@ set(ALL_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP

1
cmake/presets/all_on.cmake
View File

@ -58,6 +58,7 @@ set(ALL_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP

7
cmake/presets/clang.cmake
View File

@ -28,10 +28,3 @@ set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

8
cmake/presets/gcc.cmake
View File

@ -19,11 +19,3 @@ set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Og -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

8
cmake/presets/intel.cmake
View File

@ -1,4 +1,4 @@
# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
# preset that will enable the classic Intel compilers with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "icpc" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)

1
cmake/presets/mingw-cross.cmake
View File

@ -47,6 +47,7 @@ set(WIN_PACKAGES
MISC
ML-HDNNP
ML-IAP
ML-POD
ML-RANN
ML-SNAP
MOFFF

1
cmake/presets/most.cmake
View File

@ -41,6 +41,7 @@ set(ALL_PACKAGES
MEAM
MISC
ML-IAP
ML-POD
ML-SNAP
MOFFF
MOLECULE

9
cmake/presets/nvhpc.cmake Normal file
View File

@ -0,0 +1,9 @@
# preset that will enable Nvidia HPC SDK compilers with support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "nvc++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "nvc" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "nvfortran" CACHE STRING "" FORCE)
set(MPI_CXX "nvc++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)

6
cmake/presets/oneapi.cmake
View File

@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)

9
cmake/presets/pedantic.cmake
View File

@ -1,4 +1,4 @@
# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
# preset that will set gcc/g++ with extra warnings enabled and support for MPI and OpenMP (on Linux boxes)
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
@ -17,10 +17,3 @@ set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "gcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

7
cmake/presets/pgi.cmake
View File

@ -7,10 +7,3 @@ set(MPI_CXX "pgc++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "pgcc" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-mp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "pgc++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-mp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

18
doc/Makefile
View File

@ -38,16 +38,14 @@ endif
# override settings for PIP commands
# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
# temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
# grab list of sources from doxygen config file.
# we only want to use explicitly listed files.
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check xmlgen fasthtml
# ------------------------------------------
@ -89,6 +87,8 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@$(MAKE) $(MFLAGS) -C graphviz all
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
touch $(RSTDIR)/Fortran.rst ;\
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;\
@ -114,7 +114,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@mkdir -p fasthtml
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
touch $(RSTDIR)/Fortran.rst ;\
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
deactivate ;\
)
@rm -rf fasthtml/_sources
@ -144,6 +146,8 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@cp src/JPG/*.* epub/JPG
@(\
. $(VENV)/bin/activate ;\
sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
touch $(RSTDIR)/Fortran.rst ;\
sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
deactivate ;\
@ -163,7 +167,9 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
touch $(RSTDIR)/Fortran.rst ;\
sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
echo "############################################" ;\
rst_anchor_check src/*.rst ;\

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "15 September 2022" "2022-9-15"
.TH LAMMPS "1" "3 November 2022" "2022-11-3"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 15 September 2022
\- Molecular Dynamics Simulator. Version 3 November 2022
.SH SYNOPSIS
.B lmp

10
doc/src/Build_development.rst
View File

@ -147,6 +147,16 @@ compile and will download and compile a specific recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.
.. admonition:: Software version requirements for testing
:class: note
The compiler and library version requirements for the testing
framework are more strict than for the main part of LAMMPS. For
example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
(version 4.8.x) are not sufficient. The CMake configuration will try
to detect compatible versions and either skip incompatible tests or
stop with an error.
After compilation is complete, the unit testing is started in the build
folder using the ``ctest`` command, which is part of the CMake software.
The output of this command will be looking something like this::

133
doc/src/Build_extras.rst
View File

@ -36,6 +36,7 @@ This is the list of packages that may require additional steps.
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COMPRESS <compress>`
* :ref:`ELECTRODE <electrode>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`INTEL <intel>`
@ -48,6 +49,7 @@ This is the list of packages that may require additional steps.
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
@ -234,7 +236,7 @@ LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ ,
Makefile you use.
You can also build the library in one step from the ``lammps/src`` dir,
using a command like these, which simply invoke the ``lib/gpu/Install.py``
using a command like these, which simply invokes the ``lib/gpu/Install.py``
script with the specified args:
.. code-block:: bash
@ -350,7 +352,7 @@ minutes to hours) to build. Of course you only need to do that once.)
You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``. You can also do
this in one step from the lammps/src directory, using a command like
these, which simply invoke the ``lib/kim/Install.py`` script with
these, which simply invokes the ``lib/kim/Install.py`` script with
the specified args.
.. code-block:: bash
@ -483,6 +485,9 @@ They must be specified in uppercase.
* - **Arch-ID**
- **HOST or GPU**
- **Description**
* - NATIVE
- HOST
- Local machine
* - AMDAVX
- HOST
- AMD 64-bit x86 CPU (AVX 1)
@ -522,9 +527,21 @@ They must be specified in uppercase.
* - BDW
- HOST
- Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
* - SKL
- HOST
- Intel Skylake Client CPU
* - SKX
- HOST
- Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
- Intel Skylake Xeon Server CPU (AVX512)
* - ICL
- HOST
- Intel Ice Lake Client CPU (AVX512)
* - ICX
- HOST
- Intel Ice Lake Xeon Server CPU (AVX512)
* - SPR
- HOST
- Intel Sapphire Rapids Xeon Server CPU (AVX512)
* - KNC
- HOST
- Intel Knights Corner Xeon Phi
@ -596,7 +613,10 @@ They must be specified in uppercase.
- AMD GPU MI100 GFX908
* - VEGA90A
- GPU
- AMD GPU
- AMD GPU MI200 GFX90A
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
* - INTEL_DG1
- GPU
- Intel Iris XeMAX GPU
@ -611,9 +631,12 @@ They must be specified in uppercase.
- Intel GPU Gen12LP
* - INTEL_XEHP
- GPU
- Intel GPUs Xe-HP
- Intel GPU Xe-HP
* - INTEL_PVC
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 3.5.0 of the Kokkos library.
This list was last updated for version 3.7.0 of the Kokkos library.
.. tabs::
@ -933,7 +956,7 @@ more details.
You can download and build the MS-CG library manually if you
prefer; follow the instructions in ``lib/mscg/README``\ . You can
also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/mscg/Install.py`` script with the specified args:
.. code-block:: bash
@ -990,7 +1013,7 @@ POEMS package
``lib/poems``\ . You can do this manually if you prefer; follow
the instructions in ``lib/poems/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/poems/Install.py`` script with the
which simply invokes the ``lib/poems/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1079,7 +1102,7 @@ binary package provided by your operating system.
You can download and build the Voro++ library manually if you
prefer; follow the instructions in ``lib/voronoi/README``. You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/voronoi/Install.py`` script with the specified args:
.. code-block:: bash
@ -1158,7 +1181,7 @@ The ATC package requires the MANYBODY package also be installed.
``lib/atc``. You can do this manually if you prefer; follow the
instructions in ``lib/atc/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/atc/Install.py`` script with the
which simply invokes the ``lib/atc/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1209,7 +1232,7 @@ AWPMD package
``lib/awpmd``. You can do this manually if you prefer; follow the
instructions in ``lib/awpmd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/awpmd/Install.py`` script with the
which simply invokes the ``lib/awpmd/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1272,7 +1295,7 @@ be built for the most part with all major versions of the C++ language.
In general, it is safer to use build setting consistent with the
rest of LAMMPS. This is best carried out from the LAMMPS src
directory using a command like these, which simply invoke the
directory using a command like these, which simply invokes the
``lib/colvars/Install.py`` script with the specified args:
.. code-block:: bash
@ -1313,20 +1336,30 @@ This package depends on the KSPACE package.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_KSPACE=yes`` and ``-D
PKG_ELECTRODE=yes``.
No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
``-D PKG_ELECTRODE=yes``.
.. tab:: Traditional make
The package is activated with ``make yes-KSPACE`` and ``make
yes-ELECTRODE``
Before building LAMMPS, you must configure the ELECTRODE support
libraries and settings in ``lib/electrode``. You can do this
manually, if you prefer, or do it in one step from the
``lammps/src`` dir, using a command like these, which simply
invokes the ``lib/electrode/Install.py`` script with the specified
args:
.. code-block:: bash
$ make lib-electrode # print help message
$ make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
Note that the ``Makefile.lammps`` file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in ``lib/awpmd/README``
these can either exist on your system, or you can use the files provided
in ``lib/linalg``. In the latter case you also need to build the library
in ``lib/linalg`` with a command like these:
Note that the ``Makefile.lammps`` file has settings for the BLAS
and LAPACK linear algebra libraries. These can either exist on
your system, or you can use the files provided in ``lib/linalg``.
In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
.. code-block:: bash
@ -1335,6 +1368,9 @@ This package depends on the KSPACE package.
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
----------
.. _ml-pace:
@ -1377,6 +1413,49 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
----------
.. _ml-pod:
ML-POD package
-----------------------------
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_ML-POD=yes``.
.. tab:: Traditional make
Before building LAMMPS, you must configure the ML-POD support
settings in ``lib/mlpod``. You can do this manually, if you
prefer, or do it in one step from the ``lammps/src`` dir, using a
command like the following, which simply invoke the
``lib/mlpod/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-mlpod # print help message
$ make lib-mlpod args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-mlpod args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-mlpod args="-m mpi -e linalg" # same as above but use the bundled linalg lib
Note that the ``Makefile.lammps`` file has settings to use the BLAS
and LAPACK linear algebra libraries. These can either exist on
your system, or you can use the files provided in ``lib/linalg``.
In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
The package itself is activated with ``make yes-ML-POD``.
----------
.. _plumed:
PLUMED package
@ -1534,7 +1613,7 @@ the HDF5 library.
``lib/h5md``. You can do this manually if you prefer; follow the
instructions in ``lib/h5md/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/h5md/Install.py`` script with the
which simply invokes the ``lib/h5md/Install.py`` script with the
specified args:
.. code-block:: bash
@ -1590,7 +1669,7 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
You can download and build the *n2p2* library manually if you prefer;
follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
simply invokes the ``lib/hdnnp/Install.py`` script with the specified args:
.. code-block:: bash
@ -1727,7 +1806,7 @@ they will be downloaded the first time this package is installed.
Before building LAMMPS, you must build the *mesont* library in
``lib/mesont``\ . You can also do it in one step from the
``lammps/src`` dir, using a command like these, which simply
invoke the ``lib/mesont/Install.py`` script with the specified
invokes the ``lib/mesont/Install.py`` script with the specified
args:
.. code-block:: bash
@ -1896,7 +1975,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
``lib/qmmm``. You can do this manually if you prefer; follow the
first two steps explained in ``lib/qmmm/README``. You can also do
it in one step from the ``lammps/src`` dir, using a command like
these, which simply invoke the ``lib/qmmm/Install.py`` script with
these, which simply invokes the ``lib/qmmm/Install.py`` script with
the specified args:
.. code-block:: bash
@ -2004,7 +2083,7 @@ To build with this package, you must download and build the
You can download and build the ScaFaCoS library manually if you
prefer; follow the instructions in ``lib/scafacos/README``. You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/scafacos/Install.py`` script with the specified args:
.. code-block:: bash
@ -2048,7 +2127,7 @@ Eigen3 is a template library, so you do not need to build it.
You can download the Eigen3 library manually if you prefer; follow
the instructions in ``lib/smd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/smd/Install.py`` script with the
which simply invokes the ``lib/smd/Install.py`` script with the
specified args:
.. code-block:: bash

17
doc/src/Build_manual.rst
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@ -216,9 +216,20 @@ be multiple tests run automatically:
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
thus prints all offending lines with filename and line number
prepended to the screen. Special characters like the Angstrom
:math:`\mathrm{\mathring{A}}` should be typeset with embedded math
(like this ``:math:`\mathrm{\mathring{A}}```\ ).
prepended to the screen. Special characters like Greek letters
(:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
(:math:`x^2~~\mathrm{U}_{LJ}`), mathematical expressions
(:math:`\frac{1}{2}\mathrm{N}~~x\to\infty`), or the Angstrom symbol
(:math:`\AA`) should be typeset with embedded LaTeX (like this
``:math:`\alpha \sigma \epsilon```, ``:math:`x^2 \mathrm{E}_{LJ}```,
``:math:`\frac{1}{2}\mathrm{N} x\to\infty```, or ``:math:`\AA```\ ).
- Embedded LaTeX is rendered in HTML output with `MathJax
<https://www.mathjax.org/>`_ and in PDF output by passing the embedded
text to LaTeX. Some care has to be taken, though, since there are
limitations which macros and features can be used in either mode, so
it is recommended to always check whether any new or changed
documentation does translate and render correctly with either output.
- A test whether all styles are documented and listed in their
respective overview pages. A typical output with warnings looks like this:

5
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@ -31,7 +31,6 @@ table above.
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`clear <clear>`
* :doc:`comm_modify <comm_modify>`
@ -90,8 +89,7 @@ table above.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset_atoms <reset_atoms>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`
@ -127,6 +125,7 @@ additional letter in parenthesis: k = KOKKOS.
* :doc:`group2ndx <group2ndx>`
* :doc:`hyper <hyper>`
* :doc:`kim <kim_commands>`
* :doc:`fitpod <fitpod_command>`
* :doc:`mdi <mdi>`
* :doc:`ndx2group <group2ndx>`
* :doc:`neb <neb>`

1
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@ -25,7 +25,6 @@ Setup simulation box:
:columns: 4
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`create_box <create_box>`
* :doc:`dimension <dimension>`

6
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@ -69,9 +69,9 @@ OPT.
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode_conp>`
* :doc:`electrode/conq (i) <fix_electrode_conp>`
* :doc:`electrode/thermo (i) <fix_electrode_conp>`
* :doc:`electrode/conp (i) <fix_electrode>`
* :doc:`electrode/conq (i) <fix_electrode>`
* :doc:`electrode/thermo (i) <fix_electrode>`
* :doc:`electron/stopping <fix_electron_stopping>`
* :doc:`electron/stopping/fit <fix_electron_stopping>`
* :doc:`enforce2d (k) <fix_enforce2d>`

5
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@ -205,7 +205,7 @@ OPT.
* :doc:`mesont/tpm <pair_mesont_tpm>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mliap <pair_mliap>`
* :doc:`mliap (k) <pair_mliap>`
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
@ -236,6 +236,8 @@ OPT.
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation <pair_pace>`
* :doc:`pod <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
@ -294,6 +296,7 @@ OPT.
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`
* :doc:`ylz <pair_ylz>`
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`

52
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@ -2,14 +2,17 @@ Removed commands and packages
=============================
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or replacements.
LAMMPS has special dummy styles implemented, that will stop LAMMPS and
print a suitable error message in most cases, when a style/command is used
that has been removed.
the distribution and provides suggestions for alternatives or
replacements. LAMMPS has special dummy styles implemented, that will
stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
.. deprecated:: 11Dec2015
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
@ -17,10 +20,23 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
Reset_ids command
-----------------
Box command
-----------
The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
.. deprecated:: TBD
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
.. deprecated:: TBD
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
present, LAMMPS will replace the commands accordingly and print a
warning.
MEAM package
------------
@ -30,18 +46,21 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax.
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
REAX package
------------
The REAX package has been removed since it was superseded by the
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF
package has been tested to yield equivalent results to the REAX package,
offers better performance, supports OpenMP multi-threading via OPENMP,
and GPU and threading parallelization through KOKKOS. The new pair styles
are not syntax compatible with the removed reax pair style, so input
files will have to be adapted.
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF package has been tested
to yield equivalent results to the REAX package, offers better
performance, supports OpenMP multi-threading via OPENMP, and GPU and
threading parallelization through KOKKOS. The new pair styles are not
syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-CUDA package
-----------------
@ -60,5 +79,6 @@ restart2data tool
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For added
convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`

14
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@ -50,7 +50,7 @@ parallel each MPI process creates such an instance. This can be seen
in the ``main.cpp`` file where the core steps of running a LAMMPS
simulation are the following 3 lines of code:
.. code-block:: C++
.. code-block:: c++
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
lammps->input->file();
@ -78,7 +78,7 @@ LAMMPS makes extensive use of the object oriented programming (OOP)
principles of *compositing* and *inheritance*. Classes like the
``LAMMPS`` class are a **composite** containing pointers to instances
of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
``Modify``, and so on. Each of these classes implement certain
``Modify``, and so on. Each of these classes implements certain
functionality by storing and manipulating data related to the
simulation and providing member functions that trigger certain
actions. Some of those classes like ``Force`` are themselves
@ -87,9 +87,9 @@ interactions. Similarly the ``Modify`` class contains a list of
``Fix`` and ``Compute`` classes. If the input commands that
correspond to these classes include the word *style*, then LAMMPS
stores only a single instance of that class. E.g. *atom_style*,
*comm_style*, *pair_style*, *bond_style*. It the input command does
not include the word *style*, there can be many instances of that
class defined. E.g. *region*, *fix*, *compute*, *dump*.
*comm_style*, *pair_style*, *bond_style*. If the input command does
**not** include the word *style*, then there may be many instances of
that class defined, for example *region*, *fix*, *compute*, *dump*.
**Inheritance** enables creation of *derived* classes that can share
common functionality in their base class while providing a consistent
@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut"
with a factory function creating an instance of the ``PairLJCut``
class.
.. code-block:: C++
.. code-block:: c++
// from force.h
typedef Pair *(*PairCreator)(LAMMPS *);
@ -360,7 +360,7 @@ characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
argument type must be compatible or else the {fmt} formatting code will
throw an exception. Some format string examples are given below:
.. code-block:: C
.. code-block:: c++
auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",

16
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@ -105,7 +105,7 @@ list, where each pair of atoms is listed only once (except when the
pairs straddling sub-domains or periodic boundaries will be listed twice).
Thus these are the default settings when a neighbor list request is created in:
.. code-block:: C++
.. code-block:: c++
void Pair::init_style()
{
@ -129,7 +129,7 @@ neighbor list request to the specific needs of a style an additional
request flag is needed. The :doc:`tersoff <pair_tersoff>` pair style,
for example, needs a "full" neighbor list:
.. code-block:: C++
.. code-block:: c++
void PairTersoff::init_style()
{
@ -141,7 +141,7 @@ When a pair style supports r-RESPA time integration with different cutoff region
the request flag may depend on the corresponding r-RESPA settings. Here an example
from pair style lj/cut:
.. code-block:: C++
.. code-block:: c++
void PairLJCut::init_style()
{
@ -160,7 +160,7 @@ Granular pair styles need neighbor lists based on particle sizes and not cutoff
and also may require to have the list of previous neighbors available ("history").
For example with:
.. code-block:: C++
.. code-block:: c++
if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
else neighbor->add_request(this, NeighConst::REQ_SIZE);
@ -170,7 +170,7 @@ settings each request can set an id which is then used in the corresponding
``init_list()`` function to assign it to the suitable pointer variable. This is
done for example by the :doc:`pair style meam <pair_meam>`:
.. code-block:: C++
.. code-block:: c++
void PairMEAM::init_style()
{
@ -189,7 +189,7 @@ just once) and this can also be indicated by a flag. As an example here
is the request from the ``FixPeriNeigh`` class which is created
internally by :doc:`Peridynamics pair styles <pair_peri>`:
.. code-block:: C++
.. code-block:: c++
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
@ -198,7 +198,7 @@ than what is usually inferred from the pair style settings (largest cutoff of
all pair styles plus neighbor list skin). The following is used in the
:doc:`compute rdf <compute_rdf>` command implementation:
.. code-block:: C++
.. code-block:: c++
if (cutflag)
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
@ -212,7 +212,7 @@ for printing the neighbor list summary the name of the requesting command
should be set. Below is the request from the :doc:`delete atoms <delete_atoms>`
command:
.. code-block:: C++
.. code-block:: c++
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);

6
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@ -95,7 +95,7 @@ a class ``PairMorse2`` in the files ``pair_morse2.h`` and
``pair_morse2.cpp`` with the factory function and initialization
function would look like this:
.. code-block:: C++
.. code-block:: c++
#include "lammpsplugin.h"
#include "version.h"
@ -141,7 +141,7 @@ list of argument strings), then the pointer type is ``lammpsplugin_factory2``
and it must be assigned to the *creator.v2* member of the plugin struct.
Below is an example for that:
.. code-block:: C++
.. code-block:: c++
#include "lammpsplugin.h"
#include "version.h"
@ -176,7 +176,7 @@ demonstrated in the following example, which also shows that the
implementation of the plugin class may be within the same source
file as the plugin interface code:
.. code-block:: C++
.. code-block:: c++
#include "lammpsplugin.h"

10
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@ -194,7 +194,7 @@ macro. These tests operate by capturing the screen output when executing
the failing command and then comparing that with a provided regular
expression string pattern. Example:
.. code-block:: C++
.. code-block:: c++
TEST_F(SimpleCommandsTest, UnknownCommand)
{
@ -226,9 +226,9 @@ The following test programs are currently available:
* - ``test_kim_commands.cpp``
- KimCommands
- Tests for several commands from the :ref:`KIM package <PKG-KIM>`
* - ``test_reset_ids.cpp``
- ResetIDs
- Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
* - ``test_reset_atoms.cpp``
- ResetAtoms
- Tests to validate the :doc:`reset_atoms <reset_atoms>` sub-commands
Tests for the C-style library interface
@ -249,7 +249,7 @@ MPI support. These include tests where LAMMPS is run in multi-partition
mode or only on a subset of the MPI world communicator. The CMake
script code for adding this kind of test looks like this:
.. code-block:: CMake
.. code-block:: cmake
if (BUILD_MPI)
add_executable(test_library_mpi test_library_mpi.cpp)

46
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@ -7,7 +7,7 @@ source files provided as a supplement to a publication) that are written
for an older version of LAMMPS and thus need to be updated to be
compatible with the current version of LAMMPS. Due to the active
development of LAMMPS it is likely to always be incomplete. Please
contact developer@lammps.org in case you run across an issue that is not
contact developers@lammps.org in case you run across an issue that is not
(yet) listed here. Please also review the latest information about the
LAMMPS :doc:`programming style conventions <Modify_style>`, especially
if you are considering to submit the updated version for inclusion into
@ -61,7 +61,7 @@ header file needs to be updated accordingly.
Old:
.. code-block:: C++
.. code-block:: c++
int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
@ -75,7 +75,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
@ -112,14 +112,14 @@ Example from a pair style:
Old:
.. code-block:: C++
.. code-block:: c++
if (eflag || vflag) ev_setup(eflag, vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
New:
.. code-block:: C++
.. code-block:: c++
ev_init(eflag, vflag);
@ -142,14 +142,14 @@ when they are called from only one or a subset of the MPI processes.
Old:
.. code-block:: C++
.. code-block:: c++
val = force->numeric(FLERR, arg[1]);
num = force->inumeric(FLERR, arg[2]);
New:
.. code-block:: C++
.. code-block:: c++
val = utils::numeric(FLERR, true, arg[1], lmp);
num = utils::inumeric(FLERR, false, arg[2], lmp);
@ -183,14 +183,14 @@ copy them around for simulations.
Old:
.. code-block:: C++
.. code-block:: c++
fp = force->open_potential(filename);
fp = fopen(filename, "r");
New:
.. code-block:: C++
.. code-block:: c++
fp = utils::open_potential(filename, lmp);
@ -207,7 +207,7 @@ Example:
Old:
.. code-block:: C++
.. code-block:: c++
if (fptr == NULL) {
char str[128];
@ -217,7 +217,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
if (fptr == nullptr)
error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
@ -237,7 +237,7 @@ an example from the ``FixWallReflect`` class:
Old:
.. code-block:: C++
.. code-block:: c++
FixWallReflect(class LAMMPS *, int, char **);
virtual ~FixWallReflect();
@ -247,7 +247,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
FixWallReflect(class LAMMPS *, int, char **);
~FixWallReflect() override;
@ -271,7 +271,7 @@ the type of the "this" pointer argument.
Old:
.. code-block:: C++
.. code-block:: c++
comm->forward_comm_pair(this);
comm->forward_comm_fix(this);
@ -284,7 +284,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
comm->forward_comm(this);
comm->reverse_comm(this);
@ -304,7 +304,7 @@ requests can be :doc:`found here <Developer_notes>`. Example from the
Old:
.. code-block:: C++
.. code-block:: c++
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
@ -317,7 +317,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
if (cutflag) req->set_cutoff(mycutneigh);
@ -340,7 +340,7 @@ these are internal fixes, there is no user visible change.
Old:
.. code-block:: C++
.. code-block:: c++
#include "fix_store.h"
@ -351,7 +351,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
#include "fix_store_peratom.h"
@ -362,7 +362,7 @@ New:
Old:
.. code-block:: C++
.. code-block:: c++
#include "fix_store.h"
@ -373,7 +373,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
#include "fix_store_global.h"
@ -396,7 +396,7 @@ the dump directly. Example:
Old:
.. code-block:: C++
.. code-block:: c++
int idump = output->find_dump(arg[iarg+1]);
if (idump < 0)
@ -412,7 +412,7 @@ Old:
New:
.. code-block:: C++
.. code-block:: c++
auto idump = output->get_dump_by_id(arg[iarg+1]);
if (!idump) error->all(FLERR,"Dump ID {} in hyper command does not exist", arg[iarg+1]);

10
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@ -317,7 +317,7 @@ are all "whitespace" characters, i.e. the space character, the tabulator
character, the carriage return character, the linefeed character, and
the form feed character.
.. code-block:: C++
.. code-block:: c++
:caption: Tokenizer class example listing entries of the PATH environment variable
#include "tokenizer.h"
@ -349,7 +349,7 @@ tokenizer into a ``try`` / ``catch`` block to handle errors. The
when a (type of) number is requested as next token that is not
compatible with the string representing the next word.
.. code-block:: C++
.. code-block:: c++
:caption: ValueTokenizer class example with exception handling
#include "tokenizer.h"
@ -427,7 +427,7 @@ one or two array indices "[<number>]" with numbers > 0.
A typical code segment would look like this:
.. code-block:: C++
.. code-block:: c++
:caption: Usage example for ArgInfo class
int nvalues = 0;
@ -476,7 +476,7 @@ open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in
case of failures to read or to convert numbers, so that LAMMPS will be
aborted.
.. code-block:: C++
.. code-block:: c++
:caption: Use of PotentialFileReader class in pair style coul/streitz
PotentialFileReader reader(lmp, file, "coul/streitz");
@ -555,7 +555,7 @@ chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget()
its size is registered later with :cpp:func:`MyPage::vgot()
<LAMMPS_NS::MyPage::vgot>`.
.. code-block:: C++
.. code-block:: c++
:caption: Example of using :cpp:class:`MyPage <LAMMPS_NS::MyPage>`
#include "my_page.h"

14
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@ -26,7 +26,7 @@ constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
Every fix must be registered in LAMMPS by writing the following lines
of code in the header before include guards:
.. code-block:: c
.. code-block:: c++
#ifdef FIX_CLASS
// clang-format off
@ -47,7 +47,7 @@ keyword when it parses the input script.
Let's write a simple fix which will print the average velocity at the end
of each timestep. First of all, implement a constructor:
.. code-block:: C++
.. code-block:: c++
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg)
@ -72,7 +72,7 @@ in the Fix class called ``nevery`` which specifies how often the method
The next method we need to implement is ``setmask()``:
.. code-block:: C++
.. code-block:: c++
int FixPrintVel::setmask()
{
@ -87,7 +87,7 @@ during execution. The constant ``END_OF_STEP`` corresponds to the
are called during a timestep and the order in which they are called
are shown in the previous section.
.. code-block:: C++
.. code-block:: c++
void FixPrintVel::end_of_step()
{
@ -143,7 +143,7 @@ The group membership information of an atom is contained in the *mask*
property of and atom and the bit corresponding to a given group is
stored in the groupbit variable which is defined in Fix base class:
.. code-block:: C++
.. code-block:: c++
for (int i = 0; i < nlocal; ++i) {
if (atom->mask[i] & groupbit) {
@ -174,7 +174,7 @@ to store positions of atoms from previous timestep, we need to add
``double** xold`` to the header file. Than add allocation code
to the constructor:
.. code-block:: C++
.. code-block:: c++
FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
{
@ -190,7 +190,7 @@ to the constructor:
Implement the aforementioned methods:
.. code-block:: C++
.. code-block:: c++
double FixSavePos::memory_usage()
{

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@ -152,14 +152,14 @@ Creating a new instance of PyLammps
To create a PyLammps object you need to first import the class from the lammps
module. By using the default constructor, a new *lammps* instance is created.
.. code-block:: Python
.. code-block:: python
from lammps import PyLammps
L = PyLammps()
You can also initialize PyLammps on top of this existing *lammps* object:
.. code-block:: Python
.. code-block:: python
from lammps import lammps, PyLammps
lmp = lammps()
@ -180,14 +180,14 @@ For instance, let's take the following LAMMPS command:
In the original interface this command can be executed with the following
Python code if *L* was a lammps instance:
.. code-block:: Python
.. code-block:: python
L.command("region box block 0 10 0 5 -0.5 0.5")
With the PyLammps interface, any command can be split up into arbitrary parts
separated by white-space, passed as individual arguments to a region method.
.. code-block:: Python
.. code-block:: python
L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
@ -199,14 +199,14 @@ The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the original interface parameterization needed to be done
manually by creating formatted strings.
.. code-block:: Python
.. code-block:: python
L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: Python
.. code-block:: python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
@ -256,7 +256,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: Python
.. code-block:: python
L.variable("a index 2")
@ -265,14 +265,14 @@ A dictionary of all variables is returned by L.variables
you can access an individual variable by retrieving a variable object from the
L.variables dictionary by name
.. code-block:: Python
.. code-block:: python
a = L.variables['a']
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: Python
.. code-block:: python
print(a.value)
a.value = 4
@ -284,7 +284,7 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
passed string parameter can be any expression containing global thermo values,
variables, compute or fix data.
.. code-block:: Python
.. code-block:: python
result = L.eval("ke") # kinetic energy
result = L.eval("pe") # potential energy
@ -298,7 +298,7 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
Each element of this list is an object which exposes its properties (id, type,
position, velocity, force, etc.).
.. code-block:: Python
.. code-block:: python
# access first atom
L.atoms[0].id
@ -311,7 +311,7 @@ position, velocity, force, etc.).
Some properties can also be used to set:
.. code-block:: Python
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)
@ -328,7 +328,7 @@ after a run via the L.runs list. This list contains a growing list of run data.
The first element is the output of the first run, the second element that of
the second run.
.. code-block:: Python
.. code-block:: python
L.run(1000)
L.runs[0] # data of first 1000 time steps
@ -339,14 +339,14 @@ the second run.
Each run contains a dictionary of all trajectories. Each trajectory is
accessible through its thermo name:
.. code-block:: Python
.. code-block:: python
L.runs[0].thermo.Step # list of time steps in first run
L.runs[0].thermo.Ke # list of kinetic energy values in first run
Together with matplotlib plotting data out of LAMMPS becomes simple:
.. code-block:: Python
.. code-block:: python
import matplotlib.plot as plt
steps = L.runs[0].thermo.Step
@ -406,7 +406,7 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
them using a datafile. Then one of the atoms is rotated along the central axis by
setting its position from Python, which changes the dihedral angle.
.. code-block:: Python
.. code-block:: python
phi = [d \* math.pi / 180 for d in range(360)]
@ -439,7 +439,7 @@ Initially, a 2D system is created in a state with minimal energy.
It is then disordered by moving each atom by a random delta.
.. code-block:: Python
.. code-block:: python
random.seed(27848)
deltaperturb = 0.2
@ -458,7 +458,7 @@ It is then disordered by moving each atom by a random delta.
Finally, the Monte Carlo algorithm is implemented in Python. It continuously
moves random atoms by a random delta and only accepts certain moves.
.. code-block:: Python
.. code-block:: python
estart = L.eval("pe")
elast = estart
@ -517,7 +517,7 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
The following is a short example which reads in an existing LAMMPS input file and
executes it in parallel. You can find in.melt in the examples/melt folder.
.. code-block:: Python
.. code-block:: python
from mpi4py import MPI
from lammps import PyLammps

2
doc/src/Howto_structured_data.rst
View File

@ -43,7 +43,7 @@ JSON
"ke": $(ke)
}""" file current_state.json screen no
.. code-block:: JSON
.. code-block:: json
:caption: current_state.json
{

37
doc/src/Howto_tip4p.rst
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@ -8,18 +8,28 @@ This site M is located at a fixed distance away from the oxygen along
the bisector of the HOH bond angle. A bond style of *harmonic* and an
angle style of *harmonic* or *charmm* should also be used.
A TIP4P model is run with LAMMPS using either this command
A TIP4P model is run with LAMMPS using either these commands
for a cutoff model:
* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
or these two commands for a long-range model:
or these commands for a long-range model:
* :doc:`pair_style tip4p/long <pair_coul>`
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
* :doc:`pair_style lj/long/tip4p/long <pair_lj_long>`
* :doc:`pair_style tip4p/long/soft <pair_fep_soft>`
* :doc:`pair_style lj/cut/tip4p/long/soft <pair_fep_soft>`
* :doc:`kspace_style pppm/tip4p <kspace_style>`
* :doc:`kspace_style pppm/disp/tip4p <kspace_style>`
For both models, the bond lengths and bond angles should be held fixed
using the :doc:`fix shake <fix_shake>` command.
The bond lengths and bond angles should be held fixed using the
:doc:`fix shake <fix_shake>` or :doc:`fix rattle <fix_shake>` command,
unless a parameterization for a flexible TIP4P model is used. The
parameter sets listed below are all for rigid TIP4P model variants and
thus the bond and angle force constants are not used and can be set to
any legal value; only equilibrium length and angle are used.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
@ -87,15 +97,16 @@ solver (e.g. Ewald or PPPM in LAMMPS):
| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
|
Note that the when using the 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 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 trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
Note that the when using the 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
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
trade-off for your model. The OM distance and the LJ and Coulombic
cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
<pair_lj_cut_tip4p>` command.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.

5
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@ -144,11 +144,6 @@ does not change the atom positions due to non-periodicity. In this
mode, if you tilt the system to extreme angles, the simulation will
simply become inefficient, due to the highly skewed simulation box.
The limitation on not creating a simulation box with a tilt factor
skewing the box more than half the distance of the parallel box length
can be overridden via the :doc:`box <box>` command. Setting the *tilt*
keyword to *large* allows any tilt factors to be specified.
Box flips that may occur using the :doc:`fix deform <fix_deform>` or
:doc:`fix npt <fix_nh>` commands can be turned off using the *flip no*
option with either of the commands.

25
doc/src/Library.rst
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@ -2,12 +2,13 @@ LAMMPS Library Interfaces
*************************
As described on the :doc:`library interface to LAMMPS <Howto_library>`
page, LAMMPS can be built as a library (static or shared), so that
it can be called by another code, used in a :doc:`coupled manner
page, LAMMPS can be built as a library (static or shared), so that it
can be called by another code, used in a :doc:`coupled manner
<Howto_couple>` with other codes, or driven through a :doc:`Python
script <Python_head>`. Even the LAMMPS standalone executable is
essentially a thin wrapper on top of the LAMMPS library, creating a
LAMMPS instance, processing input and then existing.
script <Python_head>`. The LAMMPS standalone executable itself is
essentially a thin wrapper on top of the LAMMPS library, which creates a
LAMMPS instance, passes the input for processing to that instance, and
then exits.
Most of the APIs described below are based on C language wrapper
functions in the files ``src/library.h`` and ``src/library.cpp``, but
@ -87,6 +88,18 @@ run LAMMPS in serial mode.
message retrieved <lammps_get_last_error_message>`. We thus
recommend enabling C++ exceptions when using the library interface,
.. admonition:: Using the C library interface as a plugin
:class: note
Rather than including the C library directly and link to the LAMMPS
library at compile time, you can use the ``liblammpsplugin.h`` header
file and the ``liblammpsplugin.c`` C code in the
``examples/COUPLE/plugin`` folder for an interface to LAMMPS that is
largely identical to the regular library interface, only that it will
load a LAMMPS shared library file at runtime. This can be useful for
applications where the interface to LAMMPS would be an optional
feature.
.. warning::
No checks are made on the arguments of the function calls of the C
@ -163,5 +176,3 @@ The following links provide some examples and references to the C++ API.
:maxdepth: 1
Cplusplus

2
doc/src/Library_config.rst
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@ -39,7 +39,7 @@ crashes within LAMMPS may be recovered from by enabling
:ref:`exceptions <exceptions>`, avoiding them proactively is a safer
approach.
.. code-block:: C
.. code-block:: c
:caption: Example for using configuration settings functions
#include "library.h"

2
doc/src/Library_create.rst
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@ -22,7 +22,7 @@ as the "handle" argument in subsequent function calls until that
instance is destroyed by calling :cpp:func:`lammps_close`. Here is a
simple example demonstrating its use:
.. code-block:: C
.. code-block:: c
#include "library.h"
#include <stdio.h>

2
doc/src/Library_execute.rst
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@ -30,7 +30,7 @@ be included in the file or strings, and expansion of variables with
``${name}`` or ``$(expression)`` syntax is performed.
Below is a short example using some of these functions.
.. code-block:: C
.. code-block:: c
/* define to make the otherwise hidden prototype for "lammps_open()" visible */
#define LAMMPS_LIB_MPI

8
doc/src/Library_objects.rst
View File

@ -6,6 +6,7 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_compute`
- :cpp:func:`lammps_extract_fix`
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
@ -21,6 +22,11 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_extract_variable_datatype
:project: progguide
-----------------------
.. doxygenfunction:: lammps_extract_variable
:project: progguide
@ -36,3 +42,5 @@ fixes, or variables in LAMMPS using the following functions:
.. doxygenenum:: _LMP_STYLE_CONST
.. doxygenenum:: _LMP_TYPE_CONST
.. doxygenenum:: _LMP_VAR_CONST

12
doc/src/Library_properties.rst
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@ -16,8 +16,8 @@ This section documents the following functions:
--------------------
The library interface allows the extraction of different kinds of
information about the active simulation instance and also - in some
cases - to apply modifications to it. This enables combining of a
information about the active simulation instance and also---in some
cases---to apply modifications to it. This enables combining of a
LAMMPS simulation with other processing and simulation methods computed
by the calling code, or by another code that is coupled to LAMMPS via
the library interface. In some cases the data returned is direct
@ -25,14 +25,14 @@ reference to the original data inside LAMMPS, cast to a void pointer.
In that case the data needs to be cast to a suitable pointer for the
calling program to access it, and you may need to know the correct
dimensions and lengths. This also means you can directly change those
value(s) from the calling program, e.g. to modify atom positions. Of
course, this should be done with care. When accessing per-atom data,
please note that this data is the per-processor **local** data and is
value(s) from the calling program (e.g., to modify atom positions). Of
course, changing values should be done with care. When accessing per-atom
data, please note that these data are the per-processor **local** data and are
indexed accordingly. Per-atom data can change sizes and ordering at
every neighbor list rebuild or atom sort event as atoms migrate between
sub-domains and processors.
.. code-block:: C
.. code-block:: c
#include "library.h"
#include <stdio.h>

2
doc/src/Manual.rst
View File

@ -42,7 +42,7 @@ descriptions of all commands included in the LAMMPS code.
.. only:: html
Once you are familiar with LAMMPS, you may want to bookmark
:doc:`this page <Commands_all>` since it gives quick access
:doc:`this page <Commands_all>` since it gives quick access to
the documentation for all LAMMPS commands.
.. _lws: https://www.lammps.org

83
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@ -13,24 +13,65 @@ Here is a brief description of common methods you define in your
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
for details and specific additional methods.
+-----------------------+---------------------------------------------------------------------------------------+
| init | check if all coefficients are set, calls *init_style* (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
| init_style | check if style specific conditions are met (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
| compute | compute the molecular interactions (required) |
+-----------------------+---------------------------------------------------------------------------------------+
| settings | apply global settings for all types (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
| coeff | set coefficients for one type (required) |
+-----------------------+---------------------------------------------------------------------------------------+
| equilibrium_distance | length of bond, used by SHAKE (required, bond only) |
+-----------------------+---------------------------------------------------------------------------------------+
| equilibrium_angle | opening of angle, used by SHAKE (required, angle only) |
+-----------------------+---------------------------------------------------------------------------------------+
| write & read_restart | writes/reads coeffs to restart files (required) |
+-----------------------+---------------------------------------------------------------------------------------+
| single | force (bond only) and energy of a single bond or angle (required, bond or angle only) |
+-----------------------+---------------------------------------------------------------------------------------+
| memory_usage | tally memory allocated by the style (optional) |
+-----------------------+---------------------------------------------------------------------------------------+
+-----------------------+---------------------------------------------------------------------+
| Required | "pure" methods that *must* be overridden in a derived class |
+=======================+=====================================================================+
| compute | compute the molecular interactions for all listed items |
+-----------------------+---------------------------------------------------------------------+
| coeff | set coefficients for one type |
+-----------------------+---------------------------------------------------------------------+
| equilibrium_distance | length of bond, used by SHAKE (bond styles only) |
+-----------------------+---------------------------------------------------------------------+
| equilibrium_angle | opening of angle, used by SHAKE (angle styles only) |
+-----------------------+---------------------------------------------------------------------+
| write & read_restart | writes/reads coeffs to restart files |
+-----------------------+---------------------------------------------------------------------+
| single | force/r (bond styles only) and energy of a single bond or angle |
+-----------------------+---------------------------------------------------------------------+
+--------------------------------+----------------------------------------------------------------------+
| Optional | methods that have a default or dummy implementation |
+================================+======================================================================+
| init | check if all coefficients are set, calls init_style() |
+--------------------------------+----------------------------------------------------------------------+
| init_style | check if style specific conditions are met |
+--------------------------------+----------------------------------------------------------------------+
| settings | apply global settings for all types |
+--------------------------------+----------------------------------------------------------------------+
| write & read_restart_settings | writes/reads global style settings to restart files |
+--------------------------------+----------------------------------------------------------------------+
| write_data | write corresponding Coeffs section(s) in data file |
+--------------------------------+----------------------------------------------------------------------+
| memory_usage | tally memory allocated by the style |
+--------------------------------+----------------------------------------------------------------------+
| extract | provide access to internal data (bond or angle styles only) |
+--------------------------------+----------------------------------------------------------------------+
| reinit | reset all type-based parameters, called by fix adapt (bonds only) |
+--------------------------------+----------------------------------------------------------------------+
| pack & unpack_forward_comm | copy data to and from buffer in forward communication (bonds only) |
+--------------------------------+----------------------------------------------------------------------+
| pack & unpack_reverse_comm | copy data to and from buffer in reverse communication (bonds only) |
+--------------------------------+----------------------------------------------------------------------+
Here is a list of flags or settings that should be set in the
constructor of the derived class when they differ from the default
setting.
+---------------------------------+------------------------------------------------------------------------------+---------+
| Name of flag | Description | default |
+=================================+==============================================================================+=========+
| writedata | 1 if write_data() is implemented | 1 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| single_extra | number of extra single values calculated (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| partial_flag | 1 if bond type can be set to 0 and deleted (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 1 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| comm_forward | size of buffer (in doubles) for forward communication (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| comm_reverse | size of buffer (in doubles) for reverse communication (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+
| comm_reverse_off | size of buffer for reverse communication with newton off (bond styles only) | 0 |
+---------------------------------+------------------------------------------------------------------------------+---------+

132
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@ -1,35 +1,121 @@
Pair styles
===========
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include many-body potentials
such as EAM or Tersoff where particles interact without a static bond
topology. New styles can be created to add new pair potentials to
LAMMPS.
Classes that compute pairwise non-bonded interactions are derived from
the Pair class. In LAMMPS, pairwise calculation include many-body
potentials such as EAM, Tersoff, or ReaxFF where particles interact
without an explicit bond topology but include interactions beyond
pairwise non-bonded contributions. New styles can be created to add
support for additional pair potentials to LAMMPS. When the
modifications are small, sometimes it is more effective to derive from
an existing pair style class. This latter approach is also used by
:doc:`Accelerator packages <Speed_packages>` where the accelerated style
names differ from their base classes by an appended suffix.
Pair_lj_cut.cpp is a simple example of a Pair class, though it
includes some optional methods to enable its use with rRESPA.
The file ``src/pair_lj_cut.cpp`` is an example of a Pair class with a
very simple potential function. It includes several optional methods to
enable its use with :doc:`run_style respa <run_style>` and :doc:`compute
group/group <compute_group_group>`.
Here is a brief description of the class methods in pair.h:
Here is a brief list of some the class methods in the Pair class that
*must* be or *may* be overridden in a derived class.
+---------------------------------+---------------------------------------------------------------------+
| Required | "pure" methods that *must* be overridden in a derived class |
+=================================+=====================================================================+
| compute | workhorse routine that computes pairwise interactions |
+---------------------------------+---------------------------------------------------------------------+
| settings | reads the input script line with arguments you define |
| settings | processes the arguments to the pair_style command |
+---------------------------------+---------------------------------------------------------------------+
| coeff | set coefficients for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+---------------------------------------------------------------------+
| init_style | initialization specific to this pair style |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+---------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+---------------------------------------------------------------------+
| single | force/r and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+---------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
| coeff | set coefficients for one i,j type pair, called from pair_coeff |
+---------------------------------+---------------------------------------------------------------------+
The inner/middle/outer routines are optional.
+---------------------------------+----------------------------------------------------------------------+
| Optional | methods that have a default or dummy implementation |
+=================================+======================================================================+
| init_one | perform initialization for one i,j type pair |
+---------------------------------+----------------------------------------------------------------------+
| init_style | style initialization: request neighbor list(s), error checks |
+---------------------------------+----------------------------------------------------------------------+
| init_list | Neighbor class callback function to pass neighbor list to pair style |
+---------------------------------+----------------------------------------------------------------------+
| single | force/r and energy of a single pairwise interaction between 2 atoms |
+---------------------------------+----------------------------------------------------------------------+
| compute_inner/middle/outer | versions of compute used by rRESPA |
+---------------------------------+----------------------------------------------------------------------+
| memory_usage | return estimated amount of memory used by the pair style |
+---------------------------------+----------------------------------------------------------------------+
| modify_params | process arguments to pair_modify command |
+---------------------------------+----------------------------------------------------------------------+
| extract | provide access to internal scalar or per-type data like cutoffs |
+---------------------------------+----------------------------------------------------------------------+
| extract_peratom | provide access to internal per-atom data |
+---------------------------------+----------------------------------------------------------------------+
| setup | initialization at the beginning of a run |
+---------------------------------+----------------------------------------------------------------------+
| finish | called at the end of a run, e.g. to print |
+---------------------------------+----------------------------------------------------------------------+
| write & read_restart | write/read i,j pair coeffs to restart files |
+---------------------------------+----------------------------------------------------------------------+
| write & read_restart_settings | write/read global settings to restart files |
+---------------------------------+----------------------------------------------------------------------+
| write_data | write Pair Coeffs section to data file |
+---------------------------------+----------------------------------------------------------------------+
| write_data_all | write PairIJ Coeffs section to data file |
+---------------------------------+----------------------------------------------------------------------+
| pack & unpack_forward_comm | copy data to and from buffer if style uses forward communication |
+---------------------------------+----------------------------------------------------------------------+
| pack & unpack_reverse_comm | copy data to and from buffer if style uses reverse communication |
+---------------------------------+----------------------------------------------------------------------+
| reinit | reset all type-based parameters, called by fix adapt for example |
+---------------------------------+----------------------------------------------------------------------+
| reset_dt | called when the time step is changed by timestep or fix reset/dt |
+---------------------------------+----------------------------------------------------------------------+
Here is a list of flags or settings that should be set in the
constructor of the derived pair class when they differ from the default
setting.
+---------------------------------+-------------------------------------------------------------+---------+
| Name of flag | Description | default |
+=================================+=============================================================+=========+
| single_enable | 1 if single() method is implemented, 0 if missing | 1 |
+---------------------------------+-------------------------------------------------------------+---------+
| respa_enable | 1 if pair style has compute_inner/middle/outer() | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| restartinfo | 1 if pair style writes its settings to a restart | 1 |
+---------------------------------+-------------------------------------------------------------+---------+
| one_coeff | 1 if only a pair_coeff * * command is allowed | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| manybody_flag | 1 if pair style is a manybody potential | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| unit_convert_flag | value != 0 indicates support for unit conversion | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| no_virial_fdotr_compute | 1 if pair style does not call virial_fdotr_compute() | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| writedata | 1 if write_data() and write_data_all() are implemented | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| comm_forward | size of buffer (in doubles) for forward communication | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| comm_reverse | size of buffer (in doubles) for reverse communication | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| ghostneigh | 1 if cutghost is set and style uses neighbors of ghosts | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| finitecutflag | 1 if cutoff depends on diameter of atoms | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| reinitflag | 1 if style has reinit() and is compatible with fix adapt | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| ewaldflag | 1 if compatible with kspace_style ewald | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| pppmflag | 1 if compatible with kspace_style pppm | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| msmflag | 1 if compatible with kspace_style msm | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| dispersionflag | 1 if compatible with ewald/disp or pppm/disp | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| tip4pflag | 1 if compatible with kspace_style pppm/tip4p | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| dipoleflag | 1 if compatible with dipole kspace_style | 0 |
+---------------------------------+-------------------------------------------------------------+---------+
| spinflag | 1 if compatible with spin kspace_style | 0 |
+---------------------------------+-------------------------------------------------------------+---------+

6
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@ -359,6 +359,12 @@ you are uncertain, please ask.
- I/O is done via the C-style stdio library and **not** iostreams.
- Do not use so-called "alternative tokens" like ``and``, ``or``,
``not`` and similar, but rather use the corresponding operators
``&&``, ``||``, and ``!``. The alternative tokens are not available
by default on all compilers, and also we want to maintain a consistent
programming style.
- Output to the screen and the logfile should be using the corresponding
FILE pointers and only be done on MPI rank 0. Use the :cpp:func:`utils::logmesg`
convenience function where possible.

41
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@ -80,6 +80,7 @@ page gives those details.
* :ref:`ML-HDNNP <PKG-ML-HDNNP>`
* :ref:`ML-IAP <PKG-ML-IAP>`
* :ref:`ML-PACE <PKG-ML-PACE>`
* :ref:`ML-POD <PKG-ML-POD>`
* :ref:`ML-QUIP <PKG-ML-QUIP>`
* :ref:`ML-RANN <PKG-ML-RANN>`
* :ref:`ML-SNAP <PKG-ML-SNAP>`
@ -200,6 +201,7 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
* :doc:`Howto spherical <Howto_spherical>`
* :doc:`pair_style gayberne <pair_gayberne>`
* :doc:`pair_style resquared <pair_resquared>`
* :doc:`pair_style ylz <pair_ylz>`
* `doc/PDF/pair_gayberne_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
* examples/ASPHERE
@ -864,7 +866,7 @@ ELECTRODE package
The ELECTRODE package allows the user to enforce a constant potential method for
groups of atoms that interact with the remaining atoms as electrolyte.
**Authors:** The ELECTRODE library is written and maintained by Ludwig
**Authors:** The ELECTRODE package is written and maintained by Ludwig
Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
Robert Meissner (TUHH, Hamburg, Germany).
@ -877,7 +879,7 @@ This package has :ref:`specific installation instructions <electrode>` on the
**Supporting info:**
* :doc:`fix electrode/conp <fix_electrode_conp>`
* :doc:`fix electrode/conp <fix_electrode>`
----------
@ -1736,8 +1738,6 @@ must be installed.
.. versionadded:: 30Jun2020
.. versionadded:: 30Jun2020
**Supporting info:**
* src/ML-IAP: filenames -> commands
@ -1797,6 +1797,39 @@ This package has :ref:`specific installation instructions <ml-pace>` on the
----------
.. _PKG-ML-POD:
ML-POD package
-------------------
**Contents:**
A pair style and fitpod style for Proper Orthogonal Descriptors
(POD). POD is a methodology for deriving descriptors based on the proper
orthogonal decomposition. The ML-POD package provides an efficient
implementation for running simulations with POD potentials, along with
fitting the potentials natively in LAMMPS.
**Authors:**
Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia)
.. versionadded:: TBD
**Install:**
This package has :ref:`specific installation instructions <ml-pod>` on the
:doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/ML-POD: filenames -> commands
* :doc:`pair_style pod <pair_pod>`
* :doc:`command_style fitpod <fitpod_command>`
* examples/PACKAGES/pod
----------
.. _PKG-ML-QUIP:
ML-QUIP package

7
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@ -155,7 +155,7 @@ whether an extra library is needed to build and use the package:
- no
* - :ref:`ELECTRODE <PKG-ELECTRODE>`
- electrode charges to match potential
- :doc:`fix electrode/conp <fix_electrode_conp>`
- :doc:`fix electrode/conp <fix_electrode>`
- PACKAGES/electrode
- no
* - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
@ -298,6 +298,11 @@ whether an extra library is needed to build and use the package:
- :doc:`pair pace <pair_pace>`
- PACKAGES/pace
- ext
* - :ref:`ML-POD <PKG-ML-POD>`
- Proper orthogonal decomposition potentials
- :doc:`pair pod <pair_pod>`
- pod
- ext
* - :ref:`ML-QUIP <PKG-ML-QUIP>`
- QUIP/libatoms interface
- :doc:`pair_style quip <pair_quip>`

4
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@ -58,7 +58,7 @@ against invalid accesses.
Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
these objects provide access to their data (id, type, position, velocity, force, etc.):
.. code-block:: Python
.. code-block:: python
# access first atom
L.atoms[0].id
@ -71,7 +71,7 @@ against invalid accesses.
Some attributes can be changed:
.. code-block:: Python
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)

2
doc/src/Python_config.rst
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@ -4,7 +4,7 @@ Configuration information
The following methods can be used to query the LAMMPS library
about compile time settings and included packages and styles.
.. code-block:: Python
.. code-block:: python
:caption: Example for using configuration settings functions
from lammps import lammps

6
doc/src/Python_create.rst
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@ -74,7 +74,7 @@ Here are simple examples using all three Python interfaces:
:py:class:`PyLammps <lammps.PyLammps>` objects can also be created on top of an existing
:py:class:`lammps <lammps.lammps>` object:
.. code-block:: Python
.. code-block:: python
from lammps import lammps, PyLammps
...
@ -113,7 +113,7 @@ Here are simple examples using all three Python interfaces:
You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object:
.. code-block:: Python
.. code-block:: python
from lammps import lammps, IPyLammps
...
@ -142,7 +142,7 @@ the MPI and/or Kokkos environment if enabled and active.
Note that you can create multiple LAMMPS objects in your Python
script, and coordinate and run multiple simulations, e.g.
.. code-block:: Python
.. code-block:: python
from lammps import lammps
lmp1 = lammps()

2
doc/src/Python_error.rst
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@ -7,7 +7,7 @@ current Python process with an error message. C++ exceptions allow capturing
them on the C++ side and rethrowing them on the Python side. This way
LAMMPS errors can be handled through the Python exception handling mechanism.
.. code-block:: Python
.. code-block:: python
from lammps import lammps, MPIAbortException

8
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@ -60,7 +60,7 @@ it is possible to "compute" what the next LAMMPS command should be.
can be executed using with the lammps API with the following Python code if ``lmp`` is an
instance of :py:class:`lammps <lammps.lammps>`:
.. code-block:: Python
.. code-block:: python
from lammps import lammps
@ -73,7 +73,7 @@ it is possible to "compute" what the next LAMMPS command should be.
The arguments of the command can be passed as one string, or
individually.
.. code-block:: Python
.. code-block:: python
from lammps import PyLammps
@ -93,14 +93,14 @@ it is possible to "compute" what the next LAMMPS command should be.
parameterization. In the lammps API parameterization needed to be done
manually by creating formatted command strings.
.. code-block:: Python
.. code-block:: python
lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
In contrast, methods of PyLammps accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: Python
.. code-block:: python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)

2
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@ -56,7 +56,7 @@ and you should see the same output as if you had typed
Note that without the mpi4py specific lines from ``test.py``
.. code-block:: Python
.. code-block:: python
from lammps import lammps
lmp = lammps()

34
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@ -38,6 +38,40 @@ using the NumPy access method.
for n in np.nditer(nlist):
print(" atom {} with ID {}".format(n,tags[n]))
Another example for extracting a full neighbor list without evaluating a
potential is shown below.
.. code-block:: python
from lammps import lammps
import numpy as np
lmp = lammps()
lmp.commands_string("""
newton off
region box block -2 2 -2 2 -2 2
lattice fcc 1.0
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style zero 1.0 full
pair_coeff * *
run 0 post no""")
# look up the neighbor list
nlidx = lmp.find_pair_neighlist('zero')
nl = lmp.numpy.get_neighlist(nlidx)
tags = lmp.extract_atom('id')
print("full neighbor list with {} entries".format(nl.size))
# print neighbor list contents
for i in range(0,nl.size):
idx, nlist = nl.get(i)
print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
if nlist.size > 0:
for n in np.nditer(nlist):
pass
print(" atom {} with ID {}".format(n,tags[n]))
**Methods:**
* :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index

6
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@ -76,7 +76,7 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: Python
.. code-block:: python
L.variable("a index 2")
@ -85,14 +85,14 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
you can access an individual variable by retrieving a variable object from the
``L.variables`` dictionary by name
.. code-block:: Python
.. code-block:: python
a = L.variables['a']
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: Python
.. code-block:: python
print(a.value)
a.value = 4

2
doc/src/Python_properties.rst
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@ -105,7 +105,7 @@ against invalid accesses.
variables, compute or fix data (see :doc:`Howto_output`):
.. code-block:: Python
.. code-block:: python
result = L.eval("ke") # kinetic energy
result = L.eval("pe") # potential energy

4
doc/src/Python_scatter.rst
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@ -1,7 +1,7 @@
Scatter/gather operations
=========================
.. code-block:: Python
.. code-block:: python
data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID
# name = "x", "charge", "type", etc
@ -42,7 +42,7 @@ For the scatter methods, the array of coordinates passed to must be a
ctypes vector of ints or doubles, allocated and initialized something
like this:
.. code-block:: Python
.. code-block:: python
from ctypes import c_double
natoms = lmp.get_natoms()

9
doc/src/Run_basics.rst
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@ -30,12 +30,13 @@ executable itself can be placed elsewhere.
.. note::
The redirection operator "<" will not always work when running
in parallel with mpirun or mpiexec; for those systems the -in form is required.
The redirection operator "<" will not always work when running in
parallel with ``mpirun`` or ``mpiexec``; for those systems the -in
form is required.
As LAMMPS runs it prints info to the screen and a logfile named
*log.lammps*\ . More info about output is given on the
:doc:`screen and logfile output <Run_output>` page.
*log.lammps*\ . More info about output is given on the :doc:`screen and
logfile output <Run_output>` page.
If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING

22
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@ -93,13 +93,13 @@ switch is not set (the default), LAMMPS will operate as if the KOKKOS
package were not installed; i.e. you can run standard LAMMPS or with
the GPU or OPENMP packages, for testing or benchmarking purposes.
Additional optional keyword/value pairs can be specified which
determine how Kokkos will use the underlying hardware on your
platform. These settings apply to each MPI task you launch via the
"mpirun" or "mpiexec" command. You may choose to run one or more MPI
tasks per physical node. Note that if you are running on a desktop
machine, you typically have one physical node. On a cluster or
supercomputer there may be dozens or 1000s of physical nodes.
Additional optional keyword/value pairs can be specified which determine
how Kokkos will use the underlying hardware on your platform. These
settings apply to each MPI task you launch via the ``mpirun`` or
``mpiexec`` command. You may choose to run one or more MPI tasks per
physical node. Note that if you are running on a desktop machine, you
typically have one physical node. On a cluster or supercomputer there
may be dozens or 1000s of physical nodes.
Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
@ -148,9 +148,9 @@ one of these 4 environment variables
MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
which are initialized by the "srun", "mpirun" or "mpiexec" commands.
The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.
which are initialized by the ``srun``, ``mpirun``, or ``mpiexec``
commands. The environment variable setting for each MPI rank is used to
assign a unique GPU ID to the MPI task.
.. parsed-literal::
@ -262,6 +262,8 @@ Disable generating a citation reminder (see above) at all.
**-nonbuf**
.. versionadded:: 15Sep2022
Turn off buffering for screen and logfile output. For performance
reasons, output to the screen and logfile is usually buffered, i.e.
output is only written to a file if its buffer - typically 4096 bytes -

59
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@ -16,46 +16,47 @@ simulation. An example set of statistics is shown here:
.. parsed-literal::
Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
Loop time of 0.942801 on 4 procs for 300 steps with 2004 atoms
Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
97.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 54.985 ns/day, 0.436 hours/ns, 318.201 timesteps/s, 637.674 katom-step/s
195.2% CPU use with 2 MPI tasks x 2 OpenMP threads
MPI task timings breakdown:
MPI task timing breakdown:
Section \| min time \| avg time \| max time \|%varavg\| %total
---------------------------------------------------------------
Pair \| 1.9808 \| 2.0134 \| 2.0318 \| 1.4 \| 71.60
Bond \| 0.0021894 \| 0.0060319 \| 0.010058 \| 4.7 \| 0.21
Kspace \| 0.3207 \| 0.3366 \| 0.36616 \| 3.1 \| 11.97
Neigh \| 0.28411 \| 0.28464 \| 0.28516 \| 0.1 \| 10.12
Comm \| 0.075732 \| 0.077018 \| 0.07883 \| 0.4 \| 2.74
Output \| 0.00030518 \| 0.00042665 \| 0.00078821 \| 1.0 \| 0.02
Modify \| 0.086606 \| 0.086631 \| 0.086668 \| 0.0 \| 3.08
Other \| \| 0.007178 \| \| \| 0.26
Pair \| 0.61419 \| 0.62872 \| 0.64325 \| 1.8 \| 66.69
Bond \| 0.0028608 \| 0.0028899 \| 0.002919 \| 0.1 \| 0.31
Kspace \| 0.12652 \| 0.14048 \| 0.15444 \| 3.7 \| 14.90
Neigh \| 0.10242 \| 0.10242 \| 0.10242 \| 0.0 \| 10.86
Comm \| 0.026753 \| 0.027593 \| 0.028434 \| 0.5 \| 2.93
Output \| 0.00018341 \| 0.00030942 \| 0.00043542 \| 0.0 \| 0.03
Modify \| 0.039117 \| 0.039348 \| 0.039579 \| 0.1 \| 4.17
Other \| \| 0.001041 \| \| \| 0.11
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177007 ave 180562 max 170212 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nlocal: 1002 ave 1006 max 998 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8670.5 ave 8691 max 8650 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354010 ave 357257 max 350763 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Total # of neighbors = 708020
Ave neighs/atom = 353.30339
Ave special neighs/atom = 2.3403194
Neighbor list builds = 26
Dangerous builds = 0
----------
The first section provides a global loop timing summary. The *loop
time* is the total wall-clock time for the simulation to run. The
*Performance* line is provided for convenience to help predict how
long it will take to run a desired physical simulation. The *CPU use*
line provides the CPU utilization per MPI task; it should be close to
100% times the number of OpenMP threads (or 1 of not using OpenMP).
Lower numbers correspond to delays due to file I/O or insufficient
thread utilization.
The first section provides a global loop timing summary. The *loop time*
is the total wall-clock time for the simulation to run. The
*Performance* line is provided for convenience to help predict how long
it will take to run a desired physical simulation and to have numbers
useful for performance comparison between different simulation settings
or system sizes. The *CPU use* line provides the CPU utilization per
MPI task; it should be close to 100% times the number of OpenMP threads
(or 1 of not using OpenMP). Lower numbers correspond to delays due to
file I/O or insufficient thread utilization.
----------

13
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@ -76,10 +76,11 @@ instructions.
**Run with the GPU package from the command line:**
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the ``mpirun`` command in MPICH does this via
its ``-np`` and ``-ppn`` switches. Ditto for OpenMPI via ``-np`` and
``-npernode``.
When using the GPU package, you cannot assign more than one GPU to a
single MPI task. However multiple MPI tasks can share the same GPU,
@ -129,8 +130,8 @@ GPU package pair styles.
**Or run with the GPU package by editing an input script:**
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and use of multiple MPI tasks/GPU is the same.
The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
tasks/node, and use of multiple MPI tasks/GPU is the same.
Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
"gpu" suffix to individual styles in your input script, e.g.

17
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@ -72,12 +72,12 @@ See the :ref:`Build extras <kokkos>` page for instructions.
Running LAMMPS with the KOKKOS package
""""""""""""""""""""""""""""""""""""""
All Kokkos operations occur within the context of an individual MPI
task running on a single node of the machine. The total number of MPI
tasks used by LAMMPS (one or multiple per compute node) is set in the
usual manner via the mpirun or mpiexec commands, and is independent of
Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
-npernode switches. Ditto for MPICH via -np and -ppn.
All Kokkos operations occur within the context of an individual MPI task
running on a single node of the machine. The total number of MPI tasks
used by LAMMPS (one or multiple per compute node) is set in the usual
manner via the ``mpirun`` or ``mpiexec`` commands, and is independent of
Kokkos. E.g. the mpirun command in OpenMPI does this via its ``-np`` and
``-npernode`` switches. Ditto for MPICH via ``-np`` and ``-ppn``.
Running on a multi-core CPU
^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -168,7 +168,7 @@ for your MPI installation), binding can be forced with these flags:
.. parsed-literal::
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
For binding threads with KOKKOS OpenMP, use thread affinity environment
@ -310,7 +310,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
The discussion above for building LAMMPS with the KOKKOS package, the
mpirun/mpiexec command, and setting appropriate thread are the same.
``mpirun`` or ``mpiexec`` command, and setting appropriate thread
properties are the same.
You must still use the "-k on" :doc:`command-line switch <Run_options>`
to enable the KOKKOS package, and specify its additional arguments for

8
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@ -33,8 +33,8 @@ These examples assume one or more 16-core nodes.
mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task
The mpirun or mpiexec command sets the total number of MPI tasks used
by LAMMPS (one or multiple per compute node) and the number of MPI
The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
used by LAMMPS (one or multiple per compute node) and the number of MPI
tasks used per node. E.g. the mpirun command in MPICH does this via
its -np and -ppn switches. Ditto for OpenMPI via -np and -npernode.
@ -58,8 +58,8 @@ OMP_NUM_THREADS environment variable.
Or run with the OPENMP package by editing an input script
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
The discussion above for the mpirun/mpiexec command, MPI tasks/node,
and threads/MPI task is the same.
The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
tasks/node, and threads/MPI task is the same.
Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
"omp" suffix to individual styles in your input script, e.g.

24
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@ -117,33 +117,15 @@ script.
with all its accelerator packages installed. Note however that the
INTEL and KOKKOS packages require you to choose one of their
hardware options when building for a specific platform. I.e. CPU or
Phi option for the INTEL package. Or the OpenMP, Cuda, or Phi
option for the KOKKOS package.
Phi option for the INTEL package. Or the OpenMP, CUDA, HIP, SYCL,
or Phi option for the KOKKOS package. Or the OpenCL, HIP, or CUDA
option for the GPU package.
These are the exceptions. You cannot build a single executable with:
* both the INTEL Phi and KOKKOS Phi options
* the INTEL Phi or Kokkos Phi option, and the GPU package
See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (GPU, KOKKOS with Cuda), including
settings to build the needed auxiliary GPU libraries for Kepler GPUs:
.. code-block:: bash
Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.
Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those directories.
As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS website gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem

18
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@ -25,23 +25,25 @@ The *gaussian* angle style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(\theta-\theta_{i})^2}{w_i^2}\right) \right)
This analytical form is a suitable potential for obtaining mesoscale
effective force fields which can reproduce target atomistic
distributions :ref:`(Milano) <Milano1>`.
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`T` temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`A_1` (> 0, radians)
* :math:`w_1` (> 0, radians)
* :math:`\theta_1` (degrees)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`A_n` (> 0, radians)
* :math:`w_n` (> 0, radians)
* :math:`\theta_n` (degrees)

27
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@ -91,7 +91,7 @@ quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *charge* | charge | atomic system with charges |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dielectric* | dipole, area, curvature | system with surface polarization |
| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dipole* | charge and dipole moment | system with dipolar particles |
+--------------+-----------------------------------------------------+--------------------------------------+
@ -180,16 +180,21 @@ vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a
boundary element. For physical particles, the per-particle properties
are the same as atom_style full. For interface particles, in addition
to these properties, each particle also has an area, a normal unit
vector, a mean local curvature, the mean and difference of the
dielectric constants of two sides of the interface, and the local
dielectric constant at the boundary element. The distinction between
the physical and interface particles is only meaningful when :doc:`fix
polarize <fix_polarize>` commands are applied to the interface
particles.
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
For the *dipole* style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size

8
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@ -45,6 +45,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
The *bpm/rotational* bond style computes forces and torques based on
deviations from the initial reference state of the two atoms. The
reference state is stored by each bond when it is first computed in
@ -211,9 +213,9 @@ command, as *b1*, *b2*, ..., *b7*\ .
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the BPM
package. See the :doc:`Build package <Build_package>` doc page for
more info.
This bond style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default if pair interactions are to be disabled, this bond style
requires setting

8
doc/src/bond_bpm_spring.rst
View File

@ -45,6 +45,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
The *bpm/spring* bond style computes forces and torques based on
deviations from the initial reference state of the two atoms. The
reference state is stored by each bond when it is first computed in
@ -167,9 +169,9 @@ extra quantity can be accessed by the
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the BPM
package. See the :doc:`Build package <Build_package>` doc page for
more info.
This bond style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default if pair interactions are to be disabled, this bond style
requires setting

2
doc/src/bond_coeff.rst
View File

@ -21,7 +21,7 @@ Examples
bond_coeff 5 80.0 1.2
bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
bond_coeff 1 harmonic 200.0 1.0 # (for bond_style hybrid)
labelmap bond 5 carbonyl
bond_coeff carbonyl 80.0 1.2

25
doc/src/bond_gaussian.rst
View File

@ -25,33 +25,34 @@ The *gaussian* bond style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-2(r-r_{i})^2}{w_i^2}\right)\right)
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
This analytical form is a suitable potential for obtaining mesoscale
effective force fields which can reproduce target atomistic
distributions :ref:`(Milano) <Milano0>`
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`T` temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`r_1` (length)
* :math:`A_1` (> 0, distance)
* :math:`w_1` (> 0, distance)
* :math:`r_1` (>= 0, distance)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`r_n` (length)
* :math:`A_n` (> 0, distance)
* :math:`w_n` (> 0, distance)
* :math:`r_n` (>= 0, distance)
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>` doc
page for more info.
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""

10
doc/src/bond_mm3.rst
View File

@ -26,14 +26,14 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
.. math::
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + \frac{7}{12} 2.55^2(r-r_0)^2 \right]
where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
prefactor. The anharmonic prefactors have units angstrom\^(-n):
-2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
prefactor. The anharmonic prefactors have units :math:`\AA^{-n}`:
:math:`-2.55 \AA^{-1}` and :math:`\frac{7}{12} 2.55^2 \AA^{-2}`. The code takes
care of the necessary unit conversion for these factors internally.
Note that the MM3 papers contains an error in Eq (1):
(7/12)2.55 should be replaced with (7/12)2.55\^2
Note that the MM3 papers contain an error in Eq (1):
:math:`\frac{7}{12} 2.55` should be replaced with :math:`\frac{7}{12} 2.55^2`
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in

19
doc/src/bond_quartic.rst
View File

@ -28,11 +28,18 @@ The *quartic* bond style uses the potential
.. math::
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
E & = E_q + E_{LJ} \\
E_q & = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 \\
E_{LJ} & = \left\{ \begin{array} {l@{\quad:\quad}l}
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon & r < 2^{\frac{1}{6}}, \epsilon = 1, \sigma = 1 \\
0 & r >= 2^{\frac{1}{6}}
\end{array} \right.
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The :math:`\sigma` and :math:`\epsilon` used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
due to a polymer being stretched). The :math:`\sigma` and
:math:`\epsilon` used in the LJ portion of the formula are both set
equal to 1.0 by LAMMPS and the LJ portion is cut off at its minimum,
i.e. at :math:`r_c = 2^{\frac{1}{6}}`.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@ -46,9 +53,9 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`U_0` (energy)
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0`
are used, the following choice of parameters gives a quartic potential that
looks nearly like the FENE potential:
coarse-grained polymer chains. When monomers with :math:`\sigma =
\epsilon = 1.0` are used, the following choice of parameters gives a
quartic potential that looks nearly like the FENE potential:
.. math::

70
doc/src/box.rst
View File

@ -1,70 +0,0 @@
.. index:: box
box command
===========
Syntax
""""""
.. code-block:: LAMMPS
box keyword value ...
* one or more keyword/value pairs may be appended
* keyword = *tilt*
.. parsed-literal::
*tilt* value = *small* or *large*
Examples
""""""""
.. code-block:: LAMMPS
box tilt large
box tilt small
Description
"""""""""""
Set attributes of the simulation box.
For triclinic (non-orthogonal) simulation boxes, the *tilt* keyword
allows simulation domains to be created with arbitrary tilt factors,
e.g. via the :doc:`create_box <create_box>` or
:doc:`read_data <read_data>` commands. Tilt factors determine how
skewed the triclinic box is; see the :doc:`Howto triclinic <Howto_triclinic>` page for a discussion of triclinic
boxes in LAMMPS.
LAMMPS normally requires that no tilt factor can skew the box more
than half the distance of the parallel box length, which is the first
dimension in the tilt factor (x for xz). If *tilt* is set to
*small*, which is the default, then an error will be
generated if a box is created which exceeds this limit. If *tilt*
is set to *large*, then no limit is enforced. You can create
a box with any tilt factors you wish.
Note that if a simulation box has a large tilt factor, LAMMPS will run
less efficiently, due to the large volume of communication needed to
acquire ghost atoms around a processor's irregular-shaped sub-domain.
For extreme values of tilt, LAMMPS may also lose atoms and generate an
error.
Restrictions
""""""""""""
This command cannot be used after the simulation box is defined by a
:doc:`read_data <read_data>` or :doc:`create_box <create_box>` command or
:doc:`read_restart <read_restart>` command.
Related commands
""""""""""""""""
none
Default
"""""""
The default value is tilt = small.

15
doc/src/clear.rst
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@ -23,15 +23,16 @@ Description
"""""""""""
This command deletes all atoms, restores all settings to their default
values, and frees all memory allocated by LAMMPS. Once a clear
command has been executed, it is almost as if LAMMPS were starting
over, with only the exceptions noted below. This command enables
multiple jobs to be run sequentially from one input script.
values, and frees all memory allocated by LAMMPS. Once a clear command
has been executed, it is almost as if LAMMPS were starting over, with
only the exceptions noted below. This command enables multiple jobs to
be run sequentially from one input script.
These settings are not affected by a clear command: the working
directory (:doc:`shell <shell>` command), log file status
(:doc:`log <log>` command), echo status (:doc:`echo <echo>` command), and
input script variables (:doc:`variable <variable>` command).
directory (:doc:`shell <shell>` command), log file status (:doc:`log
<log>` command), echo status (:doc:`echo <echo>` command), and input
script variables except for *atomfile* style variables (:doc:`variable
<variable>` command).
Restrictions
""""""""""""

5
doc/src/commands_list.rst
View File

@ -13,7 +13,6 @@ Commands
bond_style
bond_write
boundary
box
change_box
clear
comm_modify
@ -43,6 +42,7 @@ Commands
echo
fix
fix_modify
fitpod_command
group
group2ndx
hyper
@ -90,8 +90,7 @@ Commands
region
replicate
rerun
reset_atom_ids
reset_mol_ids
reset_atoms
reset_timestep
restart
run

3
doc/src/compute_chunk_atom.rst
View File

@ -602,8 +602,7 @@ be used. For non-orthogonal (triclinic) simulation boxes, only the
*reduced* option may be used.
A *box* value selects standard distance units as defined by the
:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
for units = *real* or *metal*).
:doc:`units <units>` command (e.g., :math:`\AA` for units = *real* or *metal*).
A *lattice* value means the distance units are in lattice spacings.
The :doc:`lattice <lattice>` command must have been previously used to
define the lattice spacing. A *reduced* value means normalized

4
doc/src/compute_displace_atom.rst
View File

@ -17,7 +17,7 @@ Syntax
.. parsed-literal::
*replace* arg = name of per-atom variable
*refresh* arg = name of per-atom variable
Examples
""""""""
@ -95,7 +95,7 @@ something like the following commands:
refresh c_dsp delay 100
The :doc:`dump_modify thresh <dump_modify>` command will only output
atoms that have displaced more than :math:`0.6~\mathrm{\mathring A}` on each
atoms that have displaced more than :math:`0.6~\AA` on each
snapshot (assuming metal units). The dump_modify *refresh* option triggers a
call to this compute at the end of every dump.

4
doc/src/compute_entropy_atom.rst
View File

@ -97,13 +97,13 @@ by the corresponding volume. This option can be useful when dealing with
inhomogeneous systems such as those that have surfaces.
Here are typical input parameters for fcc aluminum (lattice
constant :math:`4.05~\mathrm{\mathring A}`),
constant :math:`4.05~\AA`),
.. parsed-literal::
compute 1 all entropy/atom 0.25 5.7 avg yes 3.7
and for bcc sodium (lattice constant 4.23 Angstroms),
and for bcc sodium (lattice constant :math:`4.23~\AA`),
.. parsed-literal::

7
doc/src/compute_nbond_atom.rst
View File

@ -23,6 +23,8 @@ Examples
Description
"""""""""""
.. versionadded:: 4May2022
Define a computation that computes the number of bonds each atom is
part of. Bonds which are broken are not counted in the tally. See
the :doc:`Howto broken bonds <Howto_bpm>` page for more information.
@ -40,8 +42,9 @@ LAMMPS output options.
Restrictions
""""""""""""
This fix can only be used if LAMMPS was built with the BPM package.
See the :doc:`Build package <Build_package>` doc page for more info.
This compute is part of the BPM 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
""""""""""""""""

2
doc/src/compute_pair_local.rst
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@ -59,7 +59,7 @@ 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 lower to the one with the higher id.
distance from the atom of higher to the one with the lower atom ID.
The value *eng* is the interaction energy for the pair of atoms.

22
doc/src/compute_rigid_local.rst
View File

@ -6,7 +6,7 @@ compute rigid/local command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID rigid/local rigidID input1 input2 ...
@ -25,6 +25,9 @@ Syntax
quatw, quati, quatj, quatk,
tqx, tqy, tqz,
inertiax, inertiay, inertiaz
.. parsed-literal::
id = atom ID of atom within body which owns body properties
mol = molecule ID used to define body in :doc:`fix rigid/small <fix_rigid>` command
mass = total mass of body
@ -69,8 +72,8 @@ the atoms owned on a processor. If the atom is not in the specified
the atom within a body that is assigned to store the body information
it is skipped (only one atom per body is so assigned). If it is the
assigned atom, then the info for that body is output. This means that
information for N bodies is generated. N may be less than the # of
bodies defined by the fix rigid command, if the atoms in some bodies
information for :math:`N` bodies is generated. :math:`N` may be less than the
number of bodies defined by the fix rigid command, if the atoms in some bodies
are not in the *group-ID*\ .
.. note::
@ -109,8 +112,7 @@ The *mass* attribute is the total mass of the rigid body.
There are two options for outputting the coordinates of the center of
mass (COM) of the body. The *x*, *y*, *z* attributes write the COM
"unscaled", in the appropriate distance :doc:`units <units>`
(:math:`\mathrm{\mathring A}`,
sigma, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
(:math:`\AA`, :math:`\sigma`, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
the image flags for each body. Unwrapped means that if the body
COM has passed through a periodic boundary one or more times, the value
is generated what the COM coordinate would be if it had not been
@ -120,7 +122,7 @@ The image flags for the body can be generated directly using the *ix*,
*iy*, *iz* attributes. For periodic dimensions, they specify which
image of the simulation box the COM 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
box lengths to get the true value. A value of :math:`-1` means subtract 1 box
length to get the true value. LAMMPS updates these flags as the rigid
body COMs cross periodic boundaries during the simulation.
@ -142,8 +144,8 @@ The *tqx*, *tqy*, *tqz* attributes are components of the torque acting
on the body around its COM.
The *inertiax*, *inertiay*, *inertiaz* attributes are components of
diagonalized inertia tensor for the body, i.e the 3 moments of inertia
for the body around its principal axes, as computed internally by
diagonalized inertia tensor for the body (i.e., the three moments of inertia
for the body around its principal axes), as computed internally by
LAMMPS.
----------
@ -170,10 +172,10 @@ corresponding attribute is in:
* vx,vy,vz = velocity units
* fx,fy,fz = force units
* omegax,omegay,omegaz = radians/time units
* angmomx,angmomy,angmomz = mass\*distance\^2/time units
* angmomx,angmomy,angmomz = mass\*distance\ :math:`^2`\ /time units
* quatw,quati,quatj,quatk = unitless
* tqx,tqy,tqz = torque units
* inertiax,inertiay,inertiaz = mass\*distance\^2 units
* inertiax,inertiay,inertiaz = mass\*distance\ :math:`^2` units
Restrictions
""""""""""""

2
doc/src/compute_saed.rst
View File

@ -86,7 +86,7 @@ will defined using the *c* values for the spacing along each reciprocal
lattice axis. Note that manual mapping of the reciprocal space mesh is
good for comparing diffraction results from multiple simulations; however
it can reduce the likelihood that Bragg reflections will be satisfied
unless small spacing parameters (:math:`<0.05~\mathrm{\mathring A}^-1`)
unless small spacing parameters (:math:`<0.05~\AA^-1`)
are implemented. Meshes with manual spacing do not require a periodic
boundary.

2
doc/src/compute_temp_ramp.rst
View File

@ -58,7 +58,7 @@ constant, and :math:`T` is the absolute temperature.
The *units* keyword determines the meaning of the distance units used
for coordinates (*clo*, *chi*) and velocities (*vlo*, *vhi*). A *box* value
selects standard distance units as defined by the :doc:`units <units>`
command (e.g., :math:`\mathrm{\mathring{A}}` for units = real or metal). A
command (e.g., :math:`\AA` for units = real or metal). A
*lattice* value means the distance units are in lattice spacings (i.e.,
velocity in lattice spacings per unit time). The :doc:`lattice <lattice>`
command must have been previously used to define the lattice spacing.

2
doc/src/compute_voronoi_atom.rst
View File

@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command
* voronoi/atom = style name of this compute command
* zero or more keyword/value pairs may be appended
* keyword = *only_group* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
* keyword = *only_group* or *occupation* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
.. parsed-literal::

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