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Merge branch 'develop' into gran-temp

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This commit is contained in:
jtclemm
2022-11-01 14:10:28 -06:00
committed by GitHub
parent 88be5a3781 a001707b22
commit f671cd7765
5545 changed files with 583048 additions and 69653 deletions
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1
.gitattributes vendored
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@ -3,6 +3,7 @@
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore
CITATION.cff export-ignore
* text=auto
*.jpg -text
*.pdf -text

6
.github/CODEOWNERS vendored
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@ -13,20 +13,21 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/AMOEBA/* @sjplimp
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/BROWNIAN/* @samueljmcameron
src/CG-DNA/* @ohenrich
src/CG-SDK/* @akohlmey
src/CG-SPICA/* @yskmiyazaki
src/COLVARS/* @giacomofiorin
src/DIELECTRIC/* @ndtrung81
src/ELECTRODE/* @ludwig-ahrens
src/FEP/* @agiliopadua
src/ML-HDNNP/* @singraber
src/INTEL/* @wmbrownintel
@ -133,6 +134,7 @@ tools/coding_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/offline/* @rbberger
tools/vim/* @hammondkd
# tests
unittest/* @akohlmey @rbberger

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/codecov.yml vendored
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@ -7,7 +7,7 @@ coverage:
threshold: 10%
only_pulls: false
branches:
- "master"
- "develop"
flags:
- "unit"
paths:
@ -16,14 +16,14 @@ coverage:
project:
default:
branches:
- "master"
- "develop"
paths:
- "src"
informational: true
patch:
default:
branches:
- "master"
- "develop"
paths:
- "src"
informational: true

6
.github/dependabot.yml vendored Normal file
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@ -0,0 +1,6 @@
version: 2
updates:
- package-ecosystem: "github-actions"
directory: "/"
schedule:
interval: "weekly"

13
.github/workflows/codeql-analysis.yml vendored
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@ -13,6 +13,11 @@ jobs:
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
permissions:
security-events: write
actions: read
contents: read
strategy:
fail-fast: false
matrix:
@ -20,17 +25,17 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 2
- name: Setup Python
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: '3.x'
- name: Initialize CodeQL
uses: github/codeql-action/init@v1
uses: github/codeql-action/init@v2
with:
languages: ${{ matrix.language }}
config-file: ./.github/codeql/${{ matrix.language }}.yml
@ -48,4 +53,4 @@ jobs:
cmake --build . --parallel 2
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v1
uses: github/codeql-action/analyze@v2

10
.github/workflows/compile-msvc.yml vendored
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@ -3,7 +3,11 @@ name: "Native Windows Compilation and Unit Tests"
on:
push:
branches: [develop]
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
@ -15,12 +19,12 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 2
- name: Select Python version
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: '3.10'

103
.github/workflows/coverity.yml vendored Normal file
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@ -0,0 +1,103 @@
name: "Run Coverity Scan"
on:
schedule:
- cron: "0 0 * * FRI"
workflow_dispatch:
jobs:
analyze:
name: Analyze
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
container:
image: lammps/buildenv:ubuntu20.04
steps:
- name: Checkout repository
uses: actions/checkout@v3
with:
fetch-depth: 2
- name: Create Build and Download Folder
run: mkdir build download
- name: Cache Coverity
id: cache-coverity
uses: actions/cache@v3
with:
path: ./download/
key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}
- name: Download Coverity if necessary
if: steps.cache-coverity.outputs.cache-hit != 'true'
working-directory: download
run: |
wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS" -O coverity_tool.tgz
wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS&md5=1" -O coverity_tool.md5
echo " coverity_tool.tgz" >> coverity_tool.md5
md5sum -c coverity_tool.md5
- name: Setup Coverity
run: |
tar xzf download/coverity_tool.tgz
ln -s cov-analysis-linux64-* coverity
- name: Configure LAMMPS via CMake
shell: bash
working-directory: build
run: |
cmake \
-C ../cmake/presets/clang.cmake \
-C ../cmake/presets/most.cmake \
-C ../cmake/presets/kokkos-openmp.cmake \
-D CMAKE_BUILD_TYPE="RelWithDebug" \
-D CMAKE_TUNE_FLAGS="-Wall -Wextra -Wno-unused-result" \
-D BUILD_MPI=on \
-D BUILD_OMP=on \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_SIZES=SMALLBIG \
-D LAMMPS_EXCEPTIONS=off \
-D PKG_MESSAGE=on \
-D PKG_MPIIO=on \
-D PKG_ATC=on \
-D PKG_AWPMD=on \
-D PKG_BOCS=on \
-D PKG_EFF=on \
-D PKG_H5MD=on \
-D PKG_INTEL=on \
-D PKG_LATBOLTZ=on \
-D PKG_MANIFOLD=on \
-D PKG_MGPT=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_MOLFILE=on \
-D PKG_NETCDF=on \
-D PKG_PTM=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-D PKG_TALLY=on \
../cmake
- name: Run Coverity Scan
shell: bash
working-directory: build
run: |
export PATH=$GITHUB_WORKSPACE/coverity/bin:$PATH
cov-build --dir cov-int cmake --build . --parallel 2
- name: Create tarball with scan results
shell: bash
working-directory: build
run: tar czf lammps.tgz cov-int
- name: Upload scan result to Coverity
shell: bash
run: |
curl --form token=${{ secrets.COVERITY_TOKEN }} \
--form email=${{ secrets.COVERITY_EMAIL }} \
--form file=@build/lammps.tgz \
--form version=${{ github.sha }} \
--form description="LAMMPS automated build" \
https://scan.coverity.com/builds?project=LAMMPS

11
.github/workflows/unittest-macos.yml vendored
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@ -3,7 +3,11 @@ name: "Unittest for MacOS"
on:
push:
branches: [develop]
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
@ -17,7 +21,7 @@ jobs:
steps:
- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
fetch-depth: 2
@ -28,7 +32,7 @@ jobs:
run: mkdir build
- name: Set up ccache
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}
@ -39,6 +43,7 @@ jobs:
working-directory: build
run: |
ccache -z
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -C ../cmake/presets/clang.cmake \
-C ../cmake/presets/most.cmake \

91
CITATION.cff Normal file
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@ -0,0 +1,91 @@
# YAML 1.2
---
cff-version: 1.2.0
title: "LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator"
type: software
authors:
- family-names: "Plimpton"
given-names: "Steven J."
- family-names: "Kohlmeyer"
given-names: "Axel"
orcid: "https://orcid.org/0000-0001-6204-6475"
- family-names: "Thompson"
given-names: "Aidan P."
orcid: "https://orcid.org/0000-0002-0324-9114"
- family-names: "Moore"
given-names: "Stan G."
- family-names: "Berger"
given-names: "Richard"
orcid: "https://orcid.org/0000-0002-3044-8266"
doi: 10.5281/zenodo.3726416
license: GPL-2.0-only
url: https://www.lammps.org
repository-code: https://github.com/lammps/lammps/
keywords:
- "Molecular Dynamics"
- "Materials Modeling"
message: "If you are referencing LAMMPS in a publication, please cite the paper below."
preferred-citation:
type: article
doi: "10.1016/j.cpc.2021.108171"
url: "https://www.sciencedirect.com/science/article/pii/S0010465521002836"
authors:
- family-names: "Thompson"
given-names: "Aidan P."
orcid: "https://orcid.org/0000-0002-0324-9114"
- family-names: "Aktulga"
given-names: "H. Metin"
- family-names: "Berger"
given-names: "Richard"
orcid: "https://orcid.org/0000-0002-3044-8266"
- family-names: "Bolintineanu"
given-names: "Dan S."
- family-names: "Brown"
given-names: "W. Michael"
- family-names: "Crozier"
given-names: "Paul S."
- family-names: "in 't Veld"
given-names: "Pieter J."
- family-names: "Kohlmeyer"
given-names: "Axel"
orcid: "https://orcid.org/0000-0001-6204-6475"
- family-names: "Moore"
given-names: "Stan G."
- family-names: "Nguyen"
given-names: "Trung Dac"
- family-names: "Shan"
given-names: "Ray"
- family-names: "Stevens"
given-names: "Mark J."
- family-names: "Tranchida"
given-names: "Julien"
- family-names: "Trott"
given-names: "Christian"
- family-names: "Plimpton"
given-names: "Steven J."
title: "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales"
journal: "Computer Physics Communications"
keywords:
- Molecular dynamics
- Materials modeling
- Parallel algorithms
- LAMMPS
month: 2
volume: 271
issn: 0010-4655
pages: 108171
year: 2022
references:
- title: "Fast Parallel Algorithms for Short-Range Molecular Dynamics"
type: article
journal: Journal of Computational Physics
volume: 117
number: 1
pages: "1-19"
year: 1995
issn: 0021-9991
doi: 10.1006/jcph.1995.1039
url: https://www.sciencedirect.com/science/article/pii/S002199918571039X
authors:
- family-names: "Plimpton"
given-names: "Steve"

4
README
View File

@ -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:

28
SECURITY.md
View File

@ -19,9 +19,9 @@ kinds of filesystem manipulations. And because of that LAMMPS should
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
either a user mistake or a bug in the code. Bugs can be reported in the
LAMMPS project [issue tracker on
GitHub](https://github.com/lammps/lammps/issues).
To mitigate issues with using homoglyphs or bidirectional reordering in
unicode, which have been demonstrated as a vector to obfuscate and hide
@ -30,10 +30,18 @@ for unicode characters and only all-ASCII source code is accepted.
# Version Updates
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.
LAMMPS follows continuous release development model. We aim to keep to
keep the development version (develop branch) always fully functional
and employ a variety of automatic testing procedures to detect failures
of existing functionality from adding or modifying features. Most of
those tests are run on pull requests *before* merging to the development
branch. The develop branch is protected, so all changes *must* be
submitted as a pull request and thus cannot avoid the automated tests.
Additional tests are run *after* merging. Before releases are made
*all* tests must have cleared. Then a release tag is applied and the
release branch fast-forwarded to that tag. Bug fixes and updates are
applied to the current development branch and thus will be available in
the next (patch) release. For stable releases, selected bug fixes are
back-ported and occasionally published as update releases. There are
only updates to the latest stable release.

96
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 ${CMAKE_REQUIRED_LIBRARIES} but use it
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
########################################
project(lammps CXX)
@ -100,7 +109,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost")
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
endif()
endif()
endif()
@ -135,10 +144,10 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if((CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Intel"))
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
@ -152,6 +161,19 @@ endif()
########################################################################
# User input options #
########################################################################
# set path to python interpreter and thus enforcing python version if
# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
else()
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
endif()
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
" Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)
@ -192,6 +214,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -200,7 +223,7 @@ set(STANDARD_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -356,17 +379,19 @@ pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(SCAFACOS MPI)
pkg_depends(AMOEBA KSPACE)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
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()
@ -375,8 +400,8 @@ endif()
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
find_package(OpenMP COMPONENTS CXX REQUIRED)
check_omp_h_include()
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
@ -400,9 +425,11 @@ endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
@ -631,7 +658,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -704,18 +731,17 @@ 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})
@ -724,6 +750,14 @@ 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)
@ -781,17 +815,23 @@ if(BUILD_SHARED_LIBS)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(BUILD_IS_MULTI_CONFIG)
set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/$<CONFIG>/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
else()
set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
set(MY_BUILD_DIR ${CMAKE_BINARY_DIR})
endif()
set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
if(Python_EXECUTABLE)
add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps -l ${LIBLAMMPS_SHARED_BINARY}
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
COMMENT "Installing LAMMPS Python module")
else()
add_custom_target(
@ -811,16 +851,25 @@ endif()
###############################################################################
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
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()
@ -931,9 +980,6 @@ 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
View File

@ -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
View File

@ -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()

208
cmake/Modules/LAMMPSInterfacePlugin.cmake Normal file
View File

@ -0,0 +1,208 @@
# CMake script code to define LAMMPS settings required for building LAMMPS plugins
# enforce out-of-source build
if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty"
CACHE STRING "URL for thirdparty package downloads")
# global LAMMPS/plugin build settings
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
if(NOT LAMMPS_SOURCE_DIR)
message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
endif()
# by default, install into $HOME/.local (not /usr/local),
# so that no root access (and sudo) is needed
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
endif()
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# C++11 is required
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
endif()
set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
#######
# helper functions from LAMMPSUtils.cmake
function(validate_option name values)
string(TOLOWER ${${name}} needle_lower)
string(TOUPPER ${${name}} needle_upper)
list(FIND ${values} ${needle_lower} IDX_LOWER)
list(FIND ${values} ${needle_upper} IDX_UPPER)
if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
message(FATAL_ERROR "\n########################################################################\n"
"Invalid value '${${name}}' for option ${name}\n"
"\n"
"Possible values are:\n"
"${POSSIBLE_VALUE_LIST}"
"########################################################################")
endif()
endfunction(validate_option)
# 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})
set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>")
foreach(_dir ${_dirs})
file(TIMESTAMP ${_dir} _newtime)
if(_newtime IS_NEWER_THAN _besttime)
set(_bestfile ${_dir})
set(_besttime ${_newtime})
endif()
endforeach()
if(_bestfile STREQUAL "<unknown>")
message(FATAL_ERROR "Could not find valid path at: ${path}")
endif()
set(${variable} ${_bestfile} PARENT_SCOPE)
endfunction()
# get LAMMPS version date
function(get_lammps_version version_header variable)
file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1\\2\\3" date "${line}")
set(${variable} "${date}" PARENT_SCOPE)
endfunction()
#################################################################################
# LAMMPS C++ interface. We only need the header related parts except on windows.
add_library(lammps INTERFACE)
target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
endif()
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
option(BUILD_MPI "Build MPI version" OFF)
endif()
if(BUILD_MPI)
# do not include the (obsolete) MPI C++ bindings which makes
# for leaner object files and avoids namespace conflicts
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${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)
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")
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)
if(LAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
endif()
endif()
target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
else()
add_library(mpi_stubs INTERFACE)
target_include_directories(mpi_stubs INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
target_link_libraries(lammps INTERFACE mpi_stubs)
endif()
################################################################################
# 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)
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
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)
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
(CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
else()
target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
endif()
target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
endif()
################
# integer size selection
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})

43
cmake/Modules/LAMMPSUtils.cmake
View File

@ -24,6 +24,39 @@ 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})
set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>")
foreach(_dir ${_dirs})
file(TIMESTAMP ${_dir} _newtime)
if(_newtime IS_NEWER_THAN _besttime)
set(_bestfile ${_dir})
set(_besttime ${_newtime})
endif()
endforeach()
if(_bestfile STREQUAL "<unknown>")
message(FATAL_ERROR "Could not find valid path at: ${path}")
endif()
set(${variable} ${_bestfile} PARENT_SCOPE)
endfunction()
function(get_lammps_version version_header variable)
file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
@ -92,14 +125,16 @@ function(FetchPotentials pkgfolder potfolder)
math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum)
if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
endif()
if(NOT sum STREQUAL oldsum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
endif()
endforeach()
endif()

12
cmake/Modules/Packages/GPU.cmake
View File

@ -233,7 +233,8 @@ elseif(GPU_API STREQUAL "OPENCL")
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined.\n"
"Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
@ -261,6 +262,8 @@ elseif(GPU_API STREQUAL "HIP")
if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "spirv")
set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "nvcc")
find_package(CUDA REQUIRED)
set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
@ -340,6 +343,13 @@ elseif(GPU_API STREQUAL "HIP")
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
DEPENDS ${CU_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
elseif(HIP_PLATFORM STREQUAL "spirv")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Gerating ${CU_NAME}.cubin")
endif()
add_custom_command(OUTPUT ${CUBIN_H_FILE}

11
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/3.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "b5c44ea961031795f434002cd7b31c20" 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 3.6.00 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()

5
cmake/Modules/Packages/LATTE.cmake
View File

@ -23,8 +23,9 @@ if(DOWNLOAD_LATTE)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
"Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
endif()
include(ExternalProject)

45
cmake/Modules/Packages/MDI.cmake
View File

@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
enable_language(C)
@ -26,8 +26,21 @@ if(DOWNLOAD_MDI)
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()
@ -36,6 +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
@ -44,8 +65,9 @@ if(DOWNLOAD_MDI)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL_MD5 ${MDI_MD5}
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
CMAKE_ARGS
-DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@ -54,24 +76,25 @@ if(DOWNLOAD_MDI)
-Dlanguage=C
-Dlibtype=STATIC
-Dmpi=${MDI_USE_MPI}
-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 "")

13
cmake/Modules/Packages/MISC.cmake Normal file
View File

@ -0,0 +1,13 @@
# pair style and fix srp/react depend on the fixes bond/break and bond/create from the MC package
if(NOT PKG_MC)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.h)
set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.cpp)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

6
cmake/Modules/Packages/ML-HDNNP.cmake
View File

@ -44,7 +44,9 @@ if(DOWNLOAD_N2P2)
else()
# get path to MPI include directory
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
foreach (_INCL ${N2P2_MPI_INCLUDE})
set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -I${_INCL}")
endforeach()
endif()
# prefer GNU make, if available. N2P2 lib seems to need it.
@ -75,7 +77,7 @@ if(DOWNLOAD_N2P2)
UPDATE_COMMAND ""
CONFIGURE_COMMAND ""
PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
BUILD_COMMAND ${N2P2_MAKE} -C <SOURCE_DIR>/src -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
BUILD_ALWAYS YES
INSTALL_COMMAND ""
BUILD_IN_SOURCE 1

23
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()
@ -25,16 +34,18 @@ if(MLIAP_ENABLE_PYTHON)
endif()
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
COMMAND ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
WORKING_DIRECTORY ${MLIAP_BINARY_DIR}
MAIN_DEPENDENCY ${MLIAP_CYTHON_SRC}
MAIN_DEPENDENCY ${MLIAP_CYTHON_FILE}
COMMENT "Generating C++ sources with cythonize...")
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
endforeach()
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
endif()

25
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.fix.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 "e0572de57039d4afedefb25707b6ceae" 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)
@ -13,24 +13,11 @@ execute_process(
COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
# enforce building libyaml-cpp as static library and turn off optional features
set(YAML_BUILD_SHARED_LIBS OFF)
set(YAML_CPP_BUILD_CONTRIB OFF)
set(YAML_CPP_BUILD_TOOLS OFF)
add_subdirectory(${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()

1
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -43,6 +43,7 @@ if(DOWNLOAD_QUIP)
file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
message(STATUS "QUIP download via git requested - we will build our own")
set(CMAKE_EP_GIT_REMOTE_UPDATE_STRATEGY CHECKOUT)
# QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
# The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
include(ExternalProject)

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}")

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

@ -1,8 +1,28 @@
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
else()
if(NOT Python_INTERPRETER)
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
find_package(Python REQUIRED COMPONENTS Interpreter Development)
target_link_libraries(lammps PRIVATE Python::Python)
endif()

7
cmake/Modules/Packages/VTK.cmake
View File

@ -1,4 +1,9 @@
find_package(VTK REQUIRED NO_MODULE)
include(${VTK_USE_FILE})
target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
if (VTK_MAJOR_VERSION VERSION_LESS 9.0)
include(${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()

3
cmake/presets/all_off.cmake
View File

@ -3,6 +3,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -11,7 +12,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/all_on.cmake
View File

@ -5,6 +5,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -13,7 +14,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

20
cmake/presets/clang.cmake
View File

@ -3,6 +3,13 @@
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()
set(FC_STD_VERSION "-std=f2003")
endif()
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
@ -21,10 +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)

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

@ -1,4 +1,5 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
ATC
AWPMD
@ -7,7 +8,7 @@ set(WIN_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -46,8 +47,8 @@ set(WIN_PACKAGES
MISC
ML-HDNNP
ML-IAP
ML-SNAP
ML-RANN
ML-SNAP
MOFFF
MOLECULE
MOLFILE
@ -56,6 +57,7 @@ set(WIN_PACKAGES
ORIENT
PERI
PHONON
PLUGIN
POEMS
PTM
QEQ

3
cmake/presets/most.cmake
View File

@ -3,13 +3,14 @@
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES
AMOEBA
ASPHERE
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

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)

3
cmake/presets/windows.cmake
View File

@ -1,11 +1,12 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

21
doc/Makefile
View File

@ -13,7 +13,7 @@ VENV = $(BUILDDIR)/docenv
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
MATHJAXTAG = 3.2.1
MATHJAXTAG = 3.2.2
PYTHON = $(word 3,$(shell type python3))
DOXYGEN = $(word 3,$(shell type doxygen))
@ -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 ;\
@ -163,6 +167,8 @@ 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 -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 "############################################" ;\
@ -242,7 +248,6 @@ $(MATHJAX):
$(ANCHORCHECK): $(VENV)
@( \
. $(VENV)/bin/activate; \
(cd utils/converters;\
python setup.py develop);\
pip $(PIP_OPTIONS) install -e utils/converters;\
deactivate;\
)

6
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "4 May 2022" "2022-5-4"
.TH LAMMPS "1" "15 September 2022" "2022-9-15"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 24 March 2022
\- Molecular Dynamics Simulator. Version 15 September 2022
.SH SYNOPSIS
.B lmp
@ -161,7 +161,7 @@ list references for specific cite-able features used during a
run.
.TP
\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
Invoke the \fBpackage\R command with <style> and optional arguments.
Invoke the \fBpackage\fR command with <style> and optional arguments.
The syntax is the same as if the command appeared in an input script.
For example "-pk gpu 2" is the same as "package gpu 2" in the input
script. The possible styles and options are discussed in the

14
doc/src/Bibliography.rst
View File

@ -368,7 +368,7 @@ Bibliography
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(GLE4MD)**
`http://gle4md.org/ <http://gle4md.org/>`_
`https://gle4md.org/ <https://gle4md.org/>`_
**(Gao)**
Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
@ -407,7 +407,7 @@ Bibliography
Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).
**(Gullet)**
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
**(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
@ -461,7 +461,7 @@ Bibliography
Hunt, Mol Simul, 42, 347 (2016).
**(IPI)**
`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
`https://ipi-code.org/ <https://ipi-code.org/>`
**(IPI-CPC)**
Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
@ -733,8 +733,8 @@ Bibliography
**(Mishin)**
Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).
**(Mitchell and Finchham)**
Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell and Fincham)**
Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell2011)**
Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).
@ -875,7 +875,7 @@ Bibliography
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
**(Park)**
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
@ -1373,7 +1373,7 @@ Bibliography
Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
**(Ziegler)**
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
**(Zimmerman2004)**
Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

12
doc/src/Build_development.rst
View File

@ -140,13 +140,23 @@ of the LAMMPS project on GitHub.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <http://pyyaml.org/>`_ library and development
It requires the `YAML <https://pyyaml.org/>`_ library and development
headers (if those are not found locally a recent version will be
downloaded and compiled along with LAMMPS and the test program) to
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::

145
doc/src/Build_extras.rst
View File

@ -123,6 +123,7 @@ CMake build
-D GPU_API=value # value = opencl (default) or cuda or hip
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D HIP_PATH # path to HIP installation. Must be set if GPU_API=HIP
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_50
@ -179,10 +180,17 @@ set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
should only use this option in preparations to run on Aurora system at ANL.
.. code:: bash
# AMDGPU target (ROCm <= 4.0)
export HIP_PLATFORM=hcc
export HIP_PATH=/path/to/HIP/install
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
@ -191,6 +199,7 @@ and the linker to work correctly.
# AMDGPU target (ROCm >= 4.1)
export HIP_PLATFORM=amd
export HIP_PATH=/path/to/HIP/install
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
@ -199,10 +208,20 @@ and the linker to work correctly.
# CUDA target (not recommended, use GPU_ARCH=cuda)
# !!! DO NOT set CMAKE_CXX_COMPILER !!!
export HIP_PLATFORM=nvcc
export HIP_PATH=/path/to/HIP/install
export CUDA_PATH=/usr/local/cuda
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
make -j 4
.. code:: bash
# SPIR-V target (Intel GPUs)
export HIP_PLATFORM=spirv
export HIP_PATH=/path/to/HIP/install
export CMAKE_CXX_COMPILER=<hipcc/clang++>
cmake -D PKG_GPU=on -D GPU_API=HIP ..
make -j 4
Traditional make
^^^^^^^^^^^^^^^^
@ -215,7 +234,7 @@ 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
@ -295,7 +314,7 @@ detailed information is available at:
In addition to installing the KIM API, it is also necessary to install the
library of KIM models (interatomic potentials).
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models
@ -331,7 +350,7 @@ 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
@ -413,7 +432,7 @@ Enabling the extra unit tests have some requirements,
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see
`Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
@ -464,6 +483,9 @@ 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)
@ -503,9 +525,21 @@ 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
@ -577,7 +611,10 @@ 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
@ -592,9 +629,12 @@ 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::
@ -790,6 +830,8 @@ library.
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
and built inside the CMake build directory. If the LATTE library
@ -797,6 +839,13 @@ library.
``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
file, not the directory the library file is in.
The LATTE library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the LATTE build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make
You can download and build the LATTE library manually if you
@ -905,7 +954,7 @@ 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
@ -962,7 +1011,7 @@ 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
@ -1025,7 +1074,7 @@ VORONOI package
-----------------------------
To build with this package, you must download and build the
`Voro++ library <http://math.lbl.gov/voro++>`_ or install a
`Voro++ library <https://math.lbl.gov/voro++>`_ or install a
binary package provided by your operating system.
.. tabs::
@ -1051,7 +1100,7 @@ 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
@ -1130,7 +1179,7 @@ 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
@ -1181,7 +1230,7 @@ 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
@ -1244,7 +1293,7 @@ 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
@ -1285,20 +1334,30 @@ 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
@ -1307,6 +1366,9 @@ 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:
@ -1506,7 +1568,7 @@ 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
@ -1562,7 +1624,7 @@ 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
@ -1699,7 +1761,7 @@ 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
@ -1868,7 +1930,7 @@ 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
@ -1913,14 +1975,25 @@ within CMake will download the non-commercial use version.
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub, if it is not
found on the local machine. This requires to have git installed. It will use the same compilers
and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
and installed QUIP library and CMake cannot find it.
CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git
installed. It will use the same compilers and flags as used for
compiling LAMMPS. Currently this is only supported for the GNU
and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
want to use a previously compiled and installed QUIP library and
CMake cannot find it.
The QUIP library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the QUIP build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make
@ -1965,7 +2038,7 @@ 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
@ -2009,7 +2082,7 @@ 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

43
doc/src/Build_manual.rst
View File

@ -48,18 +48,15 @@ Build using GNU make
The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
can be translated to different output format using the `Sphinx
<sphinx_>`_ document generator tool. It also incorporates programmer
documentation extracted from the LAMMPS C++ sources through the `Doxygen
<https://doxygen.nl>`_ program. Currently the translation to HTML, PDF
(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
readers) are supported. For that to work a Python 3 interpreter, the
``doxygen`` tools and internet access to download additional files and
tools are required. This download is usually only required once or
after the documentation folder is returned to a pristine state with
``make clean-all``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://www.sphinx-doc.org
<https://sphinx-doc.org>`_ document generator tool. It also
incorporates programmer documentation extracted from the LAMMPS C++
sources through the `Doxygen <https://doxygen.nl>`_ program. Currently
the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
and MOBI (for Amazon Kindle readers) are supported. For that to work a
Python 3 interpreter, the ``doxygen`` tools and internet access to
download additional files and tools are required. This download is
usually only required once or after the documentation folder is returned
to a pristine state with ``make clean-all``.
For the documentation build a python virtual environment is set up in
the folder ``doc/docenv`` and various python packages are installed into
@ -179,7 +176,7 @@ math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file (for e-book
readers, like Kindle, that cannot read ePUB), you also need to have the
``ebook-convert`` tool from the "calibre" software
installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
Typing ``make mobi`` will first create the ePUB file and then convert
it. On the Kindle readers in particular, you also have support for PDF
files, so you could download and view the PDF version as an alternative.
@ -219,9 +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:
@ -252,6 +260,5 @@ manual with ``make spelling``. This requires `a library called enchant
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://www.lammps.org
.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html

29
doc/src/Build_settings.rst
View File

@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system.
files in its default search path. You must specify ``FFT_LIB``
with the appropriate FFT libraries to include in the link.
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size
of the FFTs and the number of processors used, the other libraries listed
here can be faster.
The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
included in the LAMMPS distribution. It is portable across all
platforms. Depending on the size of the FFTs and the number of
processors used, the other libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run when using the
:doc:`kspace_style pppm <kspace_style>` command. The
:doc:`Screen and logfile output <Run_output>`
page gives more details. A more detailed (and time consuming)
report of the FFT performance is generated with the
per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
and 1d FFTs are only a portion of the FFT cost (parallel communication
can be costly). A breakdown of these timings is printed to the screen
at the end of a run when using the :doc:`kspace_style pppm
<kspace_style>` command. The :doc:`Screen and logfile output
<Run_output>` page gives more details. A more detailed (and time
consuming) report of the FFT performance is generated with the
:doc:`kspace_modify fftbench yes <kspace_modify>` command.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
platform and can be faster than the KISS FFT library. You can download
it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges

1
doc/src/Commands.rst
View File

@ -21,6 +21,7 @@ commands in it are used to define a LAMMPS simulation.
Commands_pair
Commands_bond
Commands_kspace
Commands_dump
.. toctree::
:maxdepth: 1

6
doc/src/Commands_all.rst
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@ -10,11 +10,14 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
General commands
================
An alphabetic list of general LAMMPS commands.
An alphabetic list of general LAMMPS commands. Note that style
commands with many variants, can be more easily accessed via the small
table above.
.. table_from_list::
:columns: 5
@ -60,6 +63,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
* :doc:`labelmap <labelmap>`
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`

7
doc/src/Commands_bond.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:
@ -43,6 +44,7 @@ OPT.
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
* :doc:`mesocnt <bond_mesocnt>`
* :doc:`mm3 <bond_mm3>`
* :doc:`morse (o) <bond_morse>`
* :doc:`nonlinear (o) <bond_nonlinear>`
@ -74,6 +76,7 @@ OPT.
*
*
*
* :doc:`amoeba <angle_amoeba>`
* :doc:`charmm (iko) <angle_charmm>`
* :doc:`class2 (ko) <angle_class2>`
* :doc:`class2/p6 <angle_class2>`
@ -90,9 +93,10 @@ OPT.
* :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`gaussian <angle_gaussian>`
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`spica (o) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
@ -152,6 +156,7 @@ OPT.
*
*
*
* :doc:`amoeba <improper_amoeba>`
* :doc:`class2 (ko) <improper_class2>`
* :doc:`cossq (o) <improper_cossq>`
* :doc:`cvff (io) <improper_cvff>`

3
doc/src/Commands_compute.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================
@ -138,6 +139,8 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`smd/vol <compute_smd_vol>`
* :doc:`snap <compute_sna_atom>`
* :doc:`sna/atom <compute_sna_atom>`
* :doc:`sna/grid <compute_sna_atom>`
* :doc:`sna/grid/local <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`sph/e/atom <compute_sph_e_atom>`

56
doc/src/Commands_dump.rst Normal file
View File

@ -0,0 +1,56 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
.. table_from_list::
:columns: 5
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`
* :doc:`atom/gz <dump>`
* :doc:`atom/mpiio <dump>`
* :doc:`atom/zstd <dump>`
* :doc:`cfg <dump>`
* :doc:`cfg/gz <dump>`
* :doc:`cfg/mpiio <dump>`
* :doc:`cfg/uef <dump_cfg_uef>`
* :doc:`cfg/zstd <dump>`
* :doc:`custom <dump>`
* :doc:`custom/adios <dump_adios>`
* :doc:`custom/gz <dump>`
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`deprecated <dump>`
* :doc:`h5md <dump_h5md>`
* :doc:`image <dump_image>`
* :doc:`local <dump>`
* :doc:`local/gz <dump>`
* :doc:`local/zstd <dump>`
* :doc:`molfile <dump_molfile>`
* :doc:`movie <dump_image>`
* :doc:`netcdf <dump_netcdf>`
* :doc:`netcdf/mpiio <dump>`
* :doc:`vtk <dump_vtk>`
* :doc:`xtc <dump>`
* :doc:`xyz <dump>`
* :doc:`xyz/gz <dump>`
* :doc:`xyz/mpiio <dump>`
* :doc:`xyz/zstd <dump>`
* :doc:`yaml <dump>`

6
doc/src/Commands_fix.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============
@ -28,6 +29,8 @@ OPT.
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`append/atoms <fix_append_atoms>`
* :doc:`atc <fix_atc>`
* :doc:`atom/swap <fix_atom_swap>`
@ -103,7 +106,7 @@ OPT.
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`mdi/aimd <fix_mdi_aimd>`
* :doc:`mdi/qm <fix_mdi_qm>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`mol/swap <fix_mol_swap>`
* :doc:`momentum (k) <fix_momentum>`
@ -162,6 +165,7 @@ OPT.
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>`
* :doc:`pair <fix_pair>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`

1
doc/src/Commands_kspace.rst
View File

@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
KSpace solvers
==============

17
doc/src/Commands_pair.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
@ -38,6 +39,7 @@ OPT.
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`amoeba <pair_amoeba>`
* :doc:`atm <pair_atm>`
* :doc:`awpmd/cut <pair_awpmd>`
* :doc:`beck (go) <pair_beck>`
@ -124,6 +126,7 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`hippo <pair_amoeba>`
* :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
* :doc:`ilp/tmd (t) <pair_ilp_tmd>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@ -179,9 +182,9 @@ OPT.
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@ -194,10 +197,11 @@ OPT.
* :doc:`lubricateU/poly <pair_lubricateU>`
* :doc:`mdpd <pair_mesodpd>`
* :doc:`mdpd/rhosum <pair_mesodpd>`
* :doc:`meam <pair_meam>`
* :doc:`meam (k) <pair_meam>`
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mesocnt <pair_mesocnt>`
* :doc:`mesocnt/viscous <pair_mesocnt>`
* :doc:`mesont/tpm <pair_mesont_tpm>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
@ -232,6 +236,7 @@ OPT.
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation <pair_pace>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
@ -268,7 +273,9 @@ OPT.
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`srp/react <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`sw/angle/table <pair_sw_angle_table>`
* :doc:`sw/mod (o) <pair_sw>`
* :doc:`table (gko) <pair_table>`
* :doc:`table/rx (k) <pair_table_rx>`
@ -279,6 +286,7 @@ OPT.
* :doc:`tersoff/table (o) <pair_tersoff>`
* :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
* :doc:`thole <pair_thole>`
* :doc:`threebody/table <pair_threebody_table>`
* :doc:`tip4p/cut (o) <pair_coul>`
* :doc:`tip4p/long (o) <pair_coul>`
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
@ -287,6 +295,7 @@ 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>`

22
doc/src/Commands_parse.rst
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@ -123,14 +123,15 @@ LAMMPS:
.. _six:
6. If you want text with spaces to be treated as a single argument, it
can be enclosed in either single or double or triple quotes. A long
single argument enclosed in single or double quotes can span multiple
lines if the "&" character is used, as described above. When the
lines are concatenated together (and the "&" characters and line
breaks removed), the text will become a single line. If you want
multiple lines of an argument to retain their line breaks, the text
can be enclosed in triple quotes, in which case "&" characters are
not needed. For example:
can be enclosed in either single (') or double (") or triple (""")
quotes. A long single argument enclosed in single or double quotes
can span multiple lines if the "&" character is used, as described
in :ref:`1 <one>` above. When the lines are concatenated together
by LAMMPS (and the "&" characters and line breaks removed), the
combined text will become a single line. If you want multiple lines
of an argument to retain their line breaks, the text can be enclosed
in triple quotes, in which case "&" characters are not needed and do
not function as line continuation character. For example:
.. code-block:: LAMMPS
@ -144,8 +145,9 @@ LAMMPS:
System temperature = $t
"""
In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.
In each of these cases, the single, double, or triple quotes are
removed and the enclosed text stored internally as a single
argument.
See the :doc:`dump modify format <dump_modify>`, :doc:`print
<print>`, :doc:`if <if>`, and :doc:`python <python>` commands for

1
doc/src/Developer.rst
View File

@ -17,6 +17,7 @@ of time and requests from the LAMMPS user community.
Developer_flow
Developer_write
Developer_notes
Developer_updating
Developer_plugins
Developer_unittest
Classes

29
doc/src/Developer_plugins.rst
View File

@ -276,10 +276,27 @@ Compilation of the plugin can be managed via both, CMake or traditional
GNU makefiles. Some examples that can be used as a template are in the
``examples/plugins`` folder. The CMake script code has some small
adjustments to allow building the plugins for running unit tests with
them. Another example that converts the KIM package into a plugin can be
found in the ``examples/kim/plugin`` folder. No changes to the sources
of the KIM package themselves are needed; only the plugin interface and
loader code needs to be added. This example only supports building with
CMake, but is probably a more typical example. To compile you need to
run CMake with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
them.
Another example that converts the KIM package into a plugin can be found
in the ``examples/kim/plugin`` folder. No changes to the sources of the
KIM package themselves are needed; only the plugin interface and loader
code needs to be added. This example only supports building with CMake,
but is probably a more typical example. To compile you need to run CMake
with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
configuration setting are identical to those for compiling LAMMPS.
A second example for a plugin from a package is in the
``examples/PACKAGES/pace/plugin`` folder that will create a plugin from
the ML-PACE package. In this case the bulk of the code is in a static
external library that is being downloaded and compiled first and then
combined with the pair style wrapper and the plugin loader. This
example also contains a NSIS script that can be used to create an
Installer package for Windows (the mutual licensing terms of the
external library and LAMMPS conflict when distributing binaries, so the
ML-PACE package cannot be linked statically, but the LAMMPS headers
required to build the plugin are also available under a less restrictive
license). This will automatically set the required environment variable
and launching a (compatible) LAMMPS binary will load and register the
plugin and the ML-PACE package can then be used as it was linked into
LAMMPS.

425
doc/src/Developer_updating.rst Normal file
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@ -0,0 +1,425 @@
Notes for updating code written for older LAMMPS versions
---------------------------------------------------------
This section documents how C++ source files that are available *outside
of the LAMMPS source distribution* (e.g. in external USER packages or as
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 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
the LAMMPS distribution.
Available topics in mostly chronological order are:
- `Setting flags in the constructor`_
- `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Simplify customized error messages`_
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
----
Setting flags in the constructor
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
As LAMMPS gains additional functionality, new flags may need to be set
in the constructor or a class to signal compatibility with such features.
Most of the time the defaults are chosen conservatively, but sometimes
the conservative choice is the uncommon choice, and then those settings
need to be made when updating code.
Pair styles:
- ``manybody_flag``: set to 1 if your pair style is not pair-wise additive
- ``restartinfo``: set to 0 if your pair style does not store data in restart files
Rename of pack/unpack_comm() to pack/unpack_forward_comm()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 8Aug2014
In this change set the functions to pack data into communication buffers
and to unpack data from communication buffers for :doc:`forward
communications <Developer_comm_ops>` were renamed from ``pack_comm()``
and ``unpack_comm()`` to ``pack_forward_comm()`` and
``unpack_forward_comm()``, respectively. Also the meaning of the return
value of these functions was changed: rather than returning the number
of items per atom stored in the buffer, now the total number of items
added (or unpacked) needs to be returned. Here is an example from the
`PairEAM` class. Of course the member function declaration in corresponding
header file needs to be updated accordingly.
Old:
.. code-block:: C++
int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int m = 0;
for (int i = 0; i < n; i++) {
int j = list[i];
buf[m++] = fp[j];
}
return 1;
}
New:
.. code-block:: C++
int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int m = 0;
for (int i = 0; i < n; i++) {
int j = list[i];
buf[m++] = fp[j];
}
return m;
}
.. note::
Because the various "pack" and "unpack" functions are defined in the
respective base classes as dummy functions doing nothing, and because
of the the name mismatch the custom versions in the derived class
will no longer be called, there will be no compilation error when
this change is not applied. Only calculations will suddenly produce
incorrect results because the required forward communication calls
will cease to function correctly.
Use ev_init() to initialize variables derived from eflag and vflag
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 29Mar2019
There are several variables that need to be initialized based on
the values of the "eflag" and "vflag" variables and since sometimes
there are new bits added and new variables need to be set to 1 or 0.
To make this consistent, across all styles, there is now an inline
function ``ev_init(eflag, vflag)`` that makes those settings
consistently and calls either ``ev_setup()`` or ``ev_unset()``.
Example from a pair style:
Old:
.. code-block:: C++
if (eflag || vflag) ev_setup(eflag, vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
New:
.. code-block:: C++
ev_init(eflag, vflag);
Not applying this change will not cause a compilation error, but
can lead to inconsistent behavior and incorrect tallying of
energy or virial.
Use utils::numeric() functions instead of force->numeric()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
The "numeric()" conversion functions (including "inumeric()",
"bnumeric()", and "tnumeric()") have been moved from the Force class to
the utils namespace. Also they take an additional argument that selects
whether the ``Error::all()`` or ``Error::one()`` function should be
called in case of an error. The former should be used when *all* MPI
processes call the conversion function and the latter *must* be used
when they are called from only one or a subset of the MPI processes.
Old:
.. code-block:: C++
val = force->numeric(FLERR, arg[1]);
num = force->inumeric(FLERR, arg[2]);
New:
.. code-block:: C++
val = utils::numeric(FLERR, true, arg[1], lmp);
num = utils::inumeric(FLERR, false, arg[2], lmp);
.. seealso::
:cpp:func:`utils::numeric() <LAMMPS_NS::utils::numeric>`,
:cpp:func:`utils::inumeric() <LAMMPS_NS::utils::inumeric>`,
:cpp:func:`utils::bnumeric() <LAMMPS_NS::utils::bnumeric>`,
:cpp:func:`utils::tnumeric() <LAMMPS_NS::utils::tnumeric>`
Use utils::open_potential() function to open potential files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
The :cpp:func:`utils::open_potential()
<LAMMPS_NS::utils::open_potential>` function must be used to replace
calls to ``force->open_potential()`` and should be used to replace
``fopen()`` for opening potential files for reading. The custom
function does three additional steps compared to ``fopen()``: 1) it will
try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an
error on a units mismatch and will print the date info, if present, in
the log file; 2) for pair styles that support it, it will set up
possible automatic unit conversions based on the embedded unit
information and LAMMPS' current units setting; 3) it will not only try
to open a potential file at the given path, but will also search in the
folders listed in the ``LAMMPS_POTENTIALS`` environment variable. This
allows to keep potential files in a common location instead of having to
copy them around for simulations.
Old:
.. code-block:: C++
fp = force->open_potential(filename);
fp = fopen(filename, "r");
New:
.. code-block:: C++
fp = utils::open_potential(filename, lmp);
Simplify customized error messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 14May2021
Aided by features of the bundled {fmt} library, error messages now
can have a variable number of arguments and the string will be interpreted
as a {fmt} style format string so that custom error messages can be
easily customized without having to use temporary buffers and ``sprintf()``.
Example:
Old:
.. code-block:: C++
if (fptr == NULL) {
char str[128];
sprintf(str,"Cannot open AEAM potential file %s",filename);
error->one(FLERR,str);
}
New:
.. code-block:: C++
if (fptr == nullptr)
error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
Use of "override" instead of "virtual"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 17Feb2022
Since LAMMPS requires C++11 we switched to use the "override" keyword
instead of "virtual" to indicate polymorphism in derived classes. This
allows the C++ compiler to better detect inconsistencies when an
override is intended or not. Please note that "override" has to be
added to **all** polymorph functions in derived classes and "virtual"
*only* to the function in the base class (or the destructor). Here is
an example from the ``FixWallReflect`` class:
Old:
.. code-block:: C++
FixWallReflect(class LAMMPS *, int, char **);
virtual ~FixWallReflect();
int setmask();
void init();
void post_integrate();
New:
.. code-block:: C++
FixWallReflect(class LAMMPS *, int, char **);
~FixWallReflect() override;
int setmask() override;
void init() override;
void post_integrate() override;
This change set will neither cause a compilation failure, nor will it
change functionality, but if you plan to submit the updated code for
inclusion into the LAMMPS distribution, it will be requested for achieve
a consistent :doc:`programming style <Modify_style>`.
Simplified function names for forward and reverse communication
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 24Mar2022
Rather then using the function name to distinguish between the different
forward and reverse communication functions for styles, LAMMPS now uses
the type of the "this" pointer argument.
Old:
.. code-block:: C++
comm->forward_comm_pair(this);
comm->forward_comm_fix(this);
comm->forward_comm_compute(this);
comm->forward_comm_dump(this);
comm->reverse_comm_pair(this);
comm->reverse_comm_fix(this);
comm->reverse_comm_compute(this);
comm->reverse_comm_dump(this);
New:
.. code-block:: C++
comm->forward_comm(this);
comm->reverse_comm(this);
This change is **required** or else the code will not compile.
Simplified and more compact neighbor list requests
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 24Mar2022
This change set reduces the amount of code required to request a
neighbor list. It enforces consistency and no longer requires to change
internal data of the request. More information on neighbor list
requests can be :doc:`found here <Developer_notes>`. Example from the
``ComputeRDF`` class:
Old:
.. code-block:: C++
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
if (cutflag) {
neighbor->requests[irequest]->cut = 1;
neighbor->requests[irequest]->cutoff = mycutneigh;
}
New:
.. code-block:: C++
auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
if (cutflag) req->set_cutoff(mycutneigh);
Public access to the ``NeighRequest`` class data members has been
removed so this update is **required** to avoid compilation failure.
Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 15Sep2022
This change splits the GLOBAL and PERATOM modes of fix STORE into two
separate fixes STORE/GLOBAL and STORE/PERATOM. There was very little
shared code between the two fix STORE modes and the two different code
paths had to be prefixed with if statements. Furthermore, some flags
were used differently in the two modes leading to confusion. Splitting
the code into two fix styles, makes it more easily maintainable. Since
these are internal fixes, there is no user visible change.
Old:
.. code-block:: C++
#include "fix_store.h"
FixStore *fix = dynamic_cast<FixStore *>(
modify->add_fix(fmt::format("{} {} STORE peratom 1 13",id_pole,group->names[0]));
FixStore *fix = dynamic_cast<FixStore *>(modify->get_fix_by_id(id_pole));
New:
.. code-block:: C++
#include "fix_store_peratom.h"
FixStorePeratom *fix = dynamic_cast<FixStorePeratom *>(
modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 13",id_pole,group->names[0]));
FixStorePeratom *fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_pole));
Old:
.. code-block:: C++
#include "fix_store.h"
FixStore *fix = dynamic_cast<FixStore *>(
modify->add_fix(fmt::format("{} {} STORE global 1 1",id_fix,group->names[igroup]));
FixStore *fix = dynamic_cast<FixStore *>(modify->get_fix_by_id(id_fix));
New:
.. code-block:: C++
#include "fix_store_global.h"
FixStoreGlobal *fix = dynamic_cast<FixStoreGlobal *>(
modify->add_fix(fmt::format("{} {} STORE/GLOBAL 1 1",id_fix,group->names[igroup]));
FixStoreGlobal *fix = dynamic_cast<FixStoreGlobal *>(modify->get_fix_by_id(id_fix));
This change is **required** or else the code will not compile.
Use Output::get_dump_by_id() instead of Output::find_dump()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 15Sep2022
The accessor function to individual dump style instances has been changed
from ``Output::find_dump()`` returning the index of the dump instance in
the list of dumps to ``Output::get_dump_by_id()`` returning a pointer to
the dump directly. Example:
Old:
.. code-block:: C++
int idump = output->find_dump(arg[iarg+1]);
if (idump < 0)
error->all(FLERR,"Dump ID in hyper command does not exist");
memory->grow(dumplist,ndump+1,"hyper:dumplist");
dumplist[ndump++] = idump;
[...]
if (dumpflag)
for (int idump = 0; idump < ndump; idump++)
output->dump[dumplist[idump]]->write();
New:
.. 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]);
dumplist.emplace_back(idump);
[...]
if (dumpflag) for (auto idump : dumplist) idump->write();
This change is **required** or else the code will not compile.

14
doc/src/Developer_utils.rst
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@ -154,6 +154,9 @@ and parsing files or arguments.
.. doxygenfunction:: trim_and_count_words
:project: progguide
.. doxygenfunction:: join_words
:project: progguide
.. doxygenfunction:: split_words
:project: progguide
@ -172,6 +175,12 @@ and parsing files or arguments.
.. doxygenfunction:: is_double
:project: progguide
.. doxygenfunction:: is_id
:project: progguide
.. doxygenfunction:: is_type
:project: progguide
Potential file functions
^^^^^^^^^^^^^^^^^^^^^^^^
@ -202,10 +211,13 @@ Argument processing
.. doxygenfunction:: expand_args
:project: progguide
.. doxygenfunction:: expand_type
:project: progguide
Convenience functions
^^^^^^^^^^^^^^^^^^^^^
.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &format, Args&&... args)
:project: progguide
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)

2
doc/src/Errors_debug.rst
View File

@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
There are two options to use the GDB debugger for identifying the origin
of the segmentation fault or similar crash. The GDB debugger has many
more features and options, as can be seen for example its `online
documentation <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
Run LAMMPS from within the debugger
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

166
doc/src/Errors_messages.rst
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@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Bonds defined but no bond types*
The data file header lists bonds but no bond types.
*Bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
Self-explanatory.
*Bond/react: First neighbors of chiral atoms must be of mutually different types*
Self-explanatory.
*Bond/react: Chiral atoms must have exactly four first neighbors*
Self-explanatory.
*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
The coordinates of atoms in the pre-reacted template are used to determine
chirality.
*Bond/react special bond generation overflow*
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
*Bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Both restart files must use % or neither*
Self-explanatory.
@ -1291,7 +1232,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use chosen neighbor list style with lj/gromacs/kk*
Self-explanatory.
*Cannot use chosen neighbor list style with lj/sdk/kk*
*Cannot use chosen neighbor list style with lj/spica/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with pair eam/kk*
@ -1659,10 +1600,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use newton pair with lj/gromacs/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/gpu pair style*
*Cannot use newton pair with lj/spica/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj96/cut/gpu pair style*
@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
acquire needed info, The comm_modify cutoff command can be used to
extend the communication range.
*Fix bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Fix bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Fix bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Fix bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Fix bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Fix bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Fix bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
Self-explanatory.
*Fix bond/react: First neighbors of chiral atoms must be of mutually different types*
Self-explanatory.
*Fix bond/react: Chiral atoms must have exactly four first neighbors*
Self-explanatory.
*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
The coordinates of atoms in the pre-reacted template are used to determine
chirality.
*Fix bond/react special bond generation overflow*
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
*Fix bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Fix bond/swap cannot use dihedral or improper styles*
These styles cannot be defined when using this fix.
@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Mass command must set a type from 1-N where N is the number of atom
types.
*Invalid label2type() function syntax in variable formula*
The first argument must be a label map kind (atom, bond, angle,
dihedral, or improper) and the second argument must be a valid type
label that has been assigned to a numeric type.
*Invalid use of library file() function*
This function is called through the library interface. This
error should not occur. Contact the developers if it does.
@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*LJ6 off not supported in pair_style buck/long/coul/long*
Self-explanatory.
*Label map is incomplete: all types must be assigned a unique type label*
For a given type-kind (atom types, bond types, etc.) to be written to
the data file, all associated types must be assigned a type label, and
each type label can be assigned to only one numeric type.
*Label wasn't found in input script*
Self-explanatory.
*Labelmap command before simulation box is defined*
The labelmap command cannot be used before a read_data,
read_restart, or create_box command.
*Lattice orient vectors are not orthogonal*
The three specified lattice orientation vectors must be mutually
orthogonal.
@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Must not have multiple fixes change box parameter ...*
Self-explanatory.
*Must read Angle Type Labels before Angles*
An Angle Type Labels section of a data file must come before the Angles section.
*Must read Atom Type Labels before Atoms*
An Atom Type Labels section of a data file must come before the Atoms section.
*Must read Atoms before Angles*
The Atoms section of a data file must come before an Angles section.
@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
The Atoms section of a data file must come before a Velocities
section.
*Must read Bond Type Labels before Bonds*
A Bond Type Labels section of a data file must come before the Bonds section.
*Must read Dihedral Type Labels before Dihedrals*
An Dihedral Type Labels section of a data file must come before the Dihedrals section.
*Must read Improper Type Labels before Impropers*
An Improper Type Labels section of a data file must come before the Impropers section.
*Must re-specify non-restarted pair style (xxx) after read_restart*
For pair styles, that do not store their settings in a restart file,
it must be defined with a new 'pair_style' command after read_restart.
@ -6782,7 +6811,7 @@ keyword to allow for additional bonds to be formed
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
*Pair style lj/spica/coul/long/gpu requires atom attribute q*
The atom style defined does not have this attribute.
*Pair style nb3b/harmonic requires atom IDs*
@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
Number of local atoms times number of columns must fit in a 32-bit
integer for dump.
*Topology type exceeds system topology type*
The number of bond, angle, etc types exceeds the system setting. See
the create_box or read_data command for how to specify these values.
*Tree structure in joint connections*
Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure.
@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
*Two groups cannot be the same in fix spring couple*
Self-explanatory.
*The %s type label %s is already in use for type %s*
For a given type-kind (atom types, bond types, etc.), a given type
label can be assigned to only one numeric type.
*Type label string %s for %s type %s is invalid*
See the labelmap command documentation for valid type labels.
*Unable to initialize accelerator for use*
There was a problem initializing an accelerator for the gpu package

23
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@ -68,14 +68,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch.
*Bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explanatory.
@ -212,6 +204,14 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
about changes they made at the same time step and thus it may result
in unexpected behavior.
*Fix bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/swap will ignore defined angles*
See the page for fix bond/swap for more info on this
restriction.
@ -470,6 +470,12 @@ This will most likely cause errors in kinetic fluctuations.
*More than one compute sna/atom*
Self-explanatory.
*More than one compute sna/grid*
Self-explanatory.
*More than one compute sna/grid/local*
Self-explanatory.
*More than one compute snad/atom*
Self-explanatory.
@ -804,4 +810,3 @@ This will most likely cause errors in kinetic fluctuations.
*Using pair tail corrections with pair_modify compute no*
The tail corrections will thus not be computed.

2102
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3
doc/src/Howto.rst
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@ -34,6 +34,7 @@ Settings howto
:maxdepth: 1
Howto_2d
Howto_type_labels
Howto_triclinic
Howto_thermostat
Howto_barostat
@ -65,6 +66,7 @@ Force fields howto
:maxdepth: 1
Howto_bioFF
Howto_amoeba
Howto_tip3p
Howto_tip4p
Howto_spc
@ -83,6 +85,7 @@ Packages howto
Howto_coreshell
Howto_drude
Howto_drude2
Howto_peri
Howto_manifold
Howto_spins

324
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@ -0,0 +1,324 @@
AMOEBA and HIPPO force fields
=============================
The AMOEBA and HIPPO polarizable force fields were developed by Jay
Ponder's group at the U Washington at St Louis. The LAMMPS
implementation is based on Fortran 90 code provided by the Ponder
group in their `Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
The current implementation (July 2022) of AMOEBA in LAMMPS matches the
version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
<amoeba-Ren>`, and :ref:`(Shi) <amoeba-Shi>`. Likewise the current
implementation of HIPPO in LAMMPS matches the version discussed in
:ref:`(Rackers) <amoeba-Rackers>`.
These force fields can be used when polarization effects are desired
in simulations of water, organic molecules, and biomolecules including
proteins, provided that parameterizations (Tinker PRM force field
files) are available for the systems you are interested in. Files in
the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can
be used. The Tinker distribution and website have additional force
field files as well:
`https://github.com/TinkerTools/tinker/tree/release/params
<https://github.com/TinkerTools/tinker/tree/release/params>`_.
Note that currently, HIPPO can only be used for water systems, but
HIPPO files for a variety of small organic and biomolecules are in
preparation by the Ponder group. Those force field files will be
included in the LAMMPS distribution when available.
To use the AMOEBA or HIPPO force fields, a simulation must be 3d, and
fully periodic or fully non-periodic, and use an orthogonal (not
triclinic) simulation box.
----------
The AMOEBA and HIPPO force fields contain the following terms in their
energy (U) computation. Further details for AMOEBA equations are in
:ref:`(Ponder) <amoeba-Ponder>`, further details for the HIPPO
equations are in :ref:`(Rackers) <amoeba-Rackers>`.
.. math::
U & = U_{intermolecular} + U_{intramolecular} \\
U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}
For intermolecular terms, the AMOEBA force field includes only the
:math:`U_{hal}`, :math:`U_{multipole}`, :math:`U_{polar}` terms. The
HIPPO force field includes all but the :math:`U_{hal}` term. In
LAMMPS, these are all computed by the :doc:`pair_style amoeba or hippo
<pair_style>` command. Note that the :math:`U_{multipole}` and
:math:`U_{polar}` terms in this formula are not the same for the
AMOEBA and HIPPO force fields.
For intramolecular terms, the :math:`U_{bond}`, :math:`U_{angle}`,
:math:`U_{torsion}`, :math:`U_{oop}` terms are computed by the
:doc:`bond_style class2 <bond_class2>` :doc:`angle_style amoeba
<angle_amoeba>`, :doc:`dihedral_style fourier <dihedral_fourier>`, and
:doc:`improper_style amoeba <improper_amoeba>` commands respectively.
The :doc:`angle_style amoeba <angle_amoeba>` command includes the
:math:`U_{b\theta}` bond-angle cross term, and the :math:`U_{UB}` term
for a Urey-Bradley bond contribution between the I,K atoms in the IJK
angle.
The :math:`U_{pitorsion}` term is computed by the :doc:`fix
amoeba/pitorsion <fix_amoeba_pitorsion>` command. It computes 6-body
interaction between a pair of bonded atoms which each have 2
additional bond partners.
The :math:`U_{bitorsion}` term is computed by the :doc:`fix
amoeba/bitorsion <fix_amoeba_bitorsion>` command. It computes 5-body
interaction between two 4-body torsions (dihedrals) which overlap,
having 3 atoms in common.
These command doc pages have additional details on the terms they
compute:
* :doc:`pair_style amoeba or hippo <pair_amoeba>`
* :doc:`bond_style class2 <bond_class2>`
* :doc:`angle_style amoeba <angle_amoeba>`
* :doc:`dihedral_style fourier <dihedral_fourier>`
* :doc:`improper_style amoeba <improper_amoeba>`
* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
----------
To use the AMOEBA or HIPPO force fields in LAMMPS, use commands like
the following appropriately in your input script. The only change
needed for AMOEBA vs HIPPO simulation is for the :doc:`pair_style
<pair_style>` and :doc:`pair_coeff <pair_coeff>` commands, as shown
below. See examples/amoeba for example input scripts for both AMOEBA
and HIPPO.
.. code-block:: LAMMPS
units real # required
atom_style amoeba
bond_style class2 # CLASS2 package
angle_style amoeba
dihedral_style fourier # EXTRA-MOLECULE package
improper_style amoeba
# required per-atom data
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
fix polaxe all property/atom i_polaxe
fix pit all amoeba/pitorsion # PiTorsion terms in FF
fix_modify pit energy yes
# Bitorsion terms in FF
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions
pair_style amoeba # AMOEBA FF
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
pair_style hippo # HIPPO FF
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes # 1-5 neighbors
The data file read by the :doc:`read_data <read_data>` command should
be created by the tools/tinker/tinker2lmp.py conversion program
described below. It will create a section in the data file with the
header "Tinker Types". A :doc:`fix property/atom <fix_property_atom>`
command for the data must be specified before the read_data command.
In the example above the fix ID is *amtype*.
Similarly, if the system you are simulating defines AMOEBA/HIPPO
pitorsion or bitorsion interactions, there will be entries in the data
file for those interactions. They require a :doc:`fix
amoeba/pitortion <fix_amoeba_pitorsion>` and :doc:`fix
amoeba/bitorsion <fix_amoeba_bitorsion>` command be defined. In the
example above, the IDs for these two fixes are *pit* and *bit*.
Of course, if the system being modeled does not have one or more of
the following -- bond, angle, dihedral, improper, pitorsion,
bitorsion interactions -- then the corresponding style and fix
commands above do not need to be used. See the example scripts in
examples/amoeba for water systems as examples; they are simpler than
what is listed above.
The two :doc:`fix property/atom <fix_property_atom>` commands with IDs
(in the example above) *extra* and *polaxe* are also needed to define
internal per-atom quantities used by the AMOEBA and HIPPO force
fields.
The :doc:`pair_coeff <pair_coeff>` command used for either the AMOEBA
or HIPPO force field takes two arguments for Tinker force field files,
namely a PRM and KEY file. The keyfile can be specified as NULL and
default values for a various settings will be used. Note that these 2
files are meant to allow use of native Tinker files as-is. However
LAMMPS does not support all the options which can be included
in a Tinker PRM or KEY file. See specifics below.
A :doc:`special_bonds <special_bonds>` command with the *one/five*
option is required, since the AMOEBA/HIPPO force fields define
weighting factors for not only 1-2, 1-3, 1-4 interactions, but also
1-5 interactions. This command will trigger a per-atom list of 1-5
neighbors to be generated. The AMOEBA and HIPPO force fields define
their own custom weighting factors for all the 1-2, 1-3, 1-4, 1-5
terms which in the Tinker PRM and KEY files; they can be different for
different terms in the force field.
In addition to the list above, these command doc pages have additional
details:
* :doc:`atom_style amoeba <atom_style>`
* :doc:`fix property/atom <fix_property_atom>`
* :doc:`special_bonds <special_bonds>`
----------
Tinker PRM and KEY files
A Tinker PRM file is composed of sections, each of which has multiple
lines. This is the list of PRM sections LAMMPS knows how to parse and
use. Any other sections are skipped:
* Angle Bending Parameters
* Atom Type Definitions
* Atomic Multipole Parameters
* Bond Stretching Parameters
* Charge Penetration Parameters
* Charge Transfer Parameters
* Dipole Polarizability Parameters
* Dispersion Parameters
* Force Field Definition
* Literature References
* Out-of-Plane Bend Parameters
* Pauli Repulsion Parameters
* Pi-Torsion Parameters
* Stretch-Bend Parameters
* Torsion-Torsion Parameters
* Torsional Parameters
* Urey-Bradley Parameters
* Van der Waals Pair Parameters
* Van der Waals Parameters
A Tinker KEY file is composed of lines, each of which has a keyword
followed by zero or more parameters. This is the list of keywords
LAMMPS knows how to parse and use in the same manner Tinker does. Any
other keywords are skipped. The value in parenthesis is the default
value for the keyword if it is not specified, or if the keyfile in the
:doc:`pair_coeff <pair_coeff>` command is specified as NULL:
* a-axis (0.0)
* b-axis (0.0)
* c-axis (0.0)
* ctrn-cutoff (6.0)
* ctrn-taper (0.9 * ctrn-cutoff)
* cutoff
* delta-halgren (0.07)
* dewald (no long-range dispersion unless specified)
* dewald-alpha (0.4)
* dewald-cutoff (7.0)
* dispersion-cutoff (9.0)
* dispersion-taper (9.0 * dispersion-cutoff)
* dpme-grid
* dpme-order (4)
* ewald (no long-range electrostatics unless specified)
* ewald-alpha (0.4)
* ewald-cutoff (7.0)
* gamma-halgren (0.12)
* mpole-cutoff (9.0)
* mpole-taper (0.65 * mpole-cutoff)
* pcg-guess (enabled by default)
* pcg-noguess (disable pcg-guess if specified)
* pcg-noprecond (disable pcg-precond if specified)
* pcg-peek (1.0)
* pcg-precond (enabled by default)
* pewald-alpha (0.4)
* pme-grid
* pme-order (5)
* polar-eps (1.0e-6)
* polar-iter (100)
* polar-predict (no prediction operation unless specified)
* ppme-order (5)
* repulsion-cutoff (6.0)
* repulsion-taper (0.9 * repulsion-cutoff)
* taper
* usolve-cutoff (4.5)
* usolve-diag (2.0)
* vdw-cutoff (9.0)
* vdw-taper (0.9 * vdw-cutoff)
----------
Tinker2lmp.py tool
This conversion tool is found in the tools/tinker directory.
As shown in examples/amoeba/README, these commands produce
the data files found in examples/amoeba, and also illustrate
all the options available to use with the tinker2lmp.py script:
.. code-block:: bash
% python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba # AMOEBA non-periodic system
% python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo # HIPPO non-periodic system
% python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643 # AMOEBA periodic system
% python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643 # HIPPO periodic system
% python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new # system with bitorsions
Switches and their arguments may be specified in any order.
The -xyz switch is required and specifies an input XYZ file as an
argument. The format of this file is an extended XYZ format defined
and used by Tinker for its input. Example \*.xyz files are in the
examples/amoeba directory. The file lists the atoms in the system.
Each atom has the following information: Tinker species name (ignored
by LAMMPS), xyz coordinates, Tinker numeric type, and a list of atom
IDs the atom is bonded to.
Here is more information about the extended XYZ format defined and
used by Tinker, and links to programs that convert standard PDB files
to the extended XYZ format:
* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
* `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
* `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_
The -amoeba or -hippo switch is required. It specifies an input
AMOEBA or HIPPO PRM force field file as an argument. This should be
the same file used by the :doc:`pair_style <pair_style>` command in
the input script.
The -data switch is required. It specifies an output file name for
the LAMMPS data file that will be produced.
For periodic systems, the -pbc switch is required. It specifies the
periodic box size for each dimension (x,y,z). For a Tinker simulation
these are specified in the KEY file.
The -bitorsion switch is only needed if the system contains Tinker
bitorsion interactions. The data for each type of bitorsion
interaction will be written to the specified file, and read by the
:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>` command. The data
includes 2d arrays of values to which splines are fit, and thus is not
compatible with the LAMMPS data file format.
----------
.. _howto-Ponder:
**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
.. _howto-Rackers:
**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
.. _howto-Ren:
**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
.. _howto-Shi:
**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.

33
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@ -3,24 +3,20 @@ CHARMM, AMBER, COMPASS, and DREIDING force fields
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly
used in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
formulas implemented in LAMMPS that correspond to formulas commonly used
in the CHARMM, AMBER, COMPASS, and DREIDING force fields. Setting
coefficients is done either from special sections in an input data file
via the :doc:`read_data <read_data>` command or in the input script with
commands like :doc:`pair_coeff <pair_coeff>` or
:doc:`bond_coeff <bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc
page for additional tools that can use CHARMM, AMBER, or Materials
Studio generated files to assign force field coefficients and convert
their output into LAMMPS input.
commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
<bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
additional tools that can use CHARMM, AMBER, or Materials Studio
generated files to assign force field coefficients and convert their
output into LAMMPS input.
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
field. See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
force field. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
force field.
.. _charmm: http://www.scripps.edu/brooks
.. _amber: http://amber.scripps.edu
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
force field. See :ref:`(Cornell) <howto-Cornell>` for a description of
the AMBER force field. See :ref:`(Sun) <howto-Sun>` for a description
of the COMPASS force field.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
@ -41,9 +37,10 @@ command's documentation for the formula it computes.
.. note::
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
in March 2017. We recommend they be used instead of the older *charmm*
styles. See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
March 2017. We recommend they be used instead of the older *charmm*
styles. See discussion of the differences on the :doc:`pair charmm
<pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
pages.
COMPASS is a general force field for atomistic simulation of common

113
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@ -33,46 +33,6 @@ reference state of a bond. Bonds that are created midway into a run,
such as those created by pouring grains using :doc:`fix pour
<fix_pour>`, are initialized on that timestep.
As bonds can be broken between neighbor list builds, the
:doc:`special_bonds <special_bonds>` command works differently for BPM
bond styles. There are two possible settings which determine how pair
interactions work between bonded particles. First, one can turn off
all pair interactions between bonded particles. Unlike :doc:`bond
quartic <bond_quartic>`, this is not done by subtracting pair forces
during the bond computation but rather by dynamically updating the
special bond list. This is the default behavior of BPM bond styles and
is done by updating the 1-2 special bond list as bonds break. To do
this, LAMMPS requires :doc:`newton <newton>` bond off such that all
processors containing an atom know when a bond breaks. Additionally,
one must do either (A) or (B).
A) Use the following special bond settings
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1
These settings accomplish two goals. First, they turn off 1-3 and 1-4
special bond lists, which are not currently supported for BPMs. As
BPMs often have dense bond networks, generating 1-3 and 1-4 special
bond lists is expensive. By setting the lj weight for 1-2 bonds to
zero, this turns off pairwise interactions. Even though there are no
charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds.
B) Alternatively, one can simply overlay pair interactions such that all
bonded particles also feel pair interactions. This can be
accomplished by using the *overlay/pair* keyword present in all bpm
bond styles and by using the following special bond settings
.. code-block:: LAMMPS
special_bonds lj/coul 1 1 1
See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
more information.
----------
Currently there are two types of bonds included in the BPM
@ -91,12 +51,6 @@ This also requires a unique integrator :doc:`fix nve/bpm/sphere
<fix_nve_bpm_sphere>` which numerically integrates orientation similar
to :doc:`fix nve/asphere <fix_nve_asphere>`.
To monitor the fracture of bonds in the system, all BPM bond styles
have the ability to record instances of bond breakage to output using
the :doc:`dump local <dump>` command. Additionally, one can use
:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
number of bonds per atom.
In addition to bond styles, a new pair style :doc:`pair bpm/spring
<pair_bpm_spring>` was added to accompany the bpm/spring bond
style. This pair style is simply a hookean repulsion with similar
@ -104,6 +58,73 @@ velocity damping as its sister bond style.
----------
Bond data can be output using a combination of standard LAMMPS commands.
A list of IDs for bonded atoms can be generated using the
:doc:`compute property/local <compute_property_local>` command.
Various properties of bonds can be computed using the
:doc:`compute bond/local <compute_bond_local>` command. This
command allows one to access data saved to the bond's history
such as the reference length of the bond. More information on
bond history data can be found on the documentation pages for the specific
BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
command. As one may output many columns from the same compute, the
:doc:`dump modify <dump_modify>` *colname* option may be used to provide
more helpful column names. An example of this procedure is found in
/examples/bpm/pour/. External software, such as OVITO, can read these dump
files to render bond data.
----------
As bonds can be broken between neighbor list builds, the
:doc:`special_bonds <special_bonds>` command works differently for BPM
bond styles. There are two possible settings which determine how pair
interactions work between bonded particles. First, one can overlay
pair forces with bond forces such that all bonded particles also
feel pair interactions. This can be accomplished by using the *overlay/pair*
keyword present in all bpm bond styles and by using the following special
bond settings
.. code-block:: LAMMPS
special_bonds lj/coul 1 1 1
Alternatively, one can turn off all pair interactions between bonded
particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
by subtracting pair forces during the bond computation but rather by
dynamically updating the special bond list. This is the default behavior
of BPM bond styles and is done by updating the 1-2 special bond list as
bonds break. To do this, LAMMPS requires :doc:`newton <newton>` bond off
such that all processors containing an atom know when a bond breaks.
Additionally, one must use the following special bond settings
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1
These settings accomplish two goals. First, they turn off 1-3 and 1-4
special bond lists, which are not currently supported for BPMs. As
BPMs often have dense bond networks, generating 1-3 and 1-4 special
bond lists is expensive. By setting the lj weight for 1-2 bonds to
zero, this turns off pairwise interactions. Even though there are no
charges in BPM models, setting a nonzero coul weight for 1-2 bonds
ensures all bonded neighbors are still included in the neighbor list
in case bonds break between neighbor list builds.
To monitor the fracture of bonds in the system, all BPM bond styles
have the ability to record instances of bond breakage to output using
the :doc:`dump local <dump>` command. Since one may frequently output
a list of broken bonds and the time they broke, the
:doc:`dump modify <dump_modify>` option *header no* may be useful to
avoid repeatedly printing the header of the dump file. An example of
this procedure is found in /examples/bpm/impact/. Additionally,
one can use :doc:`compute nbond/atom <compute_nbond_atom>` to tally the
current number of bonds per atom.
See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
more information.
----------
While LAMMPS has many utilities to create and delete bonds, *only*
the following are currently compatible with BPM bond styles:

2
doc/src/Howto_github.rst
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@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS
distribution. It uses the process of updating this very tutorial as an
example to describe the individual steps and options. You need to be
familiar with git and you may want to have a look at the `git book
<http://git-scm.com/book/>`_ to familiarize yourself with some of the
<https://git-scm.com/book/>`_ to familiarize yourself with some of the
more advanced git features used below.
As of fall 2016, submitting contributions to LAMMPS via pull requests

2
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@ -47,4 +47,4 @@ to the relevant fixes.
.. _Paquay1:
**(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

63
doc/src/Howto_mdi.rst
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@ -5,9 +5,9 @@ Client/server coupling of two (or more) codes is where one code is the
"client" and sends request messages (data) to one (or more) "server"
code(s). A server responds to each request with a reply message
(data). This enables two (or more) codes to work in tandem to perform
a simulation. LAMMPS can act as either a client or server code; it
does this by using the `MolSSI Driver Interface (MDI) library
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
a simulation. In this context, LAMMPS can act as either a client or
server code. It does this by using the `MolSSI Driver Interface (MDI)
library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
developed by the `Molecular Sciences Software Institute (MolSSI)
<https://molssi.org>`_, which is supported by the :ref:`MDI <PKG-MDI>`
package.
@ -63,22 +63,39 @@ The package also provides a :doc:`mdi plugin <mdi>` command which
enables LAMMPS to operate as an MDI driver and load an MDI engine as a
plugin library.
The package also has a `fix mdi/aimd <fix_mdi_aimd>` command in which
LAMMPS operates as an MDI driver to perform *ab initio* MD simulations
in conjunction with a quantum mechanics code. Its post_force() method
illustrates how a driver issues MDI commands to another code. This
command can be used to couple to an MDI engine which is either a
stand-alone code or a plugin library.
The package also has a `fix mdi/qm <fix_mdi_qm>` command in which
LAMMPS operates as an MDI driver in conjunction with a quantum
mechanics code as an MDI engine. The post_force() method of the
fix_mdi_qm.cpp file shows how a driver issues MDI commands to another
code. This command can be used to couple to an MDI engine which is
either a stand-alone code or a plugin library.
As explained on the `fix mdi/qm <fix_mdi_qm>` command doc page, it can
be used to perform *ab initio* MD simulations or energy minimizations,
or to evaluate the quantum energy and forces for a series of
independent systems. The examples/mdi directory has example input
scripts for all of these use cases.
----------
The examples/mdi directory contains Python scripts and LAMMPS input
script which use LAMMPS as either an MDI driver or engine or both.
Three example use cases are provided:
Currently, 5 example use cases are provided:
* Run ab initio MD (AIMD) using 2 instances of LAMMPS, one as driver
and one as an engine. As an engine, LAMMPS is a surrogate for a
quantum code.
* Run ab initio MD (AIMD) using 2 instances of LAMMPS. As a driver
LAMMPS performs the timestepping in either NVE or NPT mode. As an
engine, LAMMPS computes forces and is a surrogate for a quantum
code.
* As a driver, LAMMPS runs an MD simulation. Every N steps it passes
the current snapshot to an MDI engine to evaluate the energy,
virial, and peratom forces. As the engine LAMMPS is a surrogate for
a quantum code.
* As a driver, LAMMPS loops over a series of data files and passes the
configuration to an MDI engine to evaluate the energy, virial, and
peratom forces. As the engine LAMMPS is a surrogate for a quantum
code.
* A Python script driver invokes a sequence of unrelated LAMMPS
calculations. Calculations can be single-point energy/force
@ -91,20 +108,22 @@ Three example use cases are provided:
Note that in any of these example where LAMMPS is used as an engine,
an actual QM code (which supports MDI) could be used in its place,
without modifying other code or scripts, except to specify the name of
the QM code.
without modifying the input scripts or launch commands, except to
specify the name of the QM code.
The examples/mdi/README file explains how to launch both driver and
The examples/mdi/Run.sh file illustrates how to launch both driver and
engine codes so that they communicate using the MDI library via either
MPI or sockets.
MPI or sockets. Or using the engine as a stand-alone code or plugin
library.
-------------
Currently there are two quantum DFT codes which have direct MDI
support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
and `INQ <https://qsg.llnl.gov/node/101.html>`_. There are also
several QM codes which have indirect support through QCEngine or i-PI.
The former means they require a wrapper program (QCEngine) with MDI
Currently there are at least two quantum DFT codes which have direct
MDI support, `Quantum ESPRESSO (QE)
<https://www.quantum-espresso.org/>`_ and `INQ
<https://qsg.llnl.gov/node/101.html>`_. There are also several QM
codes which have indirect support through QCEngine or i-PI. The
former means they require a wrapper program (QCEngine) with MDI
support which writes/read files to pass data to the quantum code
itself. The list of QCEngine-supported and i-PI-supported quantum
codes is on the `MDI webpage

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@ -38,7 +38,7 @@ the partial charge assignments change:
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
the SPC and SPC/E models.
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
----------

16
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@ -30,9 +30,11 @@ can be coupled to another Langevin thermostat applied to the atoms
using :doc:`fix langevin <fix_langevin>` in order to simulate
thermostatted spin-lattice systems.
The magnetic Gilbert damping can also be applied using :doc:`fix langevin/spin <fix_langevin_spin>`. It allows to either dissipate
the thermal energy of the Langevin thermostat, or to perform a
relaxation of the magnetic configuration toward an equilibrium state.
The magnetic damping can also be applied
using :doc:`fix langevin/spin <fix_langevin_spin>`.
It allows to either dissipate the thermal energy of the Langevin
thermostat, or to perform a relaxation of the magnetic configuration
toward an equilibrium state.
The command :doc:`fix setforce/spin <fix_setforce>` allows to set the
components of the magnetic precession vectors (while erasing and
@ -52,9 +54,11 @@ All the computed magnetic properties can be output by two main
commands. The first one is :doc:`compute spin <compute_spin>`, that
enables to evaluate magnetic averaged quantities, such as the total
magnetization of the system along x, y, or z, the spin temperature, or
the magnetic energy. The second command is :doc:`compute property/atom <compute_property_atom>`. It enables to output all the
per atom magnetic quantities. Typically, the orientation of a given
magnetic spin, or the magnetic force acting on this spin.
the magnetic energy. The second command
is :doc:`compute property/atom <compute_property_atom>`.
It enables to output all the per atom magnetic quantities. Typically,
the orientation of a given magnetic spin, or the magnetic force
acting on this spin.
----------

4
doc/src/Howto_structured_data.rst
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@ -184,7 +184,7 @@ frame.
.. code-block:: python
import re, yaml
import yaml
import pandas as pd
try:
@ -193,7 +193,7 @@ frame.
from yaml import SafeLoader as Loader
with open("ave.yaml") as f:
ave = yaml.load(docs, Loader=Loader)
ave = yaml.load(f, Loader=Loader)
keys = ave['keywords']
df = {}

2
doc/src/Howto_tip3p.rst
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@ -49,7 +49,7 @@ details:
| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
|
Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
----------

39
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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
@ -87,17 +97,18 @@ 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 <http://en.wikipedia.org/wiki/Water_model>`_.
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
----------

126
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@ -0,0 +1,126 @@
Type labels
===========
.. versionadded:: 15Sep2022
Each atom in LAMMPS has an associated numeric atom type. Similarly,
each bond, angle, dihedral, and improper is assigned a bond type,
angle type, and so on. The primary use of these types is to map
potential (force field) parameters to the interactions of the atom,
bond, angle, dihedral, and improper.
By default, type values are entered as integers from 1 to Ntypes
wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box
is created.
A recent addition to LAMMPS is the option to use strings - referred
to as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through
the :doc:`include command <include>` for different systems with different
numerical values assigned to types. This generality also applies to
other inputs like data files read by :doc:`read_data <read_data>` or
molecule template files read by the :doc:`molecule <molecule>`
command. See below for a list of other commands that can use
type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total
number of types is locked in when creating the simulation box, and
potential parameters for each type must be provided even if not used
by any interactions.
A collection of type labels for all type-kinds (atom types, bond types,
etc.) is stored as a "label map" which is simply a list of numeric types
and their associated type labels. Within a type-kind, each type label
must be unique. It can be assigned to only one numeric type. To read
and write type labels to data files for a given type-kind, *all*
associated numeric types need have a type label assigned. Partial
maps can be saved with the :doc:`labelmap write <labelmap>` command
and read back with the :doc:`include <include>` command.
Valid type labels can contain most ASCII characters, but cannot start
with a number, a '#', or a '*'. Also, labels must not contain whitespace
characters. When using the :doc:`labelmap command <labelmap>` in the
LAMMPS input, if certain characters appear in the type label, such as
the single (') or double (") quote or the '#' character, the label
must be put in either double, single, or triple (""") quotes. Triple
quotes allow for the most generic type label strings, but they require
to have a leading and trailing blank space. When defining type labels
the blanks will be ignored. Example:
.. code-block:: LAMMPS
labelmap angle 1 """ C1'-C2"-C3# """
This command will map the string ```C1'-C2"-C3#``` to the angle type 1.
There are two ways to define label maps. One is via the :doc:`labelmap
<labelmap>` command. The other is via the :doc:`read_data <read_data>`
command. A data file can have sections such as *Atom Type Labels*, *Bond
Type Labels*, etc., which assign type labels to numeric types. The
label map can be written out to data files by the :doc:`write_data
<write_data>` command. This map is also written to and read from
restart files, by the :doc:`write_restart <write_restart>` and
:doc:`read_restart <read_restart>` commands.
----------
Use of type labels in LAMMPS input or output
""""""""""""""""""""""""""""""""""""""""""""
Many LAMMPS input script commands that take a numeric type as an
argument can use the associated type label instead. If a type label
is not defined for a particular numeric type, only its numeric type
can be used.
This example assigns labels to the atom types, and then uses the type
labels to redefine the pair coefficients.
.. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 # numeric types
labelmap atom 1 C 2 H
pair_coeff C H 1.0 1.0 # type labels
Adding support for type labels to various commands is an ongoing
project. If an input script command (or a section in a file read by a
command) allows substituting a type label for a numeric type argument,
it will be explicitly mentioned in that command's documentation page.
As a temporary measure, input script commands can take advantage of
variables and how they can be expanded during processing of the input.
The variables can use functions that will translate type label strings
to their respective number as defined in the current label map. See the
:doc:`variable <variable>` command for details.
For example, here is how the pair_coeff command could be used with
type labels if it did not yet support them, either with an explicit
variable command or an implicit variable used in the pair_coeff
command.
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
variable atom1 equal label2type(atom,C)
variable atom2 equal label2type(atom,H)
pair_coeff ${atom1} ${atom2} 1.0 1.0
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
pair_coeff $(label2type(atom,C)) $(label2type(atom,H)) 80.0 1.2
----------
Commands that can use label types
"""""""""""""""""""""""""""""""""
Any workflow that involves reading multiple data files, molecule
templates or a combination of the two can be streamlined by using type
labels instead of numeric types, because types are automatically synced
between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without
modification in multiple simulations or different systems.

17
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@ -68,7 +68,8 @@ liquid Ar via the GK formalism:
# Sample LAMMPS input script for viscosity of liquid Ar
units real
variable T equal 86.4956
variable T equal 200.0 # run temperature
variable Tinit equal 250.0 # equilibration temperature
variable V equal vol
variable dt equal 4.0
variable p equal 400 # correlation length
@ -99,12 +100,14 @@ liquid Ar via the GK formalism:
# equilibration and thermalization
velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
velocity all create ${Tinit} 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp ${Tinit} ${Tinit} 10 drag 0.2
run 8000
# viscosity calculation, switch to NVE if desired
velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
#unfix NVT
#fix NVE all nve
@ -122,7 +125,7 @@ liquid Ar via the GK formalism:
run 100000
variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol
print "average viscosity: $v [Pa.s] @ $T K, ${ndens} /A^3"
print "average viscosity: $v [Pa.s] @ $T K, ${ndens} atoms/A^3"
The fifth method is related to the above Green-Kubo method,
but uses the Einstein formulation, analogous to the Einstein
@ -131,9 +134,9 @@ time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times.
The sixth is periodic perturbation method. It is also a non-equilibrium MD method.
However, instead of measure the momentum flux in response of applied velocity gradient,
it measures the velocity profile in response of applied stress.
The sixth is the periodic perturbation method, which is also a non-equilibrium MD method.
However, instead of measuring the momentum flux in response to an applied velocity gradient,
it measures the velocity profile in response to applied stress.
A cosine-shaped periodic acceleration is added to the system via the
:doc:`fix accelerate/cos <fix_accelerate_cos>` command,
and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the

7
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@ -17,9 +17,10 @@ formats. See the :doc:`Tools <Tools>` page for details.
A Python-based toolkit distributed by our group can read native LAMMPS
dump files, including custom dump files with additional columns of
user-specified atom information, and convert them to various formats
or pipe them into visualization software directly. See the `Pizza.py WWW site <pizza_>`_ for details. Specifically, Pizza.py can convert
LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
user-specified atom information, and convert them to various formats or
pipe them into visualization software directly. See the `Pizza.py WWW
site <pizza_>`_ for details. Specifically, Pizza.py can convert LAMMPS
dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
RasMol visualization programs. Pizza.py has tools that do interactive
3d OpenGL visualization and one that creates SVG images of dump file

18
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@ -3,10 +3,20 @@ Install LAMMPS
You can download LAMMPS as an executable or as source code.
With source code, you also have to :doc:`build LAMMPS <Build>`. But you
have more flexibility as to what features to include or exclude in the
build. If you plan to :doc:`modify or extend LAMMPS <Modify>`, then you
need the source code.
When downloading the LAMMPS source code, you also have to :doc:`build
LAMMPS <Build>`. But you have more flexibility as to what features to
include or exclude in the build. When you download and install
pre-compiled LAMMPS executables, you are limited to install which
version of LAMMPS is available and which features are included of these
builds. If you plan to :doc:`modify or extend LAMMPS <Modify>`, then
you **must** build LAMMPS from the source code.
.. note::
If you have questions about the pre-compiled LAMMPS executables, you
need to contact the people preparing those executables. The LAMMPS
developers have no control over their choices of how they configure
and build their packages and when they update them.
.. toctree::
:maxdepth: 1

11
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@ -5,7 +5,7 @@ Binaries are available for MacOS or Linux via `Conda <conda_>`_.
First, one must setup the Conda package manager on your system. Follow the
instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
environment (named `my-lammps-env` or whatever you prefer) for your lammps
environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS
install:
.. code-block:: bash
@ -13,7 +13,7 @@ install:
% conda config --add channels conda-forge
% conda create -n my-lammps-env
Then, you can install lammps on your system with the following command:
Then, you can install LAMMPS on your system with the following command:
.. code-block:: bash
@ -38,3 +38,10 @@ up the Conda capability.
.. _openkim: https://openkim.org
.. _conda: https://docs.conda.io/en/latest/index.html
.. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
.. note::
If you have questions about these pre-compiled LAMMPS executables,
you need to contact the people preparing those packages. The LAMMPS
developers have no control over their choices of how they configure
and build their packages and when they update them.

130
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@ -3,13 +3,19 @@ Download an executable for Linux
Binaries are available for different versions of Linux:
| :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
| :ref:`Pre-built Fedora Linux executables <fedora>`
| :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
| :ref:`Pre-built OpenSuse Linux executables <opensuse>`
| :ref:`Gentoo Linux executable <gentoo>`
| :ref:`Arch Linux build-script <arch>`
|
- :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
- :ref:`Pre-built Fedora Linux executables <fedora>`
- :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
- :ref:`Pre-built OpenSuse Linux executables <opensuse>`
- :ref:`Gentoo Linux executable <gentoo>`
- :ref:`Arch Linux build-script <arch>`
.. note::
If you have questions about these pre-compiled LAMMPS executables,
you need to contact the people preparing those packages. The LAMMPS
developers have no control over their choices of how they configure
and build their packages and when they update them.
----------
@ -18,41 +24,28 @@ Binaries are available for different versions of Linux:
Pre-built Ubuntu Linux executables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
A pre-built LAMMPS executable suitable for running on the latest
Ubuntu Linux versions, can be downloaded as a Debian package. This
allows you to install LAMMPS with a single command, and stay
up-to-date with the current stable version of LAMMPS by simply updating
your operating system. Please note, that the repository below offers
two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``. The
LAMMPS developers recommend to use the ``lammps-stable`` package for
any production simulations. The ``lammps-daily`` package is built
from the LAMMPS development sources, and those versions may have known
issues and bugs when new features are added and the software has not
undergone full release testing.
To install the appropriate personal-package archives (PPAs), do the
following once:
.. code-block:: bash
$ sudo add-apt-repository ppa:gladky-anton/lammps
$ sudo add-apt-repository ppa:openkim/latest
$ sudo apt-get update
A pre-built LAMMPS executable suitable for running on the latest Ubuntu
Linux versions, can be downloaded as a Debian package. This allows you
to install LAMMPS with a single command, and stay (mostly) up-to-date
with the current stable version of LAMMPS by simply updating your
operating system.
To install LAMMPS do the following once:
.. code-block:: bash
$ sudo apt-get install lammps-stable
$ sudo apt-get install lammps
This downloads an executable named ``lmp_stable`` to your box, which
can then be used in the usual way to run input scripts:
This downloads an executable named ``lmp`` to your box and multiple
packages with supporting data, examples and libraries as well as any
missing dependencies. This executable can then be used in the usual way
to run input scripts:
.. code-block:: bash
$ lmp_stable -in in.lj
$ lmp -in in.lj
To update LAMMPS to the most current stable version, do the following:
To update LAMMPS to the latest packaged version, do the following:
.. code-block:: bash
@ -60,44 +53,24 @@ To update LAMMPS to the most current stable version, do the following:
which will also update other packages on your system.
To get a copy of the current documentation and examples:
.. code-block:: bash
$ sudo apt-get install lammps-stable-doc
which will download the doc files in
``/usr/share/doc/lammps-stable-doc/doc`` and example problems in
``/usr/share/doc/lammps-doc/examples``.
To get a copy of the current potentials files:
.. code-block:: bash
$ sudo apt-get install lammps-stable-data
which will download the potentials files to
``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is
hard-coded to look for potential files in this directory (it does not
use the ``LAMMPS_POTENTIALS`` environment variable, as described
in :doc:`pair_coeff <pair_coeff>` command).
The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
results in the above command also installing the ``kim-api`` binaries when LAMMPS
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
can install the ``openkim-models`` package
The ``lmp`` binary is built with the :ref:`KIM package <kim>` included,
which results in the above command also installing the ``kim-api``
binaries when LAMMPS is installed. In order to use potentials from
`openkim.org <openkim_>`_, you can also install the ``openkim-models``
package
.. code-block:: bash
$ sudo apt-get install openkim-models
Or use the KIM-API commands to download and install individual models.
To un-install LAMMPS, do the following:
.. code-block:: bash
$ sudo apt-get remove lammps-stable
$ sudo apt-get remove lammps
Please use ``lmp_stable -help`` to see which compilation options, packages,
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
@ -110,21 +83,21 @@ Ubuntu package capability.
Pre-built Fedora Linux executables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pre-built LAMMPS packages for stable releases are available
in the Fedora Linux distribution as of version 28. The packages
can be installed via the dnf package manager. There are 3 basic
varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
lammps-openmpi = OpenMPI MPI library) and for each support for
linking to the C library interface (lammps-devel, lammps-mpich-devel,
lammps-openmpi-devel), the header for compiling programs using
the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``
or ``lmp_mpich`` respectively. By default, ``lmp`` will refer to the
serial executable, unless one of the MPI environment modules is loaded
(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).
Then the corresponding parallel LAMMPS executable can be used.
The same mechanism applies when loading the LAMMPS python module.
Pre-built LAMMPS packages for stable releases are available in the
Fedora Linux distribution as of Fedora version 28. The packages can be
installed via the dnf package manager. There are 3 basic varieties
(lammps = no MPI, lammps-mpich = MPICH MPI library, lammps-openmpi =
OpenMPI MPI library) and for each support for linking to the C library
interface (lammps-devel, lammps-mpich-devel, lammps-openmpi-devel), the
header for compiling programs using the C library interface
(lammps-headers), and the LAMMPS python module for Python 3. All
packages can be installed at the same time and the name of the LAMMPS
executable is ``lmp`` and ``lmp_openmpi`` or ``lmp_mpich`` respectively.
By default, ``lmp`` will refer to the serial executable, unless one of
the MPI environment modules is loaded (``module load mpi/mpich-x86_64``
or ``module load mpi/openmpi-x86_64``). Then the corresponding parallel
LAMMPS executable can be used. The same mechanism applies when loading
the LAMMPS python module.
To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
@ -273,3 +246,10 @@ Alternatively, you may use an AUR helper to install these packages.
Note that the AUR provides build-scripts that download the source and
the build the package on your machine.
.. note::
It looks like the Arch Linux AUR repository build scripts for LAMMPS
have not been updated since the 29 October 2020 version. You may want
to consider installing a more current version of LAMMPS from source
directly.

2
doc/src/Install_windows.rst
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@ -6,7 +6,7 @@ Windows system can be downloaded from this site:
.. parsed-literal::
`http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
`https://packages.lammps.org/windows.html <https://packages.lammps.org/windows.html>`_
Note that each installer package has a date in its name, which
corresponds to the LAMMPS version of the same date. Installers for

4
doc/src/Intro_authors.rst
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@ -4,13 +4,13 @@ Authors of LAMMPS
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
* `Steve Plimpton <sjp_>`_, sjplimp at sandia.gov
* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
* Aidan Thompson, athomps at sandia.gov
* Stan Moore, stamoor at sandia.gov
* Axel Kohlmeyer, akohlmey at gmail.com
* Richard Berger, richard.berger at outlook.com
.. _sjp: http://www.cs.sandia.gov/~sjplimp
.. _sjp: https://sjplimp.github.io
.. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia,

6
doc/src/Intro_citing.rst
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@ -27,14 +27,14 @@ namely https://www.lammps.org.
The original publication describing the parallel algorithms used in the
initial versions of LAMMPS is:
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
`S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <https://doi.org/10.1006/jcph.1995.1039>`_
DOI for the LAMMPS source code
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
to create digital object identifies (DOI) for stable releases of the
The LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
to create digital object identifiers (DOI) for stable releases of the
LAMMPS source code. There are two types of DOIs for the LAMMPS source code.
The canonical DOI for **all** versions of LAMMPS, which will always

4
doc/src/Intro_features.rst
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@ -95,7 +95,7 @@ commands)
* metal-organic framework potentials (QuickFF, MO-FF)
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>`
* access to the `OpenKIM Repository <https://openkim.org>`_ of potentials via the :doc:`kim command <kim_commands>`
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
@ -205,7 +205,7 @@ Pre- and post-processing
.. _pizza: https://lammps.github.io/pizza
.. _python: http://www.python.org
.. _python: https://www.python.org
.. _special:

6
doc/src/Intro_nonfeatures.rst
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@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
linear bead-spring polymer chains. The moltemplate program is a true
molecular builder that will generate complex molecular models. See
the :doc:`Tools <Tools>` page for details on tools packaged with
LAMMPS. The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
LAMMPS. The `Pre/post processing page <https:/www.lammps.org/prepost.html>`_ of the LAMMPS website
describes a variety of third party tools for this task. Furthermore,
some LAMMPS internal commands allow to reconstruct, or selectively add
topology information, as well as provide the option to insert molecule
@ -80,5 +80,5 @@ Here are suggestions on how to perform these tasks:
`Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in `Python <http://www.python.org>`_
and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
above bullets. Pizza.py is written in `Python <https://www.python.org>`_
and is available for download from `this page <https://sjplimp.github.io/download.html>`_.

4
doc/src/Intro_opensource.rst
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@ -23,9 +23,9 @@ applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
.. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
.. _gnuorg: http://www.gnu.org
.. _gnuorg: https://www.gnu.org
.. _opensource: http://www.opensource.org
.. _opensource: https://www.opensource.org
Here is a more specific summary of what the GPL means for LAMMPS users:

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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

6
doc/src/Library_create.rst
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@ -11,6 +11,7 @@ This section documents the following functions:
- :cpp:func:`lammps_mpi_finalize`
- :cpp:func:`lammps_kokkos_finalize`
- :cpp:func:`lammps_python_finalize`
- :cpp:func:`lammps_error`
--------------------
@ -115,3 +116,8 @@ calling program.
.. doxygenfunction:: lammps_python_finalize
:project: progguide
-----------------------
.. doxygenfunction:: lammps_error
:project: progguide

8
doc/src/Library_objects.rst
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@ -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

30
doc/src/Library_properties.rst
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@ -15,21 +15,21 @@ This section documents the following functions:
--------------------
The library interface allows extraction of different kinds of
information about the active simulation instance and also
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 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 indexed
accordingly. Per-atom data can change sizes and ordering at every
neighbor list rebuild or atom sort event as atoms migrate between
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
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
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, 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

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