ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'develop' into bond/react-molmap_option

Browse Source
This commit is contained in:
Axel Kohlmeyer
2025-03-30 23:27:50 -04:00
parent 05521d38d9 285baf27b5
commit 935e323d08
2010 changed files with 177765 additions and 51686 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
.github/CODEOWNERS vendored
View File

@ -72,6 +72,8 @@ src/EXTRA-COMMAND/ndx_group.* @akohlmey
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
src/EXTRA-PAIR/d3_parameters.h @soniasolomoni @arthurfl
src/MISC/*_tracker.* @jtclemm
src/MC/fix_gcmc.* @athomps
src/MC/fix_sgcmc.* @athomps

372
.github/release_steps.md vendored
View File

@ -1,42 +1,54 @@
# LAMMPS Release Steps
The following notes chronicle the current steps for preparing and publishing LAMMPS releases. For
definitions of LAMMPS versions and releases mean, please refer to [the corresponding section in the
LAMMPS manual](https://docs.lammps.org/Manual_version.html).
The following notes chronicle the current steps for preparing and
publishing LAMMPS releases. For definitions of LAMMPS versions and
releases, please refer to [the corresponding section in the LAMMPS
manual](https://docs.lammps.org/Manual_version.html).
## LAMMPS Feature Release
A LAMMPS feature release is currently prepared after about 500 to 750 commits to the 'develop'
branch or after a period of four weeks up to two months. This is not a fixed rule, though, since
external circumstances can cause delays in preparing a release, or pull requests that are desired to
be merged for the release are not yet completed.
A LAMMPS feature release is currently prepared after about 500 to 750
commits to the 'develop' branch or after a period of four weeks up to
two months. This is not a fixed rule, though, since external
circumstances can cause delays in preparing a release, or pull requests
that are desired to be merged for the release are not yet completed.
### Preparing a 'next\_release' branch
Create a 'next\_release' branch off 'develop' and make the following changes:
- set the LAMMPS\_VERSION define to the planned release date in src/version.h in the format
"D Mmm YYYY" or "DD Mmm YYYY"
- set the LAMMPS\_VERSION define to the planned release date in
src/version.h in the format "D Mmm YYYY" or "DD Mmm YYYY"
- remove the LAMMPS\_UPDATE define in src/version.h
- update the release date in doc/lammps.1
- update all TBD arguments for ..versionadded::, ..versionchanged:: ..deprecated:: to the
planned release date in the format "DMmmYYYY" or "DDMmmYYYY"
- check release notes for merged new features and check if ..versionadded:: or ..versionchanged::
are missing and need to be added
Submit this pull request, rebase if needed. This is the last pull request merged for the release
and should not contain any other changes. (Exceptions: this document, last minute trivial(!) changes).
- update all TBD arguments for ..versionadded::, ..versionchanged::
..deprecated:: to the planned release date in the format "DMmmYYYY" or
"DDMmmYYYY"
- check release notes for merged new features and check if
..versionadded:: or ..versionchanged:: are missing and need to be
added
This PR shall not be merged before **all** pending tests have completed and cleared. If needed, a
bugfix pull request should be created and merged to clear all tests.
Submit this pull request. This is the last pull request merged for the
release and should not contain any other changes. (Exceptions: this
document, last minute trivial(!) changes).
This PR shall not be merged before **all** pending tests have completed
and cleared. We currently use a mix of automated tests running on
either Temple's Jenkins cluster or GitHub workflows. Those include time
consuming tests not run on pull requests. If needed, a bug-fix pull
request should be created and merged to clear all tests.
### Create release on GitHub
When all pending pull requests for the release are merged and have cleared testing, the
'next\_release' branch is merged into 'develop'.
When all pending pull requests for the release are merged and have
cleared testing, the 'next\_release' branch is merged into 'develop'.
Check out 'develop' locally, pull the latest changes, merge them into 'release', apply a suitable
release tag (for historical reasons the tag starts with "patch_" followed by the date, and finally
push everything back to GitHub. Example:
Check out or update the 'develop' branch locally, pull the latest
changes, merge them into 'release' with a fast forward(!) merge, and
apply a suitable release tag (for historical reasons the tag starts with
"patch_" followed by the date, and finally push everything back to
GitHub. There should be no commits made to 'release' but only
fast forward merges. Example:
```
git checkout develop
@ -44,65 +56,315 @@ git pull
git checkout release
git pull
git merge --ff-only develop
git tag -s -m "LAMMPS feature release 19 November 2024" patch_19Nov2024
git tag -s -m "LAMMPS feature release 4 February 2025" patch_4Feb2025
git push git@github.com:lammps/lammps.git --tags develop release
```
Go to https://github.com/lammps/lammps/releases and create a new (draft) release page or check the
existing draft for any necessary changes from pull requests that were merged but are not listed.
Then select the applied tag for the release in the "Choose a tag" dropdown list. Go to the bottom of
the list and select the "Set as pre-release" checkbox. The "Set as the latest release" button is
Applying this tag will trigger two actions on the Temple Jenkins cluster:
- The online manual at https://docs.lammps.org/ will be updated to the
state of the 'release' branch. Merges to the 'develop' branch will
trigger updating https://docs.lammps.org/latest/ so by reviewing the
version of the manual under the "latest" URL, it is possible to preview
what the updated release documentation will look like.
- A downloadable tar archive of the LAMMPS distribution that includes the
html format documentation and a PDF of the manual will be created and
uploaded to the download server at https://download.lammps.org/tars
Note that the file is added, but the `index.html` file is not updated,
so it is not yet publicly visible.
Go to https://github.com/lammps/lammps/releases and create a new (draft)
release page with a summary of all the changes included and references
to the pull requests they were merged from or check the existing draft
for any necessary changes from pull requests that were merged but are
not listed. Then select the applied tag for the release in the "Choose
a tag" drop-down list. Go to the bottom of the list and select the "Set
as pre-release" checkbox. The "Set as the latest release" button is
reserved for stable releases and updates to them.
If everything is in order, you can click on the "Publish release" button. Otherwise, click on "Save
draft" and finish pending tasks until you can return to edit the release page and publish it.
If everything is in order, you can click on the "Publish release"
button. Otherwise, click on "Save draft" and finish pending tasks until
you can return to edit the release page and publish it.
### Update download website, prepare pre-compiled packages, update packages to GitHub
### Prepare pre-compiled packages, update packages to GitHub
Publishing the release on GitHub will trigger the Temple Jenkins cluster to update
the https://docs.lammps.org/ website with the documentation for the new feature release
and it will create a tarball for download (which contains the translated manual).
A suitable build environment is provided with the
https://download.lammps.org/static/fedora41_musl_mingw.sif container
image. The corresponding container build definition file is maintained
in the tools/singularity folder of the LAMMPS source distribution.
Build a fully static LAMMPS installation using a musl-libc cross-compiler, install into a
lammps-static folder, and create a tarball called lammps-linux-x86_64-19Nov2024.tar.gz (or using a
corresponding date with a future release) from the lammps-static folder and upload it to GitHub
#### Fully portable static Linux x86_64 non-MPI binaries
The following commands use the Fedora container to build a fully static
LAMMPS installation using a musl-libc cross-compiler, install it into a
`lammps-static` folder, and create a tarball called
`lammps-linux-x86_64-4Feb2025.tar.gz` (or using a corresponding date
with a future release) from the `lammps-static` folder.
``` sh
rm -rf release-packages
mkdir release-packages
cd release-packages
wget https://download.lammps.org/static/fedora41_musl.sif
apptainer shell fedora41_musl.sif
git clone -b release --depth 10 https://github.com/lammps/lammps.git lammps-release
cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
cmake --build build-release --target all
cmake --build build-release --target install
/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
exit # fedora 41 container
cd ..
```
The resulting tar archive can be uploaded to the GitHub release page with:
``` sh
gh release upload patch_4Feb2025 lammps-linux-x86_64-4Feb2025.tar.gz
```
#### Linux x86_64 Flatpak bundle with GUI included
Make sure you have the `flatpak` and `flatpak-builder` packages
installed locally (they require binaries that run with elevated
privileges and thus cannot be used from the container) and build a
LAMMPS and LAMMPS-GUI flatpak bundle in the `release-packages` folder
with:
```
gh release upload patch_19Nov2024 ~/Downloads/lammps-linux-x86_64-19Nov2024.tar.gz
``` sh
cd release-packages
flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
flatpak-builder --force-clean --verbose --repo=$PWD/flatpak-repo --install-deps-from=flathub --state-dir=$PWD --user --ccache --default-branch=release flatpak-build lammps-release/tools/lammps-gui/org.lammps.lammps-gui.yml
flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo --verbose $PWD/flatpak-repo ../LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak org.lammps.lammps-gui release
cd ..
```
The resulting flatpak bundle file can be uploaded to the GitHub release page with:
``` sh
gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak
```
#### LAMMPS Source tarball
The container for the static binary can also be used to prepare the source
tarball including the HTML and PDF manual (this is currently done automatically
when the releases is created and the tarball uploaded to https://download.lammps.org/tars/).
The steps are as follows:
``` sh
cd release-packages
apptainer shell fedora41_musl_mingw.sif
cd lammps-release
rm -f ../release.tar*
git archive --output=../release.tar --prefix=lammps-4Feb2025/ HEAD
cd doc
make clean-all
make html pdf
tar -rf ../../release.tar --transform 's,^,lammps-4Feb2025/doc/,' html Manual.pdf
gzip -9v ../../release.tar
mv ../../release.tar.gz ../../lammps-src-4Feb2025.tar.gz
exit # fedora41 container
cd ..
```
The resulting source tarball can be uploaded to the GitHub release page with:
``` sh
gh release upload patch_4Feb2025 lammps-src-4Feb2025.tar.gz
```
#### Build Windows Installer Packages with MinGW Linux-to-Windows Cross-compiler
The various Windows installer packages can also be built with
apptainer container image.
``` sh
cd release-packages
apptainer shell fedora41_musl_mingw.sif
git clone --depth 10 https://github.com/lammps/lammps-packages.git lammps-packages
cd lammps-packages/mingw-cross
ln -sf ../../lammps-release lammps
./buildall.sh release >& mk.log & less +F mk.log
```
The installer with the GUI included can be uploaded to the GitHub release page with:
``` sh
ln -sf LAMMPS-64bit-GUI-4Feb2025.exe LAMMPS-Win10-64bit-GUI-4Feb2025.exe
gh release upload patch_4Feb2025 LAMMPS-Win10-64bit-GUI-4Feb2025.exe
```
The symbolic link is used to have a consistent naming scheme for the packages
attached to the GitHub release page.
#### Clean up:
``` sh
cd ..
rm -r release-packages
```
#### Build Multi-arch App-bundle for macOS
Building app-bundles for macOS is not as easily automated and portable
as some of the other steps. It requires a machine actually running
macOS. In that machine the Xcode compiler package needs to be
installed. This also includes tools for building and manipulating disk
images. This compiler supports building executables for both, the
x86_64 and the arm64 architectures. This requires building with CMake
and using the CMake settings:
``` sh
-D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0
```
This will add the compiler flags `-arch arm64 -arch x86_64
-mmacosx-version-min=11.0` and thus produce object for both
architectures and support for macOS versions back to version 11 (aka Big
Sur). With these settings the following libraries should be compiled
and installed (e.g. to `$HOME/.local`) as static libraries only:
- libomp taken from the LLVM/Clang source distribution (to support OpenMP)
- jpeg
- zlib
- png
- Qt (for LAMMPS-GUI)
When configuring LAMMPS the `cmake/presets/clang.cmake` should be used
and as many packages as possible enabled. For LAMMPS-GUI, MPI should be
disabled with `-D BUILD_MPI=OFF` and LAMMPS-GUI enabled with
`-D BUILD_LAMMPS_GUI=ON`. If the CMake configuration is successful,
settings for building a macOS app-bundle are enabled and with `cmake
--build build --target dmg` extra steps will be executed that will build
a macOS application installer image under the name
`LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg`
The application image can be uploaded to the GitHub release page with:
``` sh
ln -sf LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
gh release upload patch_4Feb2025 LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
```
The symbolic link is used to have a consistent naming scheme for the packages
attached to the GitHub release page.
We are currently building the application images on macOS 12 (aka Monterey).
#### Build Linux x86_64 binary tarball on Ubuntu 20.04LTS
While the flatpak Linux version uses portable runtime libraries provided
by the flatpak environment, we also build regular Linux executables that
use a wrapper script and matching shared libraries in a tarball. To be
compatible with many Linux distributions, one has to build this on a
very old Linux distribution, since most Linux system libraries are
usually backward compatible but not forward compatible. This is
currently done on an Ubuntu 20.04LTS system. Once LAMMPS moves to
require CMake 3.20 and C++17, we will have to move to Ubuntu 22.04LTS.
This installation (either on a real or a virtual machine) should have
the packages installed that are indicated in
`tools/singularity/ubuntu20.04.def` plus Qt version 5.x with development
headers, so that LAMMPS-GUI can be compiled.
Also the building of the binary tarball and setup of the bundled
libraries and wrapper scripts is automated and can executed with `cmake
--build build --target tgz`. This should produce a file
`LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz` which can be uploaded to the
GitHub release page with:
``` sh
ln -sf LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
```
### Update download page on LAMMPS website
Check out the LAMMPS website repo
https://github.com/lammps/lammps-website.git and edit the file
`src/download.txt` for the new release. Test translation with `make
html` and review `html/download.html` Then add and commit to git and
push the changes to GitHub. The Temple Jenkis cluster will
automatically update https://www.lammps.org/download.html accordingly.
Also notify Steve of the release so he can update `src/bug.txt` on the
website from the available release notes.
## LAMMPS Stable Release
A LAMMPS stable release is prepared about once per year in the months July, August, or September.
One (or two, if needed) feature releases before the stable release shall contain only bug fixes
or minor feature updates in optional packages. Also substantial changes to the core of the code
shall be applied rather toward the beginning of a development cycle between two stable releases
than toward the end. The intention is to stablilize significant change to the core and have
outside users and developers try them out during the development cycle; the sooner the changes
are included, the better chances for spotting peripheral bugs and issues.
A LAMMPS stable release is prepared about once per year in the months
July, August, or September. One (or two, if needed) feature releases
before the stable release shall contain only bug fixes or minor feature
updates in optional packages. Also substantial changes to the core of
the code shall be applied rather toward the beginning of a development
cycle between two stable releases than toward the end. The intention is
to stablilize significant change to the core and have outside users and
developers try them out during the development cycle; the sooner the
changes are included, the better chances for spotting peripheral bugs
and issues.
### Prerequesites
Before making a stable release all remaining backported bugfixes shall be released as a (final)
stable update release (see below).
Before making a stable release all remaining backported bugfixes shall
be released as a (final) stable update release (see below).
A LAMMPS stable release process starts like a feature release (see above), only that this feature
release is called a "Stable Release Candidate" and no assets are uploaded to GitHub.
A LAMMPS stable release process starts like a feature release (see
above), only that this feature release is called a "Stable Release
Candidate" and no assets are uploaded to GitHub.
### Synchronize 'maintenance' branch with 'release'
The state of the 'release' branch is then transferred to the 'maintenance' branch (which will
have diverged significantly from 'release' due to the selectively backported bug fixes).
The state of the 'release' branch is then transferred to the
'maintenance' branch (which will have diverged significantly from
'release' due to the selectively backported bug fixes).
### Fast-forward merge of 'maintenance' into 'stable' and apply tag
At this point it should be possible to do a fast-forward merge of 'maintenance' to 'stable'
and then apply the stable\_DMmmYYYY tag.
At this point it should be possible to do a fast-forward merge of
'maintenance' to 'stable' and then apply the stable\_DMmmYYYY tag.
### Push branches and tags
## LAMMPS Stable Update Release
After making a stable release, bugfixes from the 'develop' branch
are selectively backported to the 'maintenance' branch. This is
done with "git cherry-pick \<commit hash\>' wherever possible.
The LAMMPS\_UPDATE define in "src/version.h" is set to "Maintenance".
### Prerequesites
When a sufficient number of bugfixes has accumulated or an urgent
or important bugfix needs to be distributed a new stable update
release is made. To make this publicly visible a pull request
is submitted that will merge 'maintenance' into 'stable'. Before
merging, set LAMMPS\_UPDATE in "src/version.h" to "Update #" with
"#" indicating the update count (1, 2, and so on).
Also draft suitable release notes under https://github.com/lammps/lammps/releases
### Fast-forward merge of 'maintenance' into 'stable', apply tag, and publish
Do a fast-forward merge of 'maintenance' to 'stable' and then
apply the stable\_DMmmYYYY\_update# tag and push branch and tag
to GitHub. The corresponding pull request will be automatically
closed. Example:
```
git checkout maintenance
git pull
git checkout stable
git pull
git merge --ff-only maintenance
git tag -s -m 'Update 2 for Stable LAMMPS version 29 August 2024' stable_29Aug2024_update2
git push git@github.com:lammps/lammps.git --tags maintenance stable
```
Associate draft release notes with new tag and publish as "latest release".
On https://ci.lammps.org/ go to "dev", "stable" and manually execute
the "update\_release" task. This will update https://docs.lammps.org/stable
and prepare a stable tarball.
### Build and upload binary packages and source tarball to GitHub
The build procedure is the same as for the feature releases, only
that packages are built from the 'stable' branch.

2
.github/workflows/check-vla.yml vendored
View File

@ -77,7 +77,7 @@ jobs:
-D PKG_MDI=on \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=off \
-D PKG_ML-RANN=on \
-D PKG_MOLFILE=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \

1
.github/workflows/coverity.yml vendored
View File

@ -67,7 +67,6 @@ jobs:
-D PKG_MANIFOLD=on \
-D PKG_MDI=on \
-D PKG_MGPT=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_MOLFILE=on \
-D PKG_NETCDF=on \

53
.github/workflows/lammps-gui-flatpak.yml vendored Normal file
View File

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

1
.github/workflows/style-check.yml vendored
View File

@ -35,3 +35,4 @@ jobs:
make check-permissions
make check-homepage
make check-errordocs
make check-fmtlib

81
.github/workflows/unittest-arm64.yml vendored Normal file
View File

@ -0,0 +1,81 @@
# GitHub action to build LAMMPS on Linux with ARM64 and run standard unit tests
name: "Unittest for Linux on ARM64"
on:
push:
branches: [develop]
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Linux ARM64 Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-22.04-arm
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
- name: Install extra packages
run: |
sudo apt-get update
sudo apt-get install -y ccache \
libeigen3-dev \
libcurl4-openssl-dev \
mold \
ninja-build \
python3-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-unit-ccache-${{ github.sha }}
restore-keys: linux-unit-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=on \
-D DOWNLOAD_POTENTIALS=off \
-D ENABLE_TESTING=on \
-D MLIAP_ENABLE_ACE=on \
-D MLIAP_ENABLE_PYTHON=off \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Tests
working-directory: build
shell: bash
run: ctest -V -LE unstable

15
README
View File

@ -23,17 +23,20 @@ more information about the code and its uses.
The LAMMPS distribution includes the following files and directories:
README this file
LICENSE the GNU General Public License (GPL)
bench benchmark problems
LICENSE the GNU General Public License (GPLv2)
CITATION.cff Citation information for LAMMPS in CFF format
bench benchmark inputs
cmake CMake build files
doc documentation
examples simple test problems
fortran Fortran wrapper for LAMMPS
examples example inputs for many LAMMPS commands
fortran Fortran 2003 module for LAMMPS
lib additional provided or external libraries
potentials interatomic potential files
python Python wrappers for LAMMPS
python Python module for LAMMPS
src source files
tools pre- and post-processing tools
unittest test programs for use with CTest
.github Git and GitHub related files and tools
Point your browser at any of these files to get started:
@ -42,6 +45,8 @@ https://docs.lammps.org/Intro.html hi-level introduction
https://docs.lammps.org/Build.html how to build LAMMPS
https://docs.lammps.org/Run_head.html how to run LAMMPS
https://docs.lammps.org/Commands_all.html Table of available commands
https://docs.lammps.org/Howto.html Short tutorials and HowTo discussions
https://docs.lammps.org/Errors.html How to interpret and debug errors
https://docs.lammps.org/Library.html LAMMPS library interfaces
https://docs.lammps.org/Modify.html how to modify and extend LAMMPS
https://docs.lammps.org/Developer.html LAMMPS developer info

52
cmake/CMakeLists.txt
View File

@ -3,6 +3,9 @@
# CMake build system
# This file is part of LAMMPS
cmake_minimum_required(VERSION 3.16)
if(CMAKE_VERSION VERSION_LESS 3.20)
message(WARNING "LAMMPS is planning to require at least CMake version 3.20 by Summer 2025. Please upgrade!")
endif()
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
@ -144,16 +147,28 @@ if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
endif()
# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
# we *require* C++11 without extensions but prefer C++17.
# Kokkos requires at least C++17 (currently)
if(NOT CMAKE_CXX_STANDARD)
if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
set(CMAKE_CXX_STANDARD 17)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(CMAKE_CXX_STANDARD LESS 17)
message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
# turn off C++17 check in lmptype.h
if(LAMMPS_CXX11)
add_compile_definitions(LAMMPS_CXX11)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
@ -194,7 +209,7 @@ endif()
########################################################################
# User input options #
########################################################################
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
# backward compatibility with older LAMMPS documentation
if (PYTHON_EXECUTABLE)
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
endif()
@ -210,6 +225,12 @@ if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
" Setting Python interpreter to: ${Python_EXECUTABLE}")
endif()
find_package(Python COMPONENTS Interpreter QUIET)
# NOTE: RHEL 8.0 and Ubuntu 18.04LTS ship with Python 3.6, Python 3.8 was EOL in 2024
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "LAMMPS requires Python 3.6 or later")
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)
@ -347,6 +368,17 @@ foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
set(DEPRECATED_PACKAGES AWPMD ATC POEMS)
foreach(PKG ${DEPRECATED_PACKAGES})
if(PKG_${PKG})
message(WARNING
"The ${PKG} package will be removed from LAMMPS in Summer 2025 due to lack of "
"maintenance and use of code constructs that conflict with modern C++ compilers "
"and standards. Please contact developers@lammps.org if you have any concerns "
"about this step.")
endif()
endforeach()
######################################################
# packages with special compiler needs or external libs
######################################################
@ -399,8 +431,8 @@ else()
target_link_libraries(lammps PUBLIC mpi_stubs)
endif()
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(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
set(LAMMPS_SIZES_VALUES smallbig bigbig)
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
@ -579,6 +611,16 @@ foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE
endif()
endforeach()
# settings for misc packages and styles
if(PKG_MISC)
option(LAMMPS_ASYNC_IMD "Asynchronous IMD processing" OFF)
mark_as_advanced(LAMMPS_ASYNC_IMD)
if(LAMMPS_ASYNC_IMD)
target_compile_definitions(lammps PRIVATE -DLAMMPS_ASYNC_IMD)
message(STATUS "Using IMD in asynchronous mode")
endif()
endif()
# optionally enable building script wrappers using swig
option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
if(WITH_SWIG)
@ -894,7 +936,7 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
find_package(ClangFormat 11.0)
find_package(ClangFormat 11.0 QUIET)
if(ClangFormat_FOUND)
add_custom_target(format-src

7
cmake/Modules/CodingStandard.cmake
View File

@ -1,11 +1,11 @@
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
# use default (or custom) Python executable.
# Python version check is in main CMakeLists.txt file
if(Python_EXECUTABLE)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 COMPONENTS Interpreter)
if(Python3_EXECUTABLE)
if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
add_custom_target(
check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
@ -37,4 +37,3 @@ if(Python3_EXECUTABLE)
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix permission errors")
endif()
endif()

6
cmake/Modules/Documentation.cmake
View File

@ -13,7 +13,7 @@ if(BUILD_DOC)
endif()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.8)
message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
message(FATAL_ERROR "Python 3.8 and up is required to build the LAMMPS HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
@ -65,8 +65,8 @@ if(BUILD_DOC)
find_package(Sphinx)
endif()
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.2.2.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "08dd6ef33ca08870220d9aade2a62845" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL)
GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)

24
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -34,8 +34,26 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# C++11 is required
if(NOT CMAKE_CXX_STANDARD)
if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
set(CMAKE_CXX_STANDARD 17)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(CMAKE_CXX_STANDARD LESS 17)
message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
# turn off C++17 check in lmptype.h
if(LAMMPS_CXX11)
add_compile_definitions(LAMMPS_CXX11)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
# Need -restrict with Intel compilers
@ -242,8 +260,8 @@ 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(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
set(LAMMPS_SIZES_VALUES smallbig bigbig)
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)

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

@ -72,6 +72,10 @@ if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture")
endif()
message(WARNING, "Support for Intel Xeon Phi accelerators and Knight's Landing CPUs "
"will be removed from LAMMPS in Summer 2025 due to lack of available machines "
"in labs and HPC centers and removed support in recent compilers "
"Please contact developers@lammps.org if you have any concerns about this step.")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
target_compile_options(lammps PRIVATE -xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})

22
cmake/Modules/Packages/KOKKOS.cmake
View File

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

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

@ -24,9 +24,7 @@ if(MLIAP_ENABLE_PYTHON)
if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif()
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
# Python version check is in main CMakeLists.txt file
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)

16
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,12 +1,17 @@
# PACE library support for ML-PACE package
find_package(pace QUIET)
if(pace_FOUND)
find_package(pace)
target_link_libraries(lammps PRIVATE pace::pace)
else()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "a53bd87cfee8b07d9f44bc17aad69c3f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
@ -42,9 +47,16 @@ else()
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
endif()
# some preinstalled yaml-cpp versions don't provide a namespaced target
find_package(yaml-cpp QUIET)
if(TARGET yaml-cpp AND NOT TARGET yaml-cpp::yaml-cpp)
add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
endif()
endif()

2
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -37,7 +37,7 @@ if(DOWNLOAD_QUIP)
endforeach()
# Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
set(temp "${temp} -L/_DUMMY_PATH_\n")
set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
set(temp "${temp}PYTHON=${Python_EXECUTABLE}\nPIP=pip\nEXTRA_LINKOPTS=\n")
set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")

15
cmake/Modules/Packages/PLUMED.cmake
View File

@ -32,14 +32,21 @@ endif()
# Note: must also adjust check for supported API versions in
# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-src-2.9.2.tgz"
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.3/plumed-src-2.9.3.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "ee1249805fe94bccee17d10610d3f6f1" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
# adjust C++ standard support for self-compiled Plumed2
if(CMAKE_CXX_STANDARD GREATER 11)
set(PLUMED_CXX_STANDARD 14)
else()
set(PLUMED_CXX_STANDARD 11)
endif()
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
set(CROSS_CONFIGURE mingw64-configure)
@ -55,7 +62,7 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
URL_MD5 ${PLUMED_MD5}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
--disable-python --enable-cxx=11
--disable-python --enable-cxx=${PLUMED_CXX_STANDARD}
--enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
${PLUMED_CONFIG_OMP}
${PLUMED_CONFIG_MPI}
@ -142,7 +149,7 @@ else()
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
--enable-cxx=11
--enable-cxx=${PLUMED_CXX_STANDARD}
--disable-python
${PLUMED_CONFIG_MPI}
${PLUMED_CONFIG_OMP}

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

@ -1,6 +1,6 @@
if(NOT Python_INTERPRETER)
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
# backward compatibility with older LAMMPS documentation
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()

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

@ -1,6 +1,5 @@
# preset that enables KOKKOS and selects CUDA compilation with OpenMP
# enabled as well. This preselects CC 5.0 as default GPU arch, since
# that is compatible with all higher CC, but not the default CC 3.5
# enabled as well. The GPU architecture *must* match your hardware
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)

41
doc/Makefile
View File

@ -17,9 +17,11 @@ MATHJAXTAG = 3.2.2
PYTHON = $(word 3,$(shell type python3))
DOXYGEN = $(word 3,$(shell type doxygen))
PANDOC = $(word 3,$(shell type pandoc))
HAS_PYTHON3 = NO
HAS_DOXYGEN = NO
HAS_PDFLATEX = NO
HAS_PANDOC = NO
ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0)
HAS_PYTHON3 = YES
@ -35,6 +37,10 @@ HAS_PDFLATEX = YES
endif
endif
ifeq ($(shell type pandoc >/dev/null 2>&1; echo $$?), 0)
HAS_PANDOC = YES
endif
# override settings for PIP commands
# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
@ -45,8 +51,9 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
# 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 html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml fasthtml-init
FASTHTMLFILES = $(patsubst $(RSTDIR)/%.rst,fasthtml/%.html,$(wildcard $(RSTDIR)/*rst))
# ------------------------------------------
help:
@ -116,25 +123,23 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
@rm -rf html/PDF/.[sg]*
@echo "Build finished. The HTML pages are in doc/html."
fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@$(MAKE) $(MFLAGS) -C graphviz all
@mkdir -p fasthtml
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
deactivate ;\
)
@rm -rf fasthtml/_sources
@rm -rf fasthtml/PDF
@rm -rf fasthtml/USER
@rm -rf fasthtml/JPG
@cp -r src/PDF fasthtml/PDF
@rm -rf fasthtml/PDF/.[sg]*
fasthtml: fasthtml-init $(FASTHTMLFILES)
@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
fasthtml-init:
@mkdir -p fasthtml/JPG
@cp src/JPG/*.* fasthtml/JPG
@cp $(RSTDIR)/accel_styles.rst $(RSTDIR)/lepton_expression.rst fasthtml/
@cp $(BUILDDIR)/utils/pandoc.css fasthtml/
fasthtml/%.html: $(RSTDIR)/%.rst
@if [ "$(HAS_PANDOC)" == "NO" ] ; then echo "Make 'fasthtml' requires the 'pandoc' software" 1>&2; exit 1; fi
@mkdir -p fasthtml
@echo converting $< to $@
@sed -e 's/\\AA/\\mathring{\\mathrm{A}}/g' $< > fasthtml/$*.temp.rst
@pandoc -s --mathml --css="pandoc.css" --template=$(BUILDDIR)/utils/pandoc.html --metadata title="$@" -o $@ fasthtml/$*.temp.rst
@rm -f fasthtml/$*.temp.rst
spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@(\

20
doc/README
View File

@ -22,12 +22,12 @@ doxygen-warn.log logfile with warnings from running doxygen
and:
github-development-workflow.md notes on the LAMMPS development workflow
include-file-conventions.md notes on LAMMPS' include file conventions
documentation_conventions.md notes on writing documentation for LAMMPS
If you downloaded a LAMMPS tarball from www.lammps.org, then the html
folder and the PDF manual should be included. If you downloaded LAMMPS
from GitHub then you either need to build them.
using GitHub then you either need to build them yourself or read the
online version at https://docs.lammps.org/
You can build the HTML and PDF files yourself, by typing "make html"
or by "make pdf", respectively. This requires various tools and files.
@ -39,10 +39,10 @@ environment and local folders.
Installing prerequisites for the documentation build
To run the HTML documention build toolchain, python 3.x, doxygen, git,
and the venv python module have to be installed if not already available.
Also internet access is initially required to download external files
and tools.
To run the HTML documention build toolchain, python 3.8 or later,
doxygen 1.8.10 or later, git, and the venv python module have to be
installed if not already available. Also internet access is initially
required to download external files and tools.
Building the PDF format manual requires in addition a compatible LaTeX
installation with support for PDFLaTeX and several add-on LaTeX packages
@ -52,16 +52,24 @@ installed. This includes:
- babel
- capt-of
- cmap
- dvipng
- ellipse
- fncychap
- fontawesom
- framed
- geometry
- gyre
- hyperref
- hypcap
- needspace
- pict2e
- times
- tabulary
- titlesec
- upquote
- wrapfig
- xindy
Also the latexmk script is required to run PDFLaTeX and related tools.
the required number of times to have self-consistent output and include
updated bibliography and indices.

6
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "19 November 2024" "2024-11-19"
.TH LAMMPS "1" "4 February 2025" "2025-02-04"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 19 November 2024
\- Molecular Dynamics Simulator. Version 4 February 2025
.SH SYNOPSIS
.B lmp
@ -311,7 +311,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2024 Sandia Corporation
© 2003--2025 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

35
doc/src/Build.rst
View File

@ -1,15 +1,42 @@
Build LAMMPS
============
LAMMPS is built as a library and an executable from source code using
either traditional makefiles for use with GNU make (which may require
manual editing), or using a build environment generated by CMake (Unix
Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
LAMMPS is built as a library and an executable from source code using a
build environment generated by CMake (Unix Makefiles, Ninja, Xcode,
Visual Studio, KDevelop, CodeBlocks and more depending on the platform).
Using CMake is the preferred way to build LAMMPS. In addition, LAMMPS
can be compiled using the legacy build system based on traditional
makefiles for use with GNU make (which may require manual editing).
Support for the legacy build system is slowly being phased out and may
not be available for all optional features.
As an alternative, you can download a package with pre-built executables
or automated build trees, as described in the :doc:`Install <Install>`
section of the manual.
Prerequisites
-------------
Which software you need to compile and use LAMMPS strongly depends on
which :doc:`features and settings <Build_settings>` and which
:doc:`optional packages <Packages_list>` you are trying to include.
Common to all is that you need a C++ and C compiler, where the C++
compiler has to support at least the C++11 standard (note that some
compilers require command-line flag to activate C++11 support).
Furthermore, if you are building with CMake, you need at least CMake
version 3.20 and a compatible build tool (make or ninja-build); if you
are building the the legacy GNU make based build system you need GNU
make (other make variants are not going to work since the build system
uses features unique to GNU make) and a Unix-like build environment with
a Bourne shell, and shell tools like "sed", "grep", "touch", "test",
"tr", "cp", "mv", "rm", "ln", "diff" and so on. Parts of LAMMPS
interface with or use Python version 3.6 or later.
The LAMMPS developers aim to keep LAMMPS very portable and usable -
at least in parts - on most operating systems commonly used for
running MD simulations. Please see the :doc:`section on portablility
<Intro_portability>` for more details.
.. toctree::
:maxdepth: 1

19
doc/src/Build_basics.rst
View File

@ -196,13 +196,18 @@ LAMMPS.
.. tab:: CMake build
By default CMake will use the compiler it finds according to
By default CMake will use the compiler it finds according to its
internal preferences, and it will add optimization flags
appropriate to that compiler and any :doc:`accelerator packages
<Speed_packages>` you have included in the build. CMake will
check if the detected or selected compiler is compatible with the
C++ support requirements of LAMMPS and stop with an error, if this
is not the case.
is not the case. A C++11 compatible compiler is currently
required, but a transition to require C++17 is in progress and
planned to be completed in Summer 2025. Currently, setting
``-DLAMMPS_CXX11=yes`` is required when configuring with CMake while
using a C++11 compatible compiler that does not support C++17,
otherwise setting ``-DCMAKE_CXX_STANDARD=17`` is preferred.
You can tell CMake to look for a specific compiler with setting
CMake variables (listed below) during configuration. For a few
@ -223,6 +228,8 @@ LAMMPS.
-D CMAKE_C_COMPILER=name # name of C compiler
-D CMAKE_Fortran_COMPILER=name # name of Fortran compiler
-D CMAKE_CXX_STANDARD=17 # put compiler in C++17 mode
-D LAMMPS_CXX11=yes # enforce compilation in C++11 mode
-D CMAKE_CXX_FLAGS=string # flags to use with C++ compiler
-D CMAKE_C_FLAGS=string # flags to use with C compiler
-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler
@ -321,6 +328,14 @@ LAMMPS.
you would have to install a newer compiler that supports C++11;
either as a binary package or through compiling from source.
While a C++11 compatible compiler is currently sufficient to compile
LAMMPS, a transition to require C++17 is in progress and planned to
be completed in Summer 2025. Currently, setting ``-DLAMMPS_CXX11``
in the ``LMP_INC =`` line in the machine makefile is required when
using a C++11 compatible compiler that does not support C++17.
Otherwise, to enable C++17 support (if not enabled by default) using
a compiler flag like ``-std=c++17`` in CCFLAGS may needed.
If you build LAMMPS with any :doc:`Speed_packages` included,
there may be specific compiler or linker flags that are either
required or recommended to enable required features and to

25
doc/src/Build_cmake.rst
View File

@ -16,7 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
.. note::
LAMMPS currently requires that CMake version 3.16 or later is available.
LAMMPS currently requires that CMake version 3.20 or later is available.
.. warning::
@ -32,11 +32,11 @@ environments is on a :doc:`separate page <Howto_cmake>`.
Advantages of using CMake
^^^^^^^^^^^^^^^^^^^^^^^^^
CMake is an alternative to compiling LAMMPS in the traditional way
through :doc:`(manually customized) makefiles <Build_make>`. Using
CMake has multiple advantages that are specifically helpful for
people with limited experience in compiling software or for people
that want to modify or extend LAMMPS.
CMake is the preferred way of compiling LAMMPS in contrast to the legacy
build system based on GNU make and through :doc:`(manually customized)
makefiles <Build_make>`. Using CMake has multiple advantages that are
specifically helpful for people with limited experience in compiling
software or for people that want to modify or extend LAMMPS.
- CMake can detect available hardware, tools, features, and libraries
and adapt the LAMMPS default build configuration accordingly.
@ -52,9 +52,9 @@ that want to modify or extend LAMMPS.
compilers can be configured and built concurrently from the same
source tree.
- Simplified packaging of LAMMPS for Linux distributions, environment
modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
- Integration of automated unit and regression testing (the LAMMPS side
of this is still under active development).
modules, or automated build tools like `Spack <https://spack.io>`_
or `Homebrew <https://brew.sh/>`_.
- Integration of automated unit and regression testing.
.. _cmake_build:
@ -119,6 +119,13 @@ configured) and additional files like LAMMPS API headers, manpages,
potential and force field files. The location of the installation tree
defaults to ``${HOME}/.local``.
.. note::
If you have set `-D CMAKE_INSTALL_PREFIX` to install LAMMPS into a
system location on a Linux machine , you may also have to run (as
root) the `ldconfig` program to update the cache file for fast lookup
of system shared libraries.
.. _cmake_options:
Configuration and build options

156
doc/src/Build_extras.rst
View File

@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
* :ref:`LEPTON <lepton>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MISC <misc>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
@ -254,11 +255,10 @@ Traditional make
Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
You can do this manually if you prefer; follow the instructions in
``lib/gpu/README``. Note that the GPU library uses MPI calls, so you must
use the same MPI library (or the STUBS library) settings as the main
LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ ,
``-DLAMMPS_SMALLBIG``\ , or ``-DLAMMPS_SMALLSMALL`` settings in whichever
Makefile you use.
``lib/gpu/README``. Note that the GPU library uses MPI calls, so you
must use the same MPI library (or the STUBS library) settings as the
main LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG`` or
``-DLAMMPS_SMALLBIG`` settings in whichever Makefile you use.
You can also build the library in one step from the ``lammps/src`` dir,
using a command like these, which simply invokes the ``lib/gpu/Install.py``
@ -547,16 +547,7 @@ They must be specified in uppercase.
- Local machine
* - AMDAVX
- HOST
- AMD 64-bit x86 CPU (AVX 1)
* - ZEN
- HOST
- AMD Zen class CPU (AVX 2)
* - ZEN2
- HOST
- AMD Zen2 class CPU (AVX 2)
* - ZEN3
- HOST
- AMD Zen3 class CPU (AVX 2)
- AMD chip
* - ARMV80
- HOST
- ARMv8.0 Compatible CPU
@ -572,105 +563,126 @@ They must be specified in uppercase.
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - ARMV9_GRACE
- HOST
- ARMv9 NVIDIA Grace CPU
* - SNB
- HOST
- Intel Sandy/Ivy Bridge CPU (AVX 1)
- Intel Sandy/Ivy Bridge CPUs
* - HSW
- HOST
- Intel Haswell CPU (AVX 2)
- Intel Haswell CPUs
* - BDW
- HOST
- Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
* - SKL
- HOST
- Intel Skylake Client CPU
* - SKX
- HOST
- Intel Skylake Xeon Server CPU (AVX512)
- Intel Broadwell Xeon E-class CPUs
* - ICL
- HOST
- Intel Ice Lake Client CPU (AVX512)
- Intel Ice Lake Client CPUs (AVX512)
* - ICX
- HOST
- Intel Ice Lake Xeon Server CPU (AVX512)
* - SPR
- Intel Ice Lake Xeon Server CPUs (AVX512)
* - SKL
- HOST
- Intel Sapphire Rapids Xeon Server CPU (AVX512)
- Intel Skylake Client CPUs
* - SKX
- HOST
- Intel Skylake Xeon Server CPUs (AVX512)
* - KNC
- HOST
- Intel Knights Corner Xeon Phi
* - KNL
- HOST
- Intel Knights Landing Xeon Phi
* - SPR
- HOST
- Intel Sapphire Rapids Xeon Server CPUs (AVX512)
* - POWER8
- HOST
- IBM POWER8 CPU
- IBM POWER8 CPUs
* - POWER9
- HOST
- IBM POWER9 CPU
- IBM POWER9 CPUs
* - ZEN
- HOST
- AMD Zen architecture
* - ZEN2
- HOST
- AMD Zen2 architecture
* - ZEN3
- HOST
- AMD Zen3 architecture
* - RISCV_SG2042
- HOST
- SG2042 (RISC-V) CPU
- SG2042 (RISC-V) CPUs
* - RISCV_RVA22V
- HOST
- RVA22V (RISC-V) CPUs
* - KEPLER30
- GPU
- NVIDIA Kepler generation CC 3.0 GPU
- NVIDIA Kepler generation CC 3.0
* - KEPLER32
- GPU
- NVIDIA Kepler generation CC 3.2 GPU
- NVIDIA Kepler generation CC 3.2
* - KEPLER35
- GPU
- NVIDIA Kepler generation CC 3.5 GPU
- NVIDIA Kepler generation CC 3.5
* - KEPLER37
- GPU
- NVIDIA Kepler generation CC 3.7 GPU
- NVIDIA Kepler generation CC 3.7
* - MAXWELL50
- GPU
- NVIDIA Maxwell generation CC 5.0 GPU
- NVIDIA Maxwell generation CC 5.0
* - MAXWELL52
- GPU
- NVIDIA Maxwell generation CC 5.2 GPU
- NVIDIA Maxwell generation CC 5.2
* - MAXWELL53
- GPU
- NVIDIA Maxwell generation CC 5.3 GPU
- NVIDIA Maxwell generation CC 5.3
* - PASCAL60
- GPU
- NVIDIA Pascal generation CC 6.0 GPU
- NVIDIA Pascal generation CC 6.0
* - PASCAL61
- GPU
- NVIDIA Pascal generation CC 6.1 GPU
- NVIDIA Pascal generation CC 6.1
* - VOLTA70
- GPU
- NVIDIA Volta generation CC 7.0 GPU
- NVIDIA Volta generation CC 7.0
* - VOLTA72
- GPU
- NVIDIA Volta generation CC 7.2 GPU
- NVIDIA Volta generation CC 7.2
* - TURING75
- GPU
- NVIDIA Turing generation CC 7.5 GPU
- NVIDIA Turing generation CC 7.5
* - AMPERE80
- GPU
- NVIDIA Ampere generation CC 8.0 GPU
- NVIDIA Ampere generation CC 8.0
* - AMPERE86
- GPU
- NVIDIA Ampere generation CC 8.6 GPU
- NVIDIA Ampere generation CC 8.6
* - ADA89
- GPU
- NVIDIA Ada Lovelace generation CC 8.9 GPU
- NVIDIA Ada generation CC 8.9
* - HOPPER90
- GPU
- NVIDIA Hopper generation CC 9.0 GPU
- NVIDIA Hopper generation CC 9.0
* - AMD_GFX906
- GPU
- AMD GPU MI50/MI60
- AMD GPU MI50/60
* - AMD_GFX908
- GPU
- AMD GPU MI100
* - AMD_GFX90A
- GPU
- AMD GPU MI200
* - AMD_GFX940
- GPU
- AMD GPU MI300
* - AMD_GFX942
- GPU
- AMD GPU MI300
* - AMD_GFX942_APU
- GPU
- AMD APU MI300A
* - AMD_GFX1030
- GPU
- AMD GPU V620/W6800
@ -679,7 +691,7 @@ They must be specified in uppercase.
- AMD GPU RX7900XTX
* - AMD_GFX1103
- GPU
- AMD Phoenix APU with Radeon 740M/760M/780M/880M/890M
- AMD APU Phoenix
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
@ -702,7 +714,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.3.0 of the Kokkos library.
This list was last updated for version 4.5.1 of the Kokkos library.
.. tabs::
@ -1126,11 +1138,10 @@ POEMS package
PYTHON package
---------------------------
Building with the PYTHON package requires you have a the Python development
headers and library available on your system, which needs to be a Python 2.7
version or a Python 3.x version. Since support for Python 2.x has ended,
using Python 3.x is strongly recommended. See ``lib/python/README`` for
additional details.
Building with the PYTHON package requires you have a the Python
development headers and library available on your system, which
needs to be Python version 3.6 or later. See ``lib/python/README``
for additional details.
.. tabs::
@ -1146,7 +1157,7 @@ additional details.
set the Python_EXECUTABLE variable to specify which Python
interpreter should be used. Note note that you will also need to
have the development headers installed for this version,
e.g. python2-devel.
e.g. python3-devel.
.. tab:: Traditional make
@ -2019,7 +2030,7 @@ TBB and MKL.
.. _mdi:
MDI package
-----------------------------
-----------
.. tabs::
@ -2046,6 +2057,37 @@ MDI package
----------
.. _misc:
MISC package
------------
The :doc:`fix imd <fix_imd>` style in this package can be run either
synchronously (communication with IMD clients is done in the main
process) or asynchronously (the fix spawns a separate thread that can
communicate with IMD clients concurrently to the LAMMPS execution).
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D LAMMPS_ASYNC_IMD=value # Run IMD server asynchronously
# value = no (default) or yes
.. tab:: Traditional make
To enable asynchronous mode the ``-DLAMMPS_ASYNC_IMD`` define
needs to be added to the ``LMP_INC`` variable in the
``Makefile.machine`` you are using. For example:
.. code-block:: make
LMP_INC = -DLAMMPS_ASYNC_IMD -DLAMMPS_MEMALIGN=64
----------
.. _molfile:
MOLFILE package

10
doc/src/Build_make.rst
View File

@ -8,6 +8,10 @@ Building LAMMPS with traditional makefiles requires that you have a
for customizing your LAMMPS build with a number of global compilation
options and features.
This build system is slowly being phased out and may not support all
optional features and packages in LAMMPS. It is recommended to switch
to the :doc:`CMake based build system <Build_cmake>`.
Requirements
^^^^^^^^^^^^
@ -26,9 +30,9 @@ additional tools to be available and functioning.
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* Python (optional, required for ``make lib-<pkg>`` in the ``src``
folder). Python scripts are currently tested with python 2.7 and
3.6 to 3.11. The procedure for :doc:`building the documentation
<Build_manual>` *requires* Python 3.5 or later.
folder). Python scripts are currently tested with 3.6 to 3.11.
The procedure for :doc:`building the documentation <Build_manual>`
*requires* Python 3.8 or later.
Getting started
^^^^^^^^^^^^^^^

88
doc/src/Build_manual.rst
View File

@ -78,8 +78,7 @@ folder. The following ``make`` commands are available:
make epub # generate LAMMPS.epub in ePUB format using Sphinx
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
make fasthtml # generate approximate HTML in fasthtml dir using Sphinx
# some Sphinx extensions do not work correctly with this
make fasthtml # generate approximate HTML in fasthtml dir using pandoc
make clean # remove intermediate RST files created by HTML build
make clean-all # remove entire build folder and any cached data
@ -116,9 +115,9 @@ environment variable.
Prerequisites for HTML
----------------------
To run the HTML documentation build toolchain, python 3, git, doxygen,
and virtualenv have to be installed locally. Here are instructions for
common setups:
To run the HTML documentation build toolchain, Python 3.8 or later, git,
doxygen, and virtualenv have to be installed locally. Here are
instructions for common setups:
.. tabs::
@ -128,13 +127,7 @@ common setups:
sudo apt-get install git doxygen
.. tab:: RHEL or CentOS (Version 7.x)
.. code-block:: bash
sudo yum install git doxygen
.. tab:: Fedora or RHEL/CentOS (8.x or later)
.. tab:: Fedora or RHEL/AlmaLinux/RockyLinux (8.x or later)
.. code-block:: bash
@ -154,7 +147,36 @@ Prerequisites for PDF
In addition to the tools needed for building the HTML format manual,
a working LaTeX installation with support for PDFLaTeX and a selection
of LaTeX styles/packages are required. To run the PDFLaTeX translation
of LaTeX styles/packages are required. Apart from LaTeX packages that
are usually installed by default, the following packages are required:
.. table_from_list::
:columns: 11
- amsmath
- anysize
- babel
- capt-of
- cmap
- dvipng
- ellipse
- fncychap
- fontawesome
- framed
- geometry
- gyre
- hyperref
- hypcap
- needspace
- pict2e
- times
- tabulary
- titlesec
- upquote
- wrapfig
- xindy
To run the PDFLaTeX translation
the ``latexmk`` script needs to be installed as well.
Prerequisites for ePUB and MOBI
@ -182,12 +204,42 @@ documentation is required and either existing files in the ``src``
folder need to be updated or new files added. These files are written in
`reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
Testing your contribution
^^^^^^^^^^^^^^^^^^^^^^^^^
Before contributing any documentation, please check that both the HTML
and the PDF format documentation can translate without errors. During
testing the html translation, you may use the ``make fasthtml`` command
which does an approximate translation (i.e. not all Sphinx features and
extensions will work), but runs very fast because it will only translate
files that have been changed since the last ``make fasthtml`` command.
and the PDF format documentation can translate without errors and that
there are no spelling issues. This is done with ``make html``, ``make pdf``,
and ``make spelling``, respectively.
Fast and approximate translation to HTML
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Translating the full manual to HTML or PDF can take a long time. Thus
there is a fast and approximate way to translate the reStructuredText to
HTML as a quick-n-dirty way of checking your manual page.
This translation uses `Pandoc <https://pandoc.org>`_ instead of Sphinx
and thus all special Sphinx features (cross-references, advanced tables,
embedding of Python docstrings or doxygen documentation, and so on) will
not render correctly. Most embedded math should render correctly. This
is a **very fast** way to check the syntax and layout of a documentation
file translated to HTML while writing or updating it.
To translate **all** manual pages, you can type ``make fasthtml`` at the
command line. The translated HTML files are then in the ``fasthtml``
folder. All subsequent ``make fasthtml`` commands will only translate
``.rst`` files that have been changed. The ``make fasthtml`` command
can be parallelized with make using the `-j` flag. You can also
directly translate only individual pages: e.g. to translate only the
``doc/src/pair_lj.rst`` page type ``make fasthtml/pair_lj.html``
After writing the documentation is completed, you will still need
to verify with ``make html`` and ``make pdf`` that it translates
correctly in both formats.
Tests for consistency, completeness, and other known issues
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Please also check the output to the console for any warnings or problems. There will
be multiple tests run automatically:

1
doc/src/Build_package.rst
View File

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

69
doc/src/Build_settings.rst
View File

@ -8,12 +8,13 @@ Optional build settings
LAMMPS can be built with several optional settings. Each subsection
explains how to do this for building both with CMake and make.
* `C++11 standard compliance`_ when building all of LAMMPS
* `C++11 and C++17 standard compliance`_ when building all of LAMMPS
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
* `Size of LAMMPS integer types and size limits`_
* `Read or write compressed files`_
* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `Support for downloading files`_
* `Support for downloading files from the input`_
* `Prevent download of large potential files`_
* `Memory allocation alignment`_
* `Workaround for long long integers`_
* `Exception handling when using LAMMPS as a library`_ to capture errors
@ -23,14 +24,15 @@ explains how to do this for building both with CMake and make.
.. _cxx11:
C++11 standard compliance
-------------------------
C++11 and C++17 standard compliance
-----------------------------------
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
LAMMPS version 3 March 2020 is the last version compatible with the previous
C++98 standard for the core code and most packages. Most currently used
C++ compilers are compatible with C++11, but some older ones may need extra
flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
A C++11 standard compatible compiler is currently the minimum
requirement for compiling LAMMPS. LAMMPS version 3 March 2020 is the
last version compatible with the previous C++98 standard for the core
code and most packages. Most currently used C++ compilers are compatible
with C++11, but some older ones may need extra flags to enable C++11
compliance. Example for GNU c++ 4.8.x:
.. code-block:: make
@ -40,6 +42,17 @@ Individual packages may require compliance with a later C++ standard
like C++14 or C++17. These requirements will be documented with the
:doc:`individual packages <Packages_details>`.
.. versionchanged:: 4Feb2025
Starting with LAMMPS version 4 February 2025 we are starting a
transition to require the C++17 standard. Most current compilers are
compatible and if the C++17 standard is available by default, LAMMPS
will enable C++17 and will compile normally. If the chosen compiler is
not compatible with C++17, but only supports C++11, then the define
-DLAMMPS_CXX11 is required to fall back to compiling with a C++11
compiler. After the next stable release of LAMMPS in summer 2025, the
LAMMPS development branch and future releases will require C++17.
----------
.. _fft:
@ -303,7 +316,7 @@ large counters can become before "rolling over". The default setting of
.. code-block:: bash
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
-D LAMMPS_SIZES=value # smallbig (default) or bigbig
If the variable is not set explicitly, "smallbig" is used.
@ -314,7 +327,7 @@ large counters can become before "rolling over". The default setting of
.. code-block:: make
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG
The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
@ -323,34 +336,27 @@ LAMMPS system size restrictions
.. list-table::
:header-rows: 1
:widths: 18 27 28 27
:widths: 27 36 37
:align: center
* -
- smallbig
- bigbig
- smallsmall
* - Total atom count
- :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
- :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
- :math:`2^{31}` atoms (= :math:`2.147 \cdot 10^9`)
* - Total timesteps
- :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
- :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
- :math:`2^{31}` steps (= :math:`2.147 \cdot 10^9`)
* - Atom ID values
- :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
- :math:`1 \le i \le 2^{63} (= 9.223 \cdot 10^{18})`
- :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
* - Image flag values
- :math:`-512 \le i \le 511`
- :math:`- 1\,048\,576 \le i \le 1\,048\,575`
- :math:`-512 \le i \le 511`
The "bigbig" setting increases the size of image flags and atom IDs over
"smallbig" and the "smallsmall" setting is only needed if your machine
does not support 64-bit integers or incurs performance penalties when
using them.
the default "smallbig" setting.
These are limits for the core of the LAMMPS code, specific features or
some styles may impose additional limits. The :ref:`ATC
@ -504,8 +510,8 @@ during a run.
.. _libcurl:
Support for downloading files
-----------------------------
Support for downloading files from the input
--------------------------------------------
.. versionadded:: 29Aug2024
@ -548,6 +554,25 @@ LAMMPS is compiled accordingly which needs the following settings:
----------
.. _download_pot:
Prevent download of large potential files
-----------------------------------------
.. versionadded:: 8Feb2023
LAMMPS bundles a selection of potential files in the ``potentials``
folder as examples of how those kinds of potential files look like and
for use with the provided input examples in the ``examples`` tree. To
keep the size of the distributed LAMMPS source package small, very large
potential files (> 5 MBytes) are not bundled, but only downloaded on
demand when the :doc:`corresponding package <Packages_list>` is
installed. This automatic download can be prevented when :doc:`building
LAMMPS with CMake <Build_cmake>` by adding the setting `-D
DOWNLOAD_POTENTIALS=off` when configuring.
----------
.. _align:
Memory allocation alignment

1
doc/src/Commands_all.rst
View File

@ -140,6 +140,7 @@ additional letter in parenthesis: k = KOKKOS.
* :doc:`plugin <plugin>`
* :doc:`prd <prd>`
* :doc:`python <python>`
* :doc:`region2vmd <region2vmd>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`
* :doc:`temper/grem <temper_grem>`

2
doc/src/Commands_bond.rst
View File

@ -23,6 +23,7 @@ OPT.
*
* :doc:`bpm/rotational <bond_bpm_rotational>`
* :doc:`bpm/spring <bond_bpm_spring>`
* :doc:`bpm/spring/plastic <bond_bpm_spring_plastic>`
* :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>`
@ -90,6 +91,7 @@ OPT.
* :doc:`lepton (o) <angle_lepton>`
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`mwlc <angle_mwlc>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`spica (ko) <angle_spica>`
* :doc:`table (o) <angle_table>`

6
doc/src/Commands_compute.rst
View File

@ -58,6 +58,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`fep/ta <compute_fep_ta>`
* :doc:`force/tally <compute_tally>`
* :doc:`fragment/atom <compute_cluster_atom>`
* :doc:`gaussian/grid/local (k) <compute_gaussian_grid_local>`
* :doc:`global/atom <compute_global_atom>`
* :doc:`group/group <compute_group_group>`
* :doc:`gyration <compute_gyration>`
@ -140,8 +141,8 @@ 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:`sna/grid (k) <compute_sna_atom>`
* :doc:`sna/grid/local (k) <compute_sna_atom>`
* :doc:`snad/atom <compute_sna_atom>`
* :doc:`snav/atom <compute_sna_atom>`
* :doc:`sph/e/atom <compute_sph_e_atom>`
@ -177,6 +178,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ti <compute_ti>`
* :doc:`torque/chunk <compute_torque_chunk>`
* :doc:`vacf <compute_vacf>`
* :doc:`vacf/chunk <compute_vacf_chunk>`
* :doc:`vcm/chunk <compute_vcm_chunk>`
* :doc:`viscosity/cos <compute_viscosity_cos>`
* :doc:`voronoi/atom <compute_voronoi_atom>`

3
doc/src/Commands_fix.rst
View File

@ -58,6 +58,7 @@ OPT.
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield (k) <fix_efield>`
* :doc:`efield/lepton <fix_efield_lepton>`
* :doc:`efield/tip4p <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode>`
@ -161,6 +162,8 @@ OPT.
* :doc:`phonon <fix_phonon>`
* :doc:`pimd/langevin <fix_pimd>`
* :doc:`pimd/nvt <fix_pimd>`
* :doc:`pimd/langevin/bosonic <fix_pimd>`
* :doc:`pimd/nvt/bosonic <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
* :doc:`plumed <fix_plumed>`
* :doc:`poems <fix_poems>`

3
doc/src/Commands_pair.rst
View File

@ -80,6 +80,7 @@ OPT.
* :doc:`coul/tt <pair_coul_tt>`
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dispersion/d3 <pair_dispersion_d3>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`
@ -114,7 +115,9 @@ OPT.
* :doc:`gw/zbl <pair_gw>`
* :doc:`harmonic/cut (o) <pair_harmonic_cut>`
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/lj/angleoffset (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse/angleoffset (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`hippo (g) <pair_amoeba>`
* :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`

228
doc/src/Commands_removed.rst
View File

@ -1,6 +1,10 @@
Removed commands and packages
=============================
.. contents::
------
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or
replacements. LAMMPS has special dummy styles implemented, that will
@ -8,94 +12,32 @@ stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
restart2data tool
-----------------
.. versionchanged:: 23Nov2013
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command-line flags <Run_options>`
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
.. deprecated:: 11Dec2015
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
Box command
-----------
.. deprecated:: 22Dec2022
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
.. deprecated:: 22Dec2022
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
present, LAMMPS will replace the commands accordingly and print a
warning.
LATTE package
-------------
.. deprecated:: 15Jun2023
The LATTE package with the fix latte command was removed from LAMMPS.
This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package
<PKG-MDI>`. These fixes are compatible with several quantum software
packages, including LATTE. See the ``examples/QUANTUM`` dir and the
:doc:`MDI coupling HOWTO <Howto_mdi>` page. MDI supports running LAMMPS
with LATTE as a plugin library (similar to the way fix latte worked), as
well as on a different set of MPI processors.
MEAM package
LAMMPS shell
------------
The MEAM package in Fortran has been replaced by a C++ implementation.
The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
.. versionchanged:: 29Aug2024
Minimize style fire/old
-----------------------
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
.. deprecated:: 8Feb2023
i-PI tool
---------
Minimize style *fire/old* has been removed. Its functionality can be
reproduced with *fire* with specific options. Please see the
:doc:`min_modify command <min_modify>` documentation for details.
.. versionchanged:: 27Jun2024
Pair style mesont/tpm, compute style mesont, atom style mesont
--------------------------------------------------------------
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPI via pip are provided.
.. deprecated:: 8Feb2023
USER-REAXC package
------------------
Pair style *mesont/tpm*, compute style *mesont*, and atom style
*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
The same functionality is available through
:doc:`pair style mesocnt <pair_mesocnt>`,
:doc:`bond style mesocnt <bond_mesocnt>` and
:doc:`angle style mesocnt <angle_mesocnt>`.
.. deprecated:: 7Feb2024
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use
the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
backward compatibility by providing aliases for the styles. These have
been removed, so using "reaxff" is now *required*.
MPIIO package
-------------
@ -115,7 +57,6 @@ Similarly, the "nfile" and "fileper" keywords exist for restarts:
see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
:doc:`write_restart <write_restart>`.
MSCG package
------------
@ -126,9 +67,73 @@ for many years and instead superseded by the `OpenMSCG software
<https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
University of Chicago, which can be used independent from LAMMPS.
LATTE package
-------------
.. deprecated:: 15Jun2023
The LATTE package with the fix latte command was removed from LAMMPS.
This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package
<PKG-MDI>`. These fixes are compatible with several quantum software
packages, including LATTE. See the ``examples/QUANTUM`` dir and the
:doc:`MDI coupling HOWTO <Howto_mdi>` page. MDI supports running LAMMPS
with LATTE as a plugin library (similar to the way fix latte worked), as
well as on a different set of MPI processors.
Minimize style fire/old
-----------------------
.. deprecated:: 8Feb2023
Minimize style *fire/old* has been removed. Its functionality can be
reproduced with style *fire* with specific options. Please see the
:doc:`min_modify command <min_modify>` documentation for details.
Pair style mesont/tpm, compute style mesont, atom style mesont
--------------------------------------------------------------
.. deprecated:: 8Feb2023
Pair style *mesont/tpm*, compute style *mesont*, and atom style
*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
The same functionality is available through
:doc:`pair style mesocnt <pair_mesocnt>`,
:doc:`bond style mesocnt <bond_mesocnt>` and
:doc:`angle style mesocnt <angle_mesocnt>`.
Box command
-----------
.. deprecated:: 22Dec2022
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
.. deprecated:: 22Dec2022
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
present, LAMMPS will replace the commands accordingly and print a
warning.
MESSAGE package
---------------
.. deprecated:: 4May2022
The MESSAGE package has been removed since it was superseded by the
:ref:`MDI package <PKG-MDI>`. MDI implements the same functionality
and in a more general way with direct support for more applications.
REAX package
------------
.. deprecated:: 4Jan2019
The REAX package has been removed since it was superseded by the
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF package has been tested
to yield equivalent results to the REAX package, offers better
@ -138,20 +143,25 @@ syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-REAXC package
------------------
MEAM package
------------
.. deprecated:: 7Feb2024
.. deprecated:: 4Jan2019
The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
In the process also the pair style and related fixes were renamed to use
the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
backward compatibility by providing aliases for the styles. These have
been removed, so using "reaxff" is now *required*.
The MEAM package in Fortran has been replaced by a C++ implementation.
The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
USER-CUDA package
-----------------
.. deprecated:: 31May2016
The USER-CUDA package had been removed, since it had been unmaintained
for a long time and had known bugs and problems. Significant parts of
the design were transferred to the
@ -160,19 +170,39 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
and the :ref:`GPU package <PKG-GPU>` are maintained
and allow running LAMMPS with GPU acceleration.
i-PI tool
---------
Compute atom/molecule
_____________________
.. versionchanged:: 27Jun2024
.. deprecated:: 11 Dec2015
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPI via pip are provided.
The atom/molecule command has been removed from LAMMPS since it was superseded
by the more general and extensible "chunk infrastructure". Here the system is
partitioned in one of many possible ways - including using molecule IDs -
through the :doc:`compute chunk/atom <compute_chunk_atom>` command and then
summing is done using :doc:`compute reduce/chunk <compute_reduce_chunk>` Please
refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
LAMMPS shell
------------
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
.. versionchanged:: 29Aug2024
.. deprecated:: 11Dec2015
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
restart2data tool
-----------------
.. deprecated:: 23Nov2013
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command-line flags <Run_options>`

1
doc/src/Developer.rst
View File

@ -24,4 +24,5 @@ of time and requests from the LAMMPS user community.
Classes
Developer_platform
Developer_utils
Developer_internal
Developer_grid

41
doc/src/Developer_code_design.rst
View File

@ -203,6 +203,7 @@ processed in the expected order before types are removed from dynamic
dispatch.
.. admonition:: Important Notes
:class: note
In order to be able to detect incompatibilities at compile time and
to avoid unexpected behavior, it is crucial that all member functions
@ -300,18 +301,24 @@ Formatting with the {fmt} library
The LAMMPS source code includes a copy of the `{fmt} library
<https://fmt.dev>`_, which is preferred over formatting with the
"printf()" family of functions. The primary reason is that it allows
a typesafe default format for any type of supported data. This is
"printf()" family of functions. The primary reason is that it allows a
typesafe default format for any type of supported data. This is
particularly useful for formatting integers of a given size (32-bit or
64-bit) which may require different format strings depending on
compile time settings or compilers/operating systems. Furthermore,
{fmt} gives better performance, has more functionality, a familiar
formatting syntax that has similarities to ``format()`` in Python, and
provides a facility that can be used to integrate format strings and a
variable number of arguments into custom functions in a much simpler
way than the varargs mechanism of the C library. Finally, {fmt} has
been included into the C++20 language standard, so changes to adopt it
are future-proof.
64-bit) which may require different format strings depending on compile
time settings or compilers/operating systems. Furthermore, {fmt} gives
better performance, has more functionality, a familiar formatting syntax
that has similarities to ``format()`` in Python, and provides a facility
that can be used to integrate format strings and a variable number of
arguments into custom functions in a much simpler way than the varargs
mechanism of the C library. Finally, {fmt} has been included into the
C++20 language standard as ``std::format()``, so changes to adopt it are
future-proof, for as long as they are not using any extensions that are
not (yet) included into C++.
The long-term plan is to switch to using ``std::format()`` instead of
``fmt::format()`` when the minimum C++ standard required for LAMMPS will
be set to C++20. See the :ref:`basic build instructions <compile>` for
more details.
Formatted strings are frequently created by calling the
``fmt::format()`` function, which will return a string as a
@ -319,11 +326,13 @@ Formatted strings are frequently created by calling the
``printf()``, the {fmt} library uses ``{}`` to embed format descriptors.
In the simplest case, no additional characters are needed, as {fmt} will
choose the default format based on the data type of the argument.
Otherwise, the ``fmt::print()`` function may be used instead of
``printf()`` or ``fprintf()``. In addition, several LAMMPS output
functions, that originally accepted a single string as argument have
been overloaded to accept a format string with optional arguments as
well (e.g., ``Error::all()``, ``Error::one()``, ``utils::logmesg()``).
Otherwise, the :cpp:func:`utils::print() <LAMMPS_NS::utils::print>`
function may be used instead of ``printf()`` or ``fprintf()``. In
addition, several LAMMPS output functions, that originally accepted a
single string as argument have been overloaded to accept a format string
with optional arguments as well (e.g., ``Error::all()``,
``Error::one()``, :cpp:func:`utils::logmesg()
<LAMMPS_NS::utils::logmesg>`).
Summary of the {fmt} format syntax
==================================

2
doc/src/Developer_flow.rst
View File

@ -209,7 +209,7 @@ nve, nvt, npt.
At the end of the timestep, fixes that contain an ``end_of_step()``
method are invoked. These typically perform a diagnostic calculation,
e.g. the ave/time and ave/spatial fixes. The final operation of the
e.g. the ave/time and ave/chunk fixes. The final operation of the
timestep is to perform any requested output, via the ``write()`` method
of the Output class. There are 3 kinds of LAMMPS output: thermodynamic
output to the screen and log file, snapshots of atom data to a dump

113
doc/src/Developer_internal.rst Normal file
View File

@ -0,0 +1,113 @@
Internal Styles
---------------
LAMMPS has a number of styles that are not meant to be used in an input
file and thus are not documented in the :doc:`LAMMPS command
documentation <Commands_all>`. The differentiation between user
commands and internal commands is through the case of the command name:
user commands and styles are all lower case, internal styles are all
upper case. Internal styles are not called from the input file, but
their classes are instantiated by other styles. Often they are
created by other styles to store internal data or to perform actions
regularly at specific steps of the simulation.
The paragraphs below document some of those styles that have general
utility and may be used to avoid redundant implementation.
DEPRECATED Styles
^^^^^^^^^^^^^^^^^
The styles called DEPRECATED (e.g. pair, bond, fix, compute, region, etc.)
have the purpose to inform users that a specific style has been removed
or renamed. This is achieved by creating an alias for the deprecated
style to the corresponding class. For example, the fix style DEPRECATED
is aliased to fix style ave/spatial and fix style ave/spatial/sphere with
the following code:
.. code-block:: c++
FixStyle(DEPRECATED,FixDeprecated);
FixStyle(ave/spatial,FixDeprecated);
FixStyle(ave/spatial/sphere,FixDeprecated);
The individual class will then determine based on the style name
what action to perform:
- inform that the style has been removed and what style replaces it, if any, and then error out
- inform that the style has been renamed and then either execute the replacement or error out
- inform that the style is no longer required, and it is thus ignored and continue
There is also a section in the user's guide for :doc:`removed commands
and packages <Commands_removed>` with additional explanations.
Internal fix styles
^^^^^^^^^^^^^^^^^^^
fix DUMMY
"""""""""
Most fix classes cannot be instantiated before the simulation box has
been created since they access data that is only available then.
However, in some cases it is required that a fix must be at or close to
the top of the list of all fixes. In those cases an instance of the
DUMMY fix style may be created by calling ``Modify::add_fix()`` and then
later replaced by calling ``Modify::replace_fix()``.
fix STORE/ATOM
""""""""""""""
Fix STORE/ATOM can be used as persistent storage of per-atom data.
**Syntax**
.. code-block:: LAMMPS
fix ID group-ID STORE/ATOM N1 N2 gflag rflag
* ID, group-ID are documented in :doc:`fix <fix>` command
* STORE/ATOM = style name of this fix command
* N1 = 1, N2 = 0 : data is per-atom vector = single value per atom
* N1 > 1, N2 = 0 : data is per-atom array = N1 values per atom
* N1 > 0, N2 > 0 : data is per-atom tensor = N1xN2 values per atom
* gflag = 1 communicate per-atom values with ghost atoms, 0 do not update ghost atom data
* rflag = 1 store per-atom value in restart file, 0 do not store data in restart
Similar functionality is also available through using custom per-atom
properties with :doc:`fix property/atom <fix_property_atom>`. The
choice between the two fixes should be based on whether the user should
be able to access this per-atom data: if yes, then fix property/atom is
preferred, otherwise fix STORE/ATOM.
fix STORE/GLOBAL
""""""""""""""""
Fix STORE/GLOBAL can be used as persistent storage of global data with support for restarts
**Syntax**
.. code-block:: LAMMPS
fix ID group-ID STORE/GLOBAL N1 N2
* ID, group-ID are documented in :doc:`fix <fix>` command
* STORE/GLOBAL = style name of this fix command
* N1 >=1 : number of global items to store
* N2 = 1 : data is global vector of length N1
* N2 > 1 : data is global N1xN2 array
fix STORE/LOCAL
"""""""""""""""
Fix STORE/LOCAL can be used as persistent storage for local data
**Syntax**
.. code-block:: LAMMPS
fix ID group-ID STORE/LOCAL Nreset Nvalues
* ID, group-ID are documented in :doc:`fix <fix>` command
* STORE/LOCAL = style name of this fix command
* Nreset = frequency at which local data is available
* Nvalues = number of values per local item, that is the number of columns

151
doc/src/Developer_notes.rst
View File

@ -7,13 +7,7 @@ typically document what a variable stores, what a small section of
code does, or what a function does and its input/outputs. The topics
on this page are intended to document code functionality at a higher level.
Available topics are:
- `Reading and parsing of text and text files`_
- `Requesting and accessing neighbor lists`_
- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
- `KSpace PPPM FFT grids`_
.. contents::
----
@ -218,6 +212,149 @@ command:
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
Errors, warnings, and informational messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS has specialized functionality to handle errors (which should
terminate LAMMPS), warning messages (which should indicate possible
problems *without* terminating LAMMPS), and informational text for
messages about the progress and chosen settings. We *strongly*
encourage using these facilities and to *stay away* from using
``printf()`` or ``fprintf()`` or ``std::cout`` or ``std::cerr`` and
calling ``MPI_Abort()`` or ``exit()`` directly. Warnings and
informational messages should be printed only on MPI rank 0 to avoid
flooding the output when running in parallel with many MPI processes.
**Errors**
When LAMMPS encounters an error, for example a syntax error in the
input, then a suitable error message should be printed giving a brief,
one line remark about the reason and then call either ``Error::all()``
or ``Error::one()``. ``Error::all()`` must be called when the failing
code path is executed by *all* MPI processes and the error condition
will appear for *all* MPI processes the same. If desired, each MPI
process may set a flag to either 0 or 1 and then MPI_Allreduce()
searching for the maximum can be used to determine if there was an error
on *any* of the MPI processes and make this information available to
*all*. ``Error::one()`` in contrast needs to be called when only one or
a few MPI processes execute the code path or can have the error
condition. ``Error::all()`` is generally the preferred option.
Calling these functions does not abort LAMMPS directly, but rather
throws either a ``LAMMPSException`` (from ``Error::all()``) or a
``LAMMPSAbortException`` (from ``Error::one()``). These exceptions are
caught by the LAMMPS ``main()`` program and then handled accordingly.
The reason for this approach is to support applications, especially
graphical applications like :ref:`LAMMPS-GUI <lammps_gui>`, that are
linked to the LAMMPS library and have a mechanism to avoid that an error
in LAMMPS terminates the application. By catching the exceptions, the
application can delete the failing LAMMPS class instance and create a
new one to try again. In a similar fashion, the :doc:`LAMMPS Python
module <Python_module>` checks for this and then re-throws corresponding
Python exception, which in turn can be caught by the calling Python
code.
There are multiple "signatures" that can be called:
- ``Error::all(FLERR, "Error message")``: this will abort LAMMPS with
the error message "Error message", followed by the last line of input
that was read and processed before the error condition happened.
- ``Error::all(FLERR, Error::NOLASTLINE, "Error message")``: this is the
same as before but without the last line of input. This is preferred
for errors that would happen *during* a :doc:`run <run>` or
:doc:`minimization <minimize>`, since showing the "run" or "minimize"
command would be the last line, but is unrelated to the error.
- ``Error::all(FLERR, idx, "Error message")``: this is for argument
parsing where "idx" is the index (starting at 0) of the argument for a
LAMMPS command that is causing the failure (use -1 for the command
itself). For index 0, you need to use the constant ``Error::ARGZERO``
to work around the inability of some compilers to disambiguate between
a NULL pointer and an integer constant 0, even with an added type cast.
The output may also include the last input line *before* and
*after*, if they differ due to substituting variables. A textual
indicator is pointing to the specific word that failed. Using the
constant ``Error::NOPOINTER`` in place of the *idx* argument will
suppress the marker and then the behavior is like the *idx* argument
is not provided.
FLERR is a macro containing the filename and line where the Error class
is called and that information is appended to the error message. This
allows to quickly find the relevant source code causing the error. For
all three signatures, the single string "Error message" may be replaced
with a format string using '{}' placeholders and followed by a variable
number of arguments, one for each placeholder. This format string and
the arguments are then handed for formatting to the `{fmt} library
<https://fmt.dev>`_ (which is bundled with LAMMPS) and thus allow
processing similar to the "format()" functionality in Python.
.. note::
For commands like :doc:`fix ave/time <fix_ave_time>` that accept
wildcard arguments, the :cpp:func:`utils::expand_args` function
may be passed as an optional argument where the function will provide
a map to the original arguments from the expanded argument indices.
For complex errors, that can have multiple causes and which cannot be
explained in a single line, you can append to the error message, the
string created by :cpp:func:`utils::errorurl`, which then provides a
URL pointing to a paragraph of the :doc:`Errors_details` that
corresponds to the number provided. Example:
.. code-block:: c++
error->all(FLERR, "Unknown identifier in data file: {}{}", keyword, utils::errorurl(1));
This will output something like this:
.. parsed-literal::
ERROR: Unknown identifier in data file: Massess
For more information see https://docs.lammps.org/err0001 (src/read_data.cpp:1482)
Last input line: read_data data.peptide
Where the URL points to the first paragraph with explanations on
the :doc:`Errors_details` page in the manual.
**Warnings**
To print warnings, the ``Errors::warning()`` function should be used.
It also requires the FLERR macros as first argument to easily identify
the location of the warning in the source code. Same as with the error
functions above, the function has two variants: one just taking a single
string as final argument and a second that uses the `{fmt} library
<https://fmt.dev>`_ to make it similar to, say, ``fprintf()``. One
motivation to use this function is that it will output warnings with
always the same capitalization of the leading "WARNING" string. A
second is that it has a built in rate limiter. After a given number (by
default 100), that can be set via the :doc:`thermo_modify command
<thermo_modify>` no more warnings are printed. Also, warnings are
written consistently to both screen and logfile or not, depending on the
settings for :ref:`screen <screen>` or :doc:`logfile <log>` output.
.. note::
Unlike ``Error::all()``, the warning function will produce output on
*every* MPI process, so it typically would be prefixed with an if
statement testing for ``comm->me == 0``, i.e. limiting output to MPI
rank 0.
**Informational messages**
Finally, for informational message LAMMPS has the
:cpp:func:`utils::logmesg() convenience function
<LAMMPS_NS::utils::logmesg>`. It also uses the `{fmt} library
<https://fmt.dev>`_ to support using a format string followed by a
matching number of arguments. It will output the resulting formatted
text to both, the screen and the logfile and will honor the
corresponding settings about whether this output is active and to which
file it should be send. Same as for ``Error::warning()``, it would
produce output for every MPI process and thus should usually be called
only on MPI rank 0 to avoid flooding the output when running with many
parallel processes.
Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

72
doc/src/Developer_unittest.rst
View File

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

15
doc/src/Developer_utils.rst
View File

@ -133,6 +133,9 @@ and parsing files or arguments.
.. doxygenfunction:: trim_comment
:project: progguide
.. doxygenfunction:: strcompress
:project: progguide
.. doxygenfunction:: strip_style_suffix
:project: progguide
@ -166,6 +169,9 @@ and parsing files or arguments.
.. doxygenfunction:: split_lines
:project: progguide
.. doxygenfunction:: strsame
:project: progguide
.. doxygenfunction:: strmatch
:project: progguide
@ -232,12 +238,21 @@ Convenience functions
.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
:project: progguide
.. doxygenfunction:: print(FILE *fp, const std::string &format, Args&&... args)
:project: progguide
.. doxygenfunction:: print(FILE *fp, const std::string &mesg)
:project: progguide
.. doxygenfunction:: errorurl
:project: progguide
.. doxygenfunction:: missing_cmd_args
:project: progguide
.. doxygenfunction:: point_to_error
:project: progguide
.. doxygenfunction:: flush_buffers(LAMMPS *lmp)
:project: progguide

2
doc/src/Developer_write_fix.rst
View File

@ -96,7 +96,7 @@ Here the we specify which methods of the fix should be called during
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
scale3(1.0 / globalAvgVel[3], globalAvgVel);
if ((comm->me == 0) && screen) {
fmt::print(screen,"{}, {}, {}\n",
utils::print(screen, "{}, {}, {}\n",
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
}
}

50
doc/src/Errors_debug.rst
View File

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

942
doc/src/Errors_details.rst
View File

@ -1,12 +1,244 @@
Error and warning details
=========================
Errors and warnings details
===========================
Many errors or warnings are self-explanatory and thus straightforward to
resolve. However, there are also cases, where there is no single cause
and explanation, where LAMMPS can only detect symptoms of an error but
not the exact cause, or where the explanation needs to be more detailed than
what can be fit into a message printed by the program. The following are
discussions of such cases.
Many errors and warnings that LAMMPS outputs are self-explanatory and
thus straightforward to resolve. However, there are also cases where
there is no single cause or simple explanation that can be provided in a
short message printed by LAMMPS. Therefore, more detailed discussions
of such scenarios are provided here; first on a more general level and
then for specific errors. In the latter cases, LAMMPS will output a
short message and then provide a URL that links to a specific section on
this page.
.. contents::
------
General troubleshooting advice
------------------------------
Below are suggestions that can help to understand the causes of problems
with simulations leading to errors or unexpected results.
.. _hint01:
Create a small test system
^^^^^^^^^^^^^^^^^^^^^^^^^^
Debugging problems often requires running a simulation many times with
small modifications, thus it can be a huge time saver to first assemble
a small test system input that has the same issue, but will take much
time until it triggers the error condition. Also, it will be easier to
see what happens.
.. _hint02:
Visualize your trajectory
^^^^^^^^^^^^^^^^^^^^^^^^^
To better understand what is causing problems, it is often very useful
to visualize the system close to the point of failure. It may be
necessary to have LAMMPS output trajectory frames rather frequently. To
avoid gigantic files, you can use :doc:`dump_modify delay <dump_modify>`
to delay output until the critical section is reached, and you can use a
smaller test system (see above).
.. _hint03:
Parallel versus serial
^^^^^^^^^^^^^^^^^^^^^^
Issues where something is "lost" or "missing" often exhibit that issue
only when running in parallel. That doesn't mean there is no problem,
only the symptoms are not triggering an error quickly. Correspondingly,
errors may be triggered faster with more processors and thus smaller
sub-domains.
.. _hint04:
Segmentation Fault
^^^^^^^^^^^^^^^^^^
A segmentation fault is an error reported by the **operating system**
and not LAMMPS itself. It happens when a process tries to access a
memory address that is not available. This can have **many** reasons:
memory has not been allocated, a memory buffer is not large enough, a
memory address is computed from an incorrect index, a memory buffer is
used after it has been freed, some general memory corruption. When
investigating a segmentation fault (aka segfault), it is important to
determine which process is causing it; it may not always be LAMMPS. For
example, some MPI library implementations report a segmentation fault
from their "mpirun" or "mpiexec" command when the application has been
terminated unexpectedly.
While a segmentation fault is likely an indication of a bug in LAMMPS,
it need not always be; it can also be the consequence of too aggressive
simulation settings. For time critical code paths, LAMMPS will assume
the user has chosen the settings carefully and will not make any checks
to avoid to avoid performance penalties.
A crucial step in resolving a segmentation fault is to identify the
exact location in the code where it happens. Please see `Errors_debug`
for a couple of examples showing how to do this on a Linux machine.
With this information -- a simple way to reproduce the segmentation
fault and the exact :doc:`LAMMPS version <Manual_version>` and platform
you are running on -- you can contact the LAMMPS developers or post in
the LAMMPS forum to get assistance.
.. _hint05:
Fast moving atoms
^^^^^^^^^^^^^^^^^
Fast moving atoms may be "lost" or "missing" when their velocity becomes
so large that they can cross a sub-domain within one timestep. This
often happens when atoms are too close, but atoms may also "move" too
fast from sub-domain to sub-domain if the box changes rapidly.
E.g. when setting a large an initial box with :doc:`shrink-wrap boundary
conditions <boundary>` that collapses on the first step (in this case
the solution is often using 'm' instead of 's' as a boundary condition).
To reduce the impact of "close contacts", one can remove those atoms or
molecules with something like :doc:`delete_atoms overlap 0.1 all all
<delete_atoms>`. With periodic boundaries, a close contact pair of
atoms may be on opposite sides of the simulation box. Another option
would be to first run a minimization (aka quench) before starting
the MD. Reducing the time step can also help. Many times, one just
needs to "ease" the system into a balanced state and can then switch to
more aggressive settings.
The speed of atoms during an MD run depends on the steepness of the
potential function and their mass. Since the positions and velocities
of atoms are computed with finite timesteps, the timestep needs to be
small enough for stable numeric integration of the trajectory. If the
timestep is too large during initialization (or other instances of
extreme dynamics), using :doc:`fix nve/limit <fix_nve_limit>` or
:doc:`fix dt/reset <fix_dt_reset>` temporarily can help to avoid too
large updates or adapt the timestep according to the displacements.
.. _hint06:
Ignoring lost atoms
^^^^^^^^^^^^^^^^^^^
It is tempting to use the :doc:`thermo_modify lost ignore
<thermo_modify>` to avoid LAMMPS aborting with an error on lost atoms.
This setting should, however, *only* be used when atoms *should* leave
the system. In general, ignoring a problem does not solve it.
.. _hint07:
Pressure, forces, positions becoming NaN or Inf
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Some potentials can overflow or have a division by zero with close
contacts or bad geometries (for the given force styles in use) leading
to forces that can no longer be represented as numbers. Those will show
as "NaN" or "Inf". On most machines, the program will continue, but
there is no way to recover from it and those NaN or Inf values will
propagate. So-called :doc:`"soft-core" potentials <pair_fep_soft>` or
the :doc:`"soft" repulsive-only pair style <pair_soft>` are less prone
for this behavior (depending on the settings in use) and can be used at
the beginning of a simulation. Also, single precision numbers can
overflow much faster, so for the GPU or INTEL package it may be
beneficial to run with double precision initially before switching to
mixed or single precision for faster execution when the system has
relaxed.
.. _hint08:
Communication cutoff
^^^^^^^^^^^^^^^^^^^^
The communication cutoff determines the "overlap" between sub-domains
and atoms in these regions are referred to in LAMMPS as "ghost atoms".
This region has to be large enough to contain all atoms of a bond,
angle, dihedral, or improper with just one atom in the actual
sub-domain. Typically, this cutoff is set to the largest cutoff from
the :doc:`pair style(s) <pair_style>` plus the :doc:`neighbor list skin
distance <neighbor>` and will typically be sufficient for all bonded
interactions. But if the pair style cutoff is small, this may not be
enough. LAMMPS will print a warning in this case using some heuristic
based on the equilibrium bond length, but that still may not be
sufficient for cases where the force constants are small and thus bonds
may be stretched very far. The communication cutoff can be adjusted
with :doc:`comm_modify cutoff \<value\> <comm_modify>`, but setting this
too large will waste CPU time and memory.
.. _hint09:
Neighbor list settings
^^^^^^^^^^^^^^^^^^^^^^
Every time LAMMPS rebuilds the neighbor lists, LAMMPS will also check
for "lost" or "missing" atoms. Thus it can help to use very
conservative :doc:`neighbor list settings <neigh_modify>` and then
examine the neighbor list statistics if the neighbor list rebuild can be
safely delayed. Rebuilding the neighbor list less frequently
(i.e. through increasing the *delay* or *every*) setting has diminishing
returns and increasing risks.
.. _hint10:
Units
^^^^^
A frequent cause for a variety of problems is due to using the wrong
:doc:`units <units>` settings for a particular potentials, especially
when reading them from a potential file. Most of the (example)
potentials bundled with LAMMPS have a "UNITS:" tag that allows LAMMPS to
check of the units are consistent with what is intended, but potential
files from publications or potential parameter databases may lack this
metadata information and thus will not error out or warn when using the
wrong setting. Most potential files usually use "metal" units, but some
are parameterized for other settings, most notably :doc:`ReaxFF
potentials <pair_reaxff>` that use "real" units.
Also, individual parameters for :doc:`pair_coeff <pair_coeff>` commands
taken from publications or other MD software may need to be converted
and sometimes in unexpected ways. Thus some careful checking is
recommended.
.. _hint11:
No error message printed
^^^^^^^^^^^^^^^^^^^^^^^^
In some cases -- especially when running in parallel with MPI -- LAMMPS
may stop without displaying an error. But the fact that nothing was
displayed does not mean there was not an error message. Instead it is
highly likely that the message was written to a buffer and LAMMPS was
aborted before the buffer was output. Usually, output buffers are
output for every line of output, but sometimes this is delayed until
4096 or 8192 bytes of output have been accumulated. This buffering for
screen and logfile output can be disabled by using the :ref:`-nb
or -nonbuf <nonbuf>` command-line flag. This is most often needed when
debugging crashing multi-replica calculations.
.. _hint12:
Errors before or after the simulation box is created
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
As critical step in a LAMMPS input is when the simulation box is
defined, either with a :doc:`create_box command <create_box>`, a
:doc:`read_data command <read_data>`, or a :doc:`read_restart command
<read_restart>`. After this step, certain settings are locked in (e.g.
units, or number of atom, bond, angle, dihedral, improper types) and
cannot be changed after that. Consequently, commands that change such
settings (e.g. :doc:`units <units>`) are only allowed before the box is
defined. Very few commands can be used before and after, like
:doc:`pair_style <pair_style>` (but not :doc:`pair_coeff <pair_coeff>`).
Most LAMMPS commands must be used after the simulation box is created.
Consequently, LAMMPS will stop with an error, if a command is used in
the wrong place. This is not always obvious. So index or string style
:doc:`variables <variable>` can be expanded anywhere in the input, but
equal style (or similar) variables can only be expanded before the box
is defined if they do not reference anything that cannot be defined
before the box (e.g. a compute or fix reference or a thermo keyword).
------
.. _err0001:
@ -23,19 +255,20 @@ The header section informs LAMMPS how many entries or lines are expected
in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
the data file. If there is a mismatch, LAMMPS will either keep reading
beyond the end of a section or stop reading before the section has
ended. In that case the next line will not contain a recognized keyword.
ended. In that case the next line will not contain a recognized
keyword.
Such a mismatch can also happen when the first line of the data
is *not* a comment as required by the format, but a line with a valid
header keyword. That would result in LAMMPS expecting, for instance,
0 atoms because the "atoms" header line is the first line and thus
treated as a comment.
Such a mismatch can also happen when the first line of the data is *not*
a comment as required by the format, but a line with a valid header
keyword. That would result in LAMMPS expecting, for instance, 0 atoms
because the "atoms" header line is the first line and thus treated as a
comment.
Another possibility to trigger this error is to have a keyword in the
data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
but the :doc:`read_data <read_data>` command is missing the (optional)
arguments that identify the fix and the header keyword and section
keyword or those arguments are inconsistent with the keywords in the
arguments that identify the fix and its header and section keywords.
Alternatively, those arguments are inconsistent with the keywords in the
data file.
.. _err0002:
@ -45,35 +278,676 @@ Incorrect format in ... section of data file
This error happens when LAMMPS reads the contents of a section of a
:doc:`data file <read_data>` and the number of parameters in the line
differs from what is expected. This most commonly happens, when the
atom style is different from what is expected for a specific data file
since changing the atom style usually changes the format of the line.
differs from what is expected. This most commonly happens when the atom
style is different from what is expected for a specific data file since
changing the atom style usually changes the format of the line.
This error can also happen when the number of entries indicated in the
This error can also occur when the number of entries indicated in the
header of a data file (e.g. the number of atoms) is larger than the
number of lines provided (e.g. in the corresponding Atoms section)
and then LAMMPS will continue reading into the next section and that
would have a completely different format.
causing LAMMPS to continue reading into the next section which has a
completely different format.
.. _err0003:
Illegal variable command: expected X arguments but found Y
----------------------------------------------------------
This error indicates that there are the wrong number of arguments for a
specific variable command, but a common reason for that is a variable
expression that has whitespace but is not enclosed in single or double
quotes.
This error indicates that a variable command has the wrong number of
arguments. A common reason for this is that the variable expression has
whitespace, but is not enclosed in single or double quotes.
To explain, the LAMMPS input parser reads and processes lines. The
resulting line is broken down into "words". Those are usually
individual commands, labels, names, values separated by whitespace (a
space or tab character). For "words" that may contain whitespace, they
have to be enclosed in single (') or double (") quotes. The parser will
then remove the outermost pair of quotes and then pass that string as
individual commands, labels, names, and values separated by whitespace
(a space or tab character). For "words" that may contain whitespace,
they have to be enclosed in single (') or double (") quotes. The parser
will then remove the outermost pair of quotes and pass that string as
"word" to the variable command.
Thus missing quotes or accidental extra whitespace will lead to the
error shown in the header because the unquoted whitespace will result
in the text being broken into more "words", i.e. the variable expression
being split.
Thus missing quotes or accidental extra whitespace will trigger this
error because the unquoted whitespace will result in the text being
broken into more "words", i.e. the variable expression being split.
.. _err0004:
Out of range atoms - cannot compute ...
---------------------------------------
The PPPM (and also PPPMDisp and MSM) methods need to assemble a grid of
electron density data derived from the (partial) charges assigned to the
atoms. These charges are smeared out across multiple grid points (see
:doc:`kspace_modify order <kspace_modify>`). When running in parallel
with MPI, LAMMPS uses a :doc:`domain decomposition scheme
<Developer_par_part>` where each processor manages a subset of atoms and
thus also a grid representing the density. The processor's grid covers
the actual volume of the sub-domain and some extra space corresponding
to the :doc:`neighbor list skin <neighbor>`. These are then
:doc:`combined and redistributed <Developer_par_long>` for parallel
processing of the long-range component of the Coulomb interaction.
The ``Out of range atoms`` error can happen when atoms move too fast,
the neighbor list skin is too small, or the neighbor lists are not
updated frequently enough. The smeared charges cannot then be fully
assigned to the density grid for all atoms. LAMMPS checks for this
condition and stops with an error. Most of the time, this is an
indication of a system with very high forces, often at the beginning of
a simulation or when boundary conditions are changed. The error becomes
more likely with more MPI processes.
There are multiple options to explore for avoiding the error. The best
choice depends strongly on the individual system, and often a
combination of changes is required. For example, more conservative MD
parameter settings can be used (larger neighbor skin, shorter time step,
more frequent neighbor list updates). Sometimes, it helps to revisit
the system generation and avoid close contacts when building it.
Otherwise one can use the :doc:`delete_atoms overlap<delete_atoms>`
command to delete those close contact atoms or run a minimization before
the MD. It can also help to temporarily use a cutoff-Coulomb pair style
and no kspace style until the system has somewhat equilibrated and then
switch to the long-range solver.
.. _err0005:
Bond (or angle, dihedral, improper, cmap, or shake) atoms missing
-----------------------------------------------------------------
The second atom needed to compute a particular bond (or the third or
fourth atom for angle, dihedral, or improper) is missing on the
indicated timestep and processor. Typically, this is because the two
bonded atoms have become too far apart relative to the communication
cutoff distance for ghost atoms. By default, the communication cutoff
is set by the pair cutoff. However, to accommodate larger distances
between topologically connected atoms, it can be manually adjusted using
:doc:`comm_modify <comm_modify>` at the cost of increased communication
and more ghost atoms. However, missing bond atoms may also indicate
that there are unstable dynamics which caused the atoms to blow apart.
In this scenario, increasing the communication distance will not solve
the underlying issue. Rather, see :ref:`Fast moving atoms <hint05>` and
:ref:`Neighbor list settings <hint09>` in the general troubleshooting
section above for ideas to fix unstable dynamics.
If atoms are intended to be lost during a simulation (e.g. due to open
boundary conditions or :doc:`fix evaporate <fix_evaporate>`) such that
two bonded atoms may be lost at different times from each other, this
error can be converted to a warning or turned off using the *lost/bond*
keyword in the :doc:`thermo_modify <thermo_modify>` command.
.. _err0006:
Non-numeric atom coords or pressure or box dimensions - simulation unstable
---------------------------------------------------------------------------
This error usually occurs due to overly aggressive simulation settings
or issues with the system geometry or the potential. See
:ref:`Pressure, forces, positions becoming NaN or Inf <hint07>` above in
the general troubleshooting section. This error is more likely to
happen during equilibration, so it can help to do a minimization before
or even add a second or third minimization after running a few
equilibration MD steps. It also is more likely when directly using a
Nose-Hoover (or other) barostat, and thus it may be advisable to run
with only a thermostat for a bit until the potential energy has
stabilized.
.. _err007:
Fix used in ... not computed at compatible time
-----------------------------------------------
Many fix styles are invoked only every *nevery* timesteps, which means
their data is only valid on those steps. When data from a fix is used
as input for a compute, a dump, another fix, or thermo output, it must
read that data at timesteps when the fix in question was invoked, i.e.
on timesteps that are multiples of its *nevery* setting. If this is not
the case, LAMMPS will stop with an error. To remedy this, it may be
required to change the output frequency or the *nevery* setting of the
fix.
.. _err0008:
Lost atoms ...
--------------
A simulation stopping with an error due to lost atoms can have multiple
causes. By default, LAMMPS checks for whether the total number of atoms
is consistent with the sum of atoms "owned" by MPI processors every time
that thermodynamic output is written. In the majority of cases, lost
atoms are unexpected and a result of extremely high velocities causing
instabilities in the system. Such velocities can result from a variety
of issues. For ideas on how to track down issues with unexpected lost
atoms, see :ref:`Fast moving atoms <hint05>` and :ref:`Neighbor list
settings <hint09>` in the general troubleshooting section above. In
specific situations however, losing atoms is expected material behavior
(e.g. with sputtering and surface evaporation simulations), and an
unwanted crash can be avoided by changing the :doc:`thermo_modify lost
<thermo_modify>` keyword from the default 'error' to 'warn' or 'ignore'
(though heed the advice in :ref:`Ignoring lost atoms <hint06>` above!).
.. _err0009:
Too many neighbor bins
----------------------
The simulation box is or has become too large relative to the size of a
neighbor bin (which in turn depends on the largest pair-wise cutoff by
default) such that LAMMPS is unable to store the needed number of bins.
This typically implies the simulation box has expanded too far. That
can occur when some atoms move rapidly apart with shrink-wrap boundaries
or when a fix (like fix deform or a barostat) excessively grows the
simulation box. This can also happen if the largest pair-wise cutoff is
small. In this case, the error can be avoided by using the
:doc:`neigh_modify command <neigh_modify>` to set the bin width to a
suitably large value.
.. _err0010:
Unrecognized ... style ... is part of ... package which is not enabled in this LAMMPS binary
--------------------------------------------------------------------------------------------
The LAMMPS executable (binary) being used was not compiled with a
package containing the specified style. This indicates that the
executable needs to be re-built after enabling the correct package in
the relevant Makefile or CMake build directory. See
:doc:`Section 3. Build LAMMPS <Build>` for more details. One can check
if the expected package and pair style is present in the executable by
running it with the ``-help`` (or ``-h``) flag on the command line. One
common oversight, especially for beginner LAMMPS users, is enabling the
package but forgetting to run commands to rebuild (e.g., to run the
final ``make`` or ``cmake`` command).
If this error occurs with an executable that the user does not control
(e.g., through a module on HPC clusters), the user will need to get in
contact with the relevant person or people who can update the
executable.
.. _err011:
Energy or stress was not tallied by pair style
----------------------------------------------
This warning can be printed by computes from the :ref:`TALLY package
<PKG-TALLY>`. Those use a callback mechanism that only work for regular
pair-wise additive pair styles like :doc:`Lennard-Jones <pair_lj>`,
:doc:`Morse <pair_morse>`, :doc:`Born-Meyer-Huggins <pair_born>`, and
similar. Such required callbacks have not been implemented for
many-body potentials so one would have to implement them to add
compatibility with these computes (which may be difficult to do in a
generic fashion). Whether this warning indicates that contributions to
the computed properties are missing depends on the groups used. At any
rate, careful testing of the results is advised when this warning
appears.
.. _err0012:
fmt::format_error
-----------------
LAMMPS uses the `{fmt} library <https://fmt.dev>`_ for advanced string
formatting tasks. This is similar to the ``printf()`` family of
functions from the standard C library, but more flexible. If there is a
bug in the LAMMPS code and the format string does not match the list of
arguments or has some other error, this error message will be shown.
You should contact the LAMMPS developers and report the bug as a `GitHub
Bug Report Issue <https://github.com/lammps/lammps/issues>`_ along with
sufficient information to easily reproduce it.
.. _err0013:
Substitution for illegal variable
---------------------------------
A variable in an input script or a variable expression was not found in
the list of valid variables. The most common reason for this is a typo
somewhere in the input file such that the expression uses an invalid
variable name. The second most common reason is omitting the curly
braces for a direct variable with a name that is not a single letter.
For example:
.. code-block:: LAMMPS
variable cutoff index 10.0
pair_style lj/cut ${cutoff} # this is correct
pair_style lj/cut $cutoff # this is incorrect, LAMMPS looks for 'c' instead of 'cutoff'
variable c index 5.0 # if $c is defined, LAMMPS subsitutes only '$c' and reads: 5utoff
Another potential source of this error may be invalid command line
variables (-var or -v argument) used when launching LAMMPS from an
interactive shell or shell scripts. An uncommon source for this error
is using the :doc:`next command <next>` to advance through a list of
values provided by an index style variable. If there is no remaining
element in the list, LAMMPS will delete the variable and any following
expansion or reference attempt will trigger the error.
Users with harder-to-track variable errors might also find reading the
:doc:`Parsing rules for input scripts <Commands_parse>` helpful.
.. _err0014:
Bond atom missing in image check or box size check
--------------------------------------------------
This can be either an error or a warning depending on your
:doc:`thermo_modify settings <thermo_modify>`. It is flagged in a part
of the LAMMPS code where it updates the domain decomposition and before
it builds the neighbor lists. It checks that both atoms of a bond are
within the communication cutoff of a subdomain. It is usually caused by
atoms moving too fast (see the :ref:`paragraph on fast moving atoms
<hint05>`), or by the :doc:`communication cutoff being too small
<comm_modify>`, or by waiting too long between :doc:`sub-domain and
neighbor list updates <neigh_modify>`.
.. _err0015:
Cannot use neighbor bins - box size \<\< cutoff
-----------------------------------------------
LAMMPS is unable to build neighbor bins since the size of the box is
much smaller than an interaction cutoff in at least one of its
dimensions. Typically, this error is triggered when the simulation box
has one very thin dimension. If a cubic neighbor bin had to fit exactly
within the thin dimension, then an inordinate amount of bins would be
created to fill space. This error can be avoided using the generally
slower :doc:`nsq neighbor style <neighbor>` or by increasing the size of
the smallest box lengths.
.. _err0016:
Did not assign all atoms correctly
----------------------------------
This error happens most commonly when :doc:`reading a data file
<read_data>` under :doc:`non-periodic boundary conditions<boundary>`.
Only atoms with positions **inside** the simulation box will be read and
thus any atoms outside the box will be skipped and the total atom count
will not match, which triggers the error. This does not happen with
periodic boundary conditions where atoms outside the principal box will
be "wrapped" into the principal box and their image flags set
accordingly.
Similar errors can happen with the :doc:`replicate command<replicate>`
or the :doc:`read_restart command<read_restart>`. In these cases the
cause may be a problematic geometry, an insufficient communication
cutoff, or a bug in the LAMMPS source code. In these cases it is
advisable to set up :ref:`small test case <hint01>` for testing and
debugging. This will be required in case you need to get help from a
LAMMPS developer.
.. _err0017:
Domain too large for neighbor bins
----------------------------------
The domain has become extremely large so that neighbor bins cannot be
used. Too many neighbor bins would need to be created to fill space.
Most likely, one or more atoms have been blown a great distance out of
the simulation box or a fix (like fix deform or a barostat) has
excessively grown the simulation box.
.. _err0018:
Step X: (h)bondchk failed
-------------------------
This error is a consequence of the heuristic memory allocations for
buffers of the regular ReaxFF version. In ReaxFF simulations, the lists
of bonds and hydrogen bonds can change due to chemical reactions. The
default approach, however, assumes that these changes are not very
large, so it allocates buffers for the current system setup plus a
safety margin. This can be adjusted with the :doc:`safezone, mincap,
and minhbonds settings of the pair style <pair_reaxff>`, but only to
some extent. When equilibrating a new system, or simulating a sparse
system in parallel, this can be difficult to control and become
wasteful. A simple workaround is often to break a simulation down in
multiple chunks. A better approach, however, is to compile and use the
KOKKOS package version of ReaxFF (you do not need a GPU for that, but
can also compile it in serial or OpenMP mode), which uses a more robust
memory allocation approach.
.. _err0019:
Numeric index X is out of bounds
--------------------------------
This error most commonly happens when setting force field coefficients
with either the :doc:`pair_coeff <pair_coeff>`, the :doc:`bond_coeff
<bond_coeff>`, the :doc:`angle_coeff <angle_coeff>`, the
:doc:`dihedral_coeff <dihedral_coeff>`, or the :doc:`improper_coeff
<improper_coeff>` command. These commands accept type labels, explicit
numbers, and wildcards for ranges of numbers. If the numeric value of
any of these is outside the valid range (defined by the number of
corresponding types), LAMMPS will stop with this error. A few other
commands and styles also allow ranges of numbers and check using the
same method and thus print the same kind of error.
The cause is almost always a typo in the input or a logic error when
defining the values or ranges. So one needs to carefully review the
input. Along with the error, LAMMPS will print the valid range as a
hint.
.. _err0020:
Compute, fix, or variable vector or array is accessed out-of-range
------------------------------------------------------------------
When accessing an individual element of a global vector or array or a
per-atom vector or array provided by a compute or fix or atom-style or
vector-style variable or data from a specific atom, an index in square
brackets ("[ ]") (or two indices) must be provided to determine which
element to access and it must be in a valid range or else LAMMPS would
access invalid data or crash with a segmentation fault. In the two most
common cases, where this data is accessed, :doc:`variable expressions
<variable>` and :doc:`thermodynamic output <thermo_style>`, LAMMPS will
check for valid indices and stop with an error otherwise.
While LAMMPS is written in C++ (which uses 0 based indexing) these
indices start at 1 (i.e. similar to Fortran). Any index smaller than 1
or larger than the maximum allowed value should trigger this error.
Since this kind of error frequently happens with rather complex
expressions, it is recommended to test these with small test systems,
where the values can be tracked with output files for all relevant
properties at every step.
.. _err0021:
Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients)
-------------------------------------------------------------------------------------
The parameters in the :doc:`pair_coeff <pair_coeff>` command for a
specified :doc:`pair_style <pair_style>` have a missing or erroneous
argument. The same applies when seeing this error for :doc:`bond_coeff
<bond_coeff>`, :doc:`angle_coeff <angle_coeff>`, :doc:`dihedral_coeff
<dihedral_coeff>`, or :doc:`improper_coeff <improper_coeff>` and their
respective style commands when using the MOLECULE or EXTRA-MOLECULE
packages. The cases below describe some ways to approach pair
coefficient errors, but the same strategies apply to bonded systems as
well.
Outside of normal typos, this error can have several sources. In all
cases, the first step is to compare the command arguments to the
expected format found in the corresponding :doc:`pair_style
<pair_style>` page. This can reveal cases where, for example, a pair
style was changed, but the pair coefficients were not updated. This can
happen especially with pair style variants such as :doc:`pair_style eam
<pair_eam>` vs. :doc:`pair_style eam/alloy <pair_style>` that look very
similar but accept different parameters (the latter 'eam/alloy' variant
takes element type names while 'eam' does not).
Another common source of coefficient errors is when using multiple pair
styles with commands such as :doc:`pair_style hybrid <pair_hybrid>`.
Using hybrid pair styles requires adding an extra "label" argument in
the coefficient commands that designates which pair style the command
line refers to. Moreover, if the same pair style is used multiple
times, this label must be followed by an additional numeric argument.
Also, different pair styles may require different arguments.
This error message might also require a close look at other LAMMPS input
files that are read in by the input script, such as data files or
restart files.
.. _err0022:
Energy was not tallied on needed timestep (also virial, per-atom energy, per-atom virial)
-----------------------------------------------------------------------------------------
This error is generated when LAMMPS attempts to access an out-of-date or
non-existent energy, pressure, or virial. For efficiency reasons,
LAMMPS does *not* calculate these quantities when the forces are
calculated on every timestep or iteration. Global quantities are only
calculated when they are needed for :doc:`thermo <thermo_style>` output
(at the beginning, end, and at regular intervals specified by the
:doc:`thermo <thermo>` command). Similarly, per-atom quantities are
only calculated if they are needed to write per-atom energy or virial to
a dump file. This system works fine for simple input scripts. However,
the many user-specified `variable`, `fix`, and `compute` commands that
LAMMPS provides make it difficult to anticipate when a quantity will be
requested. In some use cases, LAMMPS will figure out that a quantity is
needed and arrange for it to be calculated on that timestep e.g. if it
is requested by :doc:`fix ave/time <fix_ave_time>` or similar commands.
If that fails, it can be detected by a mismatch between the current
timestep and when a quantity was last calculated, in which case an error
message of this type is generated.
The most common cause of this type of error is requesting a quantity
before the start of the simulation.
.. code-block:: LAMMPS
# run 0 post no # this will fix the error
variable e equal pe # requesting energy compute
print "Potential energy = $e" # this will generate the error
run 1000 # start of simulation
This situation can be avoided by adding in a "run 0" command, as
explained in more detail in the "Variable Accuracy" section of the
:doc:`variable <variable>` doc page.
Another cause is requesting a quantity on a timestep that is not a
thermo or dump output timestep. This can often be remedied by
increasing the frequency of thermo or dump output.
.. _err0023:
Molecule auto special bond generation overflow
----------------------------------------------
In order to correctly apply the :doc:`special_bonds <special_bonds>`
settings (also known as "exclusions"), LAMMPS needs to maintain for each
atom a list of atoms that are connected to this atom, either directly
with a bond or indirectly through bonding with an intermediate atom(s).
The purpose is to either remove or tag those pairs of atoms in the
neighbor list. This information is stored with individual atoms and
thus the maximum number of such "special" neighbors is set when the
simulation box is created. When reading (relative) geometry and
topology of a 'molecule' from a :doc:`molecule file <molecule>`, LAMMPS
will build the list of such "special" neighbors for the molecule atom
(if not given in the molecule file explicitly). The error is triggered
when the resulting list is too long for the space reserved when creating
the simulation box. The solution is to increase the corresponding
setting. Overestimating this value will only consume more memory, and
is thus a safe choice.
.. _err0024:
Molecule topology/atom exceeds system topology/atom
---------------------------------------------------
LAMMPS uses :doc:`domain decomposition <Developer_par_part>` to
distribute data (i.e. atoms) across the MPI processes in parallel runs.
This includes topology data about bonds, angles, dihedrals, impropers
and :doc:`"special" neighbors <special_bonds>`. This information is
stored with either one or all atoms involved in such a topology entry
(which of the two option applies depends on the :doc:`newton <newton>`
setting for bonds). When reading a data file, LAMMPS analyzes the
requirements for this file and then the values are "locked in" and
cannot be extended.
So loading a molecule file that requires more of the topology per atom
storage or adding a data file with such needs will lead to an error. To
avoid the error, one or more of the `extra/XXX/per/atom` keywords are
required to extend the corresponding storage. It is no problem to
choose those numbers generously and have more storage reserved than
actually needed, but having these numbers set too small will lead to an
error.
.. _err0025:
Molecule topology type exceeds system topology type
---------------------------------------------------
The total number of atom, bond, angle, dihedral, and improper types is
"locked in" when LAMMPS creates the simulation box. This can happen
through either the :doc:`create_box <create_box>`, the :doc:`read_data
<read_data>`, or the :doc:`read_restart <read_restart>` command. After
this it is not possible to refer to an additional type. So loading a
molecule file that uses additional types or adding a data file that
would require additional types will lead to an error. To avoid the
error, one or more of the `extra/XXX/types` keywords are required to
extend the maximum number of the individual types.
.. _err0026:
Molecule attributes do not match system attributes
--------------------------------------------------
Choosing an :doc:`atom_style <atom_style>` in LAMMPS determines which
per-atom properties are available. In a :doc:`molecule file
<molecule>`, however, it is possible to add sections (for example Masses
or Charges) that are not supported by the atom style. Masses for
example, are usually not a per-atom property, but defined through the
atom type. Thus it would not be required to have a Masses section and
the included data would be ignored. LAMMPS prints this warning to
inform about this case.
.. _err0027:
Inconsistent image flags
------------------------
This warning happens when the distance between the *unwrapped* x-, y-,
or z-components of the coordinates of a bond is larger than half the box
with periodic boundaries or larger than the box with non-periodic
boundaries. It means that the positions and image flags have become
inconsistent. LAMMPS will still compute bonded interactions based on
the closest periodic images of the atoms and thus in most cases the
results will be correct. However they can cause problems when such
atoms are used with the fix rigid or replicate commands. Thus, it is
good practice to update the system so that the message does not appear.
It will help with future manipulations of the system.
There is one case where this warning *must* appear: when you have a
chain of connected bonds that pass through the entire box and connect
back to the first atom in the chain through periodic boundaries,
i.e. some kind of "infinite polymer". In that case, the bond image
flags *must* be inconsistent for the one bond that reaches back to the
beginning of the chain.
.. _err0028:
No fixes with time integration, atoms won't move
------------------------------------------------
This warning will be issued if LAMMPS encounters a :doc:`run <run>`
command that does not have a preceding :doc:`fix <fix>` command that
updates atom/object positions and velocities per step. In other words,
there are no fixes detected that perform velocity-Verlet time
integration, such as :doc:`fix nve <fix_nve>`. Note that this alert
does not mean that there are no active fixes. LAMMPS has a very wide
variety of fixes, many of which do not move objects but also operate
through steps, such as printing outputs (e.g. :doc:`fix print
<fix_print>`), performing calculations (e.g. :doc:`fix ave/time
<fix_ave_time>`), or changing other system parameters (e.g. :doc:`fix
dt/reset <fix_dt_reset>`). It is up to the user to determine whether
the lack of a time-integrating fix is intentional or not.
.. _err0029:
System is not charge neutral, net charge = ...
----------------------------------------------
the sum of charges in the system is not zero. When a system is not
charge-neutral, methods that evolve/manipulate per-atom charges,
evaluate Coulomb interactions, evaluate Coulomb forces, or
evaluate/manipulate other properties relying on per-atom charges may
raise this warning. A non-zero net charge most commonly arises after
setting per-atom charges :doc:`set <set>` such that the sum is non-zero
or by reading in a system through :doc:`read_data <read_data>` where the
per-atom charges do not sum to zero. However, a loss of charge
neutrality may occur in other less common ways, like when charge
equilibration methods (e.g., :doc:`fix qeq <fix_qeq>`) fail.
A similar warning/error may be raised when using certain charge
equilibration methods: :doc:`fix qeq <fix_qeq>`, :doc:`fix qeq/comb
<fix_qeq_comb>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`, and :doc:`fix
qtpie/reaxff <fix_qtpie_reaxff>`. In such cases, this warning/error
will be raised for the fix :doc:`group <group>` when the group has a
non-zero net charge.
When the system is expected to be charge-neutral, this warning often
arises due to an error in the lammps input (e.g., an incorrect :doc:`set
<set>` command, error in the data file read by :doc:`read_data
<read_data>`, incorrectly grouping atoms with charge, etc.). If the
system is NOT expected to be charge-neutral, the user should make sure
that the method(s) used are appropriate for systems with a non-zero net
charge. Some commonly used fixes for charge equilibration :doc:`fix qeq
<fix_qeq>`, pair styles that include charge interactions
:doc:`pair_style coul/XXX <pair_coul>`, and kspace methods
:doc:`kspace_style <kspace_style>` can, in theory, support systems with
non-zero net charge. However, non-zero net charge can lead to spurious
artifacts. The severity of these artifacts depends on the magnitude of
total charge, system size, and methods used. Before running simulations
or calculations for systems with non-zero net charge, users should test
for artifacts and convergence of properties.
.. _err0030:
Variable evaluation before simulation box is defined
----------------------------------------------------
This error happens, when trying to expand or use an equal- or atom-style
variable (or an equivalent style), where the expression contains a
reference to something (e.g. a compute reference, a property of an atom,
or a thermo keyword) that is not allowed to be used before the
simulation box is defined. See the paragraph on :ref:`errors before or
after the simulation box is created <hint12>` for additional
information.
.. _err0031:
Invalid thermo keyword 'X' in variable formula
----------------------------------------------
This error message is often misleading. It is caused when evaluating a
:doc:`variable command <variable>` expression and LAMMPS comes across a
string that it does not recognize. LAMMPS first checks if a string is a
reference to a compute, fix, custom property, or another variable by
looking at the first 2-3 characters (and if it is, it checks whether the
referenced item exists). Next LAMMPS checks if the string matches one
of the available functions or constants. If that fails, LAMMPS will
assume that this string is a :doc:`thermo keyword <thermo_style>` and
let the code for printing thermodynamic output return the corresponding
value. However, if this fails too, since the string is not a thermo
keyword, LAMMPS stops with the 'Invalid thermo keyword' error. But it
is also possible, that there is just a typo in the name of a valid
variable function. Thus it is recommended to check the failing variable
expression very carefully.
.. _err0032:
One or more atoms are time integrated more than once
----------------------------------------------------
This is probably an error since you typically do not want to advance the
positions or velocities of an atom more than once per timestep. This
typically happens when there are multiple fix commands that advance atom
positions with overlapping groups. Also, for some fix styles it is not
immediately obvious that they include time integration. Please check
the documentation carefully.
.. _err0033:
XXX command before simulation box is defined
--------------------------------------------
This error occurs when trying to execute a LAMMPS command that requires
information about the system dimensions, or the number atom, bond,
angle, dihedral, or improper types, or the number of atoms or similar
data that is only available *after* the simulation box has been created.
See the paragraph on :ref:`errors before or after the simulation box is
created <hint12>` for additional information.
.. _err0034:
XXX command after simulation box is defined
--------------------------------------------
This error occurs when trying to execute a LAMMPS command that changes a
global setting *after* it is locked in when the simulation box is
created (for instance defining the :doc:`atom style <atom_style>`,
:doc:`dimension <dimension>`, :doc:`newton <newton>`, or :doc:`units
<units>` setting). These settings may only be changed *before* the
simulation box has been created. See the paragraph on :ref:`errors
before or after the simulation box is created <hint12>` for additional
information.

3487
doc/src/Errors_messages.rst
View File

File diff suppressed because it is too large Load Diff

169
doc/src/Errors_warnings.rst
View File

@ -1,11 +1,15 @@
Warning messages
================
This is an alphabetic list of the WARNING messages LAMMPS prints out
and the reason why. If the explanation here is not sufficient, the
documentation for the offending command may help. Warning messages
also list the source file and line number where the warning was
generated. For example, a message like this:
This is an alphabetic list of some of the WARNING messages LAMMPS prints
out and the reason why. If the explanation here is not sufficient, the
documentation for the offending command may help. This is a historic
list and no longer updated. Instead the LAMMPS developers are trying
to provide more details right with the error message or link to a
paragraph with :doc:`detailed explanations <Errors_details>`.
Warning messages also list the source file and line number where the
warning was generated. For example, a message like this:
.. parsed-literal::
@ -14,7 +18,7 @@ generated. For example, a message like this:
means that line #187 in the file src/domain.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Doc page with :doc:`ERROR messages <Errors_messages>`
Please also see the page with :doc:`Error messages <Errors_messages>`
----------
@ -28,16 +32,10 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
cutoff is set too short or the angle has blown apart and an atom is
too far away.
*Angle style in data file differs from currently defined angle style*
Self-explanatory.
*Angles are defined but no angle style is set*
The topology contains angles, but there are no angle forces computed
since there was no angle_style command.
*Atom style in data file differs from currently defined atom style*
Self-explanatory.
*Bond atom missing in box size check*
The second atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
@ -53,9 +51,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
*Bond style in data file differs from currently defined bond style*
Self-explanatory.
*Bonds are defined but no bond style is set*
The topology contains bonds, but there are no bond forces computed
since there was no bond_style command.
@ -68,9 +63,6 @@ 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.
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explanatory.
*Calling write_dump before a full system init.*
The write_dump command is used before the system has been fully
initialized as part of a 'run' or 'minimize' command. Not all dump
@ -86,18 +78,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
This means the temperature associated with the rigid bodies may be
incorrect on this timestep.
*Cannot include log terms without 1/r terms; setting flagHI to 1*
Self-explanatory.
*Cannot include log terms without 1/r terms; setting flagHI to 1.*
Self-explanatory.
*Charges are set, but coulombic solver is not used*
Self-explanatory.
*Charges did not converge at step %ld: %lg*
Self-explanatory.
*Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost*
The communication cutoff defaults to the maximum of what is inferred from
pair and bond styles (will be zero, if none are defined) and what is specified
@ -123,9 +103,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
is not changed automatically and the warning may be ignored depending
on the specific system being simulated.
*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
Self-explanatory.
*Compute cna/atom cutoff may be too large to find ghost atom neighbors*
The neighbor cutoff used may not encompass enough ghost atoms
to perform this operation correctly.
@ -158,9 +135,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
Conformation of the 4 listed dihedral atoms is extreme; you may want
to check your simulation geometry.
*Dihedral style in data file differs from currently defined dihedral style*
Self-explanatory.
*Dihedrals are defined but no dihedral style is set*
The topology contains dihedrals, but there are no dihedral forces computed
since there was no dihedral_style command.
@ -177,9 +151,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Estimated error in splitting of dispersion coeffs is %g*
Error is greater than 0.0001 percent.
*Ewald/disp Newton solver failed, using old method to estimate g_ewald*
Self-explanatory. Choosing a different cutoff value may help.
*FENE bond too long*
A FENE bond has stretched dangerously far. It's interaction strength
will be truncated to attempt to prevent the bond from blowing up.
@ -192,9 +163,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
A FENE bond has stretched dangerously far. It's interaction strength
will be truncated to attempt to prevent the bond from blowing up.
*Fix halt condition for fix-id %s met on step %ld with value %g*
Self explanatory.
*Fix SRD walls overlap but fix srd overlap not set*
You likely want to set this in your input script.
@ -238,21 +206,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Fix property/atom mol or charge w/out ghost communication*
A model typically needs these properties defined for ghost atoms.
*Fix qeq CG convergence failed (%g) after %d iterations at %ld step*
Self-explanatory.
*Fix qeq has non-zero lower Taper radius cutoff*
Absolute value must be <= 0.01.
*Fix qeq has very low Taper radius cutoff*
Value should typically be >= 5.0.
*Fix qeq/dynamic tolerance may be too small for damped dynamics*
Self-explanatory.
*Fix qeq/fire tolerance may be too small for damped fires*
Self-explanatory.
*Fix rattle should come after all other integration fixes*
This fix is designed to work after all other integration fixes change
atom positions. Thus it should be the last integration fix specified.
@ -285,9 +244,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
The user-specified force accuracy cannot be achieved unless the table
feature is disabled by using 'pair_modify table 0'.
*Geometric mixing assumed for 1/r\^6 coefficients*
Self-explanatory.
*Group for fix_modify temp != fix group*
The fix_modify command is specifying a temperature computation that
computes a temperature on a different group of atoms than the fix
@ -310,46 +266,14 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
Conformation of the 4 listed improper atoms is extreme; you may want
to check your simulation geometry.
*Improper style in data file differs from currently defined improper style*
Self-explanatory.
*Impropers are defined but no improper style is set*
The topology contains impropers, but there are no improper forces computed
since there was no improper_style command.
*Inconsistent image flags*
The image flags for a pair on bonded atoms appear to be inconsistent.
Inconsistent means that when the coordinates of the two atoms are
unwrapped using the image flags, the two atoms are far apart.
Specifically they are further apart than half a periodic box length.
Or they are more than a box length apart in a non-periodic dimension.
This is usually due to the initial data file not having correct image
flags for the two atoms in a bond that straddles a periodic boundary.
They should be different by 1 in that case. This is a warning because
inconsistent image flags will not cause problems for dynamics or most
LAMMPS simulations. However they can cause problems when such atoms
are used with the fix rigid or replicate commands. Note that if you
have an infinite periodic crystal with bonds then it is impossible to
have fully consistent image flags, since some bonds will cross
periodic boundaries and connect two atoms with the same image
flag.
*Increasing communication cutoff for GPU style*
The pair style has increased the communication cutoff to be consistent with
the communication cutoff requirements for this pair style when run on the GPU.
*KIM Model does not provide 'energy'; Potential energy will be zero*
Self-explanatory.
*KIM Model does not provide 'forces'; Forces will be zero*
Self-explanatory.
*KIM Model does not provide 'particleEnergy'; energy per atom will be zero*
Self-explanatory.
*KIM Model does not provide 'particleVirial'; virial per atom will be zero*
Self-explanatory.
*Kspace_modify slab param < 2.0 may cause unphysical behavior*
The kspace_modify slab parameter should be larger to ensure periodic
grids padded with empty space do not overlap.
@ -401,20 +325,10 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
box, or moved further than one processor's subdomain away before
reneighboring.
*MSM mesh too small, increasing to 2 points in each direction*
Self-explanatory.
*Mismatch between velocity and compute groups*
The temperature computation used by the velocity command will not be
on the same group of atoms that velocities are being set for.
*Mixing forced for lj coefficients*
Self-explanatory.
*Molecule attributes do not match system attributes*
An attribute is specified (e.g. diameter, charge) that is
not defined for the specified atom style.
*Molecule has bond topology but no special bond settings*
This means the bonded atoms will not be excluded in pairwise
interactions.
@ -449,9 +363,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*More than one compute damage/atom*
It is not efficient to use compute ke/atom more than once.
*More than one compute dilatation/atom*
Self-explanatory.
*More than one compute erotate/sphere/atom*
It is not efficient to use compute erorate/sphere/atom more than once.
@ -464,24 +375,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*More than one compute orientorder/atom*
It is not efficient to use compute orientorder/atom more than once.
*More than one compute plasticity/atom*
Self-explanatory.
*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.
*More than one compute snav/atom*
Self-explanatory.
*More than one fix poems*
It is not efficient to use fix poems more than once.
@ -557,21 +450,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Pair COMB charge %.10f with force %.10f hit min barrier*
Something is possibly wrong with your model.
*Pair brownian needs newton pair on for momentum conservation*
Self-explanatory.
*Pair dpd needs newton pair on for momentum conservation*
Self-explanatory.
*Pair dsmc: num_of_collisions > number_of_A*
Collision model in DSMC is breaking down.
*Pair dsmc: num_of_collisions > number_of_B*
Collision model in DSMC is breaking down.
*Pair style in data file differs from currently defined pair style*
Self-explanatory.
*Pair style restartinfo set but has no restart support*
This pair style has a bug, where it does not support reading and
writing information to a restart file, but does not set the member
@ -681,9 +565,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
cluster specified by the fix shake command is numerically suspect. LAMMPS
will set it to 0.0 and continue.
*Shell command '%s' failed with error '%s'*
Self-explanatory.
*Shell command returned with non-zero status*
This may indicate the shell command did not operate as expected.
@ -694,15 +575,9 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
This will lead to invalid constraint forces in the SHAKE/RATTLE
computation.
*Simulations might be very slow because of large number of structure factors*
Self-explanatory.
*Slab correction not needed for MSM*
Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.
*Specifying an 'subset' value of '0' is equivalent to no 'subset' keyword*
Self-explanatory.
*System is not charge neutral, net charge = %g*
The total charge on all atoms on the system is not 0.0.
For some KSpace solvers this is only a warning.
@ -734,9 +609,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
assumed to also be for all atoms. Thus the pressure printed by thermo
could be inaccurate.
*The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015*
Self-explanatory.
*The minimizer does not re-orient dipoles when using fix efield*
This means that only the atom coordinates will be minimized,
not the orientation of the dipoles.
@ -745,9 +617,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
More than the maximum # of neighbors was found multiple times. This
was unexpected.
*Too many inner timesteps in fix ttm*
Self-explanatory.
*Too many neighbors in CNA for %d atoms*
More than the maximum # of neighbors was found multiple times. This
was unexpected.
@ -775,24 +644,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
The deformation will heat the SRD particles so this can
be dangerous.
*Using kspace solver on system with no charge*
Self-explanatory.
*Using largest cut-off for lj/long/dipole/long long long*
Self-explanatory.
*Using largest cutoff for buck/long/coul/long*
Self-explanatory.
*Using largest cutoff for lj/long/coul/long*
Self-explanatory.
*Using largest cutoff for pair_style lj/long/tip4p/long*
Self-explanatory.
*Using package gpu without any pair style defined*
Self-explanatory.
*Using pair potential shift with pair_modify compute no*
The shift effects will thus not be computed.

4
doc/src/Examples.rst
View File

@ -54,7 +54,7 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| body | body particles, 2d system |
+-------------+------------------------------------------------------------------+
| bpm | BPM simulations of pouring elastic grains and plate impact |
| bpm | simulations of solid elastic/plastic deformation and fracture |
+-------------+------------------------------------------------------------------+
| cmap | CMAP 5-body contributions to CHARMM force field |
+-------------+------------------------------------------------------------------+
@ -146,6 +146,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| streitz | use of Streitz/Mintmire potential with charge equilibration |
+-------------+------------------------------------------------------------------+
| stress_vcm | removing binned rigid body motion from binned stress profile |
+-------------+------------------------------------------------------------------+
| tad | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
+-------------+------------------------------------------------------------------+
| threebody | regression test input for a variety of manybody potentials |

67
doc/src/Fortran.rst
View File

@ -321,6 +321,14 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype set_string_variable: subroutine
:f set_internal_variable: :f:subr:`set_internal_variable`
:ftype set_internal_variable: subroutine
:f eval: :f:func:`eval`
:ftype eval: function
:f clearstep_compute: :f:subr:`clearstep_compute`
:ftype clearstep_compute: subroutine
:f addstep_compute: :f:subr:`addstep_compute`
:ftype addstep_compute: subroutine
:f addstep_compute_all: :f:subr:`addstep_compute_all`
:ftype addstep_compute_all: subroutine
:f gather_atoms: :f:subr:`gather_atoms`
:ftype gather_atoms: subroutine
:f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@ -954,6 +962,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:f:func:`extract_atom` between runs.
.. admonition:: Array index order
:class: tip
Two-dimensional arrays returned from :f:func:`extract_atom` will be
**transposed** from equivalent arrays in C, and they will be indexed
@ -1066,6 +1075,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
you based on data from the :cpp:class:`Compute` class.
.. admonition:: Array index order
:class: tip
Two-dimensional arrays returned from :f:func:`extract_compute` will be
**transposed** from equivalent arrays in C, and they will be indexed
@ -1324,6 +1334,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:rtype data: polymorphic
.. admonition:: Array index order
:class: tip
Two-dimensional global, per-atom, or local array data from
:f:func:`extract_fix` will be **transposed** from equivalent arrays in
@ -1448,11 +1459,62 @@ Procedures Bound to the :f:type:`lammps` Derived Type
an internal-style variable, an error is generated.
:p character(len=*) name: name of the variable
:p read(c_double) val: new value to assign to the variable
:p real(c_double) val: new value to assign to the variable
:to: :cpp:func:`lammps_set_internal_variable`
--------
.. f:function:: eval(expr)
This function is a wrapper around :cpp:func:`lammps_eval` that takes a
LAMMPS equal style variable string, evaluates it and returns the resulting
scalar value as a floating-point number.
.. versionadded:: 4Feb2025
:p character(len=\*) expr: string to be evaluated
:to: :cpp:func:`lammps_eval`
:r value [real(c_double)]: result of the evaluated string
--------
.. f:subroutine:: clearstep_compute()
Clear whether a compute has been invoked
.. versionadded:: 4Feb2025
:to: :cpp:func:`lammps_clearstep_compute`
--------
.. f:subroutine:: addstep_compute(nextstep)
Add timestep to list of future compute invocations
if the compute has been invoked on the current timestep
.. versionadded:: 4Feb2025
overloaded for 32-bit and 64-bit integer arguments
:p integer(kind=8 or kind=4) nextstep: next timestep
:to: :cpp:func:`lammps_addstep_compute`
--------
.. f:subroutine:: addstep_compute_all(nextstep)
Add timestep to list of future compute invocations
.. versionadded:: 4Feb2025
overloaded for 32-bit and 64-bit integer arguments
:p integer(kind=8 or kind=4) nextstep: next timestep
:to: :cpp:func:`lammps_addstep_compute_all`
--------
.. f:subroutine:: gather_atoms(name, count, data)
This function calls :cpp:func:`lammps_gather_atoms` to gather the named
@ -2711,8 +2773,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
END SUBROUTINE external_callback
END INTERFACE
where ``c_bigint`` is ``c_int`` if ``-DLAMMPS_SMALLSMALL`` was used and
``c_int64_t`` otherwise; and ``c_tagint`` is ``c_int64_t`` if
where ``c_bigint`` is ``c_int64_t`` and ``c_tagint`` is ``c_int64_t`` if
``-DLAMMPS_BIGBIG`` was used and ``c_int`` otherwise.
The argument *caller* to :f:subr:`set_fix_external_callback` is unlimited

2
doc/src/Howto.rst
View File

@ -40,6 +40,7 @@ Settings howto
Howto_walls
Howto_nemd
Howto_dispersion
Howto_bulk2slab
Analysis howto
==============
@ -103,6 +104,7 @@ Tutorials howto
Howto_github
Howto_lammps_gui
Howto_moltemplate
Howto_python
Howto_pylammps
Howto_wsl

15
doc/src/Howto_barostat.rst
View File

@ -10,20 +10,21 @@ and/or pressure (P) is specified by the user, and the thermostat or
barostat attempts to equilibrate the system to the requested T and/or
P.
Barostatting in LAMMPS is performed by :doc:`fixes <fix>`. Two
Barostatting in LAMMPS is performed by :doc:`fixes <fix>`. Three
barostatting methods are currently available: Nose-Hoover (npt and
nph) and Berendsen:
nph), Berendsen, and various linear controllers in deform/pressure:
* :doc:`fix npt <fix_nh>`
* :doc:`fix npt/sphere <fix_npt_sphere>`
* :doc:`fix npt/asphere <fix_npt_asphere>`
* :doc:`fix nph <fix_nh>`
* :doc:`fix press/berendsen <fix_press_berendsen>`
* :doc:`fix deform/pressure <fix_deform_pressure>`
The :doc:`fix npt <fix_nh>` commands include a Nose-Hoover thermostat
and barostat. :doc:`Fix nph <fix_nh>` is just a Nose/Hoover barostat;
it does no thermostatting. Both :doc:`fix nph <fix_nh>` and :doc:`fix press/berendsen <fix_press_berendsen>` can be used in conjunction
with any of the thermostatting fixes.
it does no thermostatting. The fixes :doc:`nph <fix_nh>`, :doc:`press/berendsen <fix_press_berendsen>`, and :doc:`deform/pressure <fix_deform_pressure>`
can be used in conjunction with any of the thermostatting fixes.
As with the :doc:`thermostats <Howto_thermostat>`, :doc:`fix npt <fix_nh>`
and :doc:`fix nph <fix_nh>` only use translational motion of the
@ -44,9 +45,9 @@ a temperature or pressure compute to a barostatting fix.
.. note::
As with the thermostats, the Nose/Hoover methods (:doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`) perform time integration.
:doc:`Fix press/berendsen <fix_press_berendsen>` does NOT, so it should
be used with one of the constant NVE fixes or with one of the NVT
fixes.
:doc:`Fix press/berendsen <fix_press_berendsen>` and :doc:`fix deform/pressure <fix_deform_pressure>`
do NOT, so they should be used with one of the constant NVE fixes or with
one of the NVT fixes.
Thermodynamic output, which can be setup via the
:doc:`thermo_style <thermo_style>` command, often includes pressure

6
doc/src/Howto_bpm.rst
View File

@ -42,12 +42,14 @@ such as those created by pouring grains using :doc:`fix pour
----------
Currently, there are two types of bonds included in the BPM package. The
Currently, there are three types of bonds included in the BPM package. The
first bond style, :doc:`bond bpm/spring <bond_bpm_spring>`, only applies
pairwise, central body forces. Point particles must have :doc:`bond atom
style <atom_style>` and may be thought of as nodes in a spring
network. An optional multibody term can be used to adjust the network's
Poisson's ratio. Alternatively, the second bond style, :doc:`bond bpm/rotational
Poisson's ratio. The :doc:`bpm/spring/plastic <bond_bpm_spring_plastic>`
bond style is similar except it adds a plastic yield strain.
Alternatively, the third bond style, :doc:`bond bpm/rotational
<bond_bpm_rotational>`, resolves tangential forces and torques arising
with the shearing, bending, and twisting of the bond due to rotation or
displacement of particles. Particles are similar to those used in the

160
doc/src/Howto_bulk2slab.rst Normal file
View File

@ -0,0 +1,160 @@
===========================
Convert bulk system to slab
===========================
A regularly encountered simulation problem is how to convert a bulk
system that has been run for a while to equilibrate into a slab system
with some vacuum space and free surfaces. The challenge here is that
one cannot just change the box dimensions with the :doc:`change_box
command <change_box>` or edit the box boundaries in a data file because
some atoms will have non-zero image flags from diffusing around.
Changing the box dimensions results in an undesired displacement of
those atoms, since the image flags indicate how many times the box
length in x-, y-, or z-direction needs to be added or subtracted to get
the "unwrapped" coordinates. By changing the box dimension this
distance is changed and thus those atoms move unphysically relative to
their neighbors with zero image flags. Setting image flags forcibly to
zero creates problems because that could break apart molecules by having
one atom of a bond on the top of the system and the other at the bottom.
.. _bulk2slab:
.. figure:: JPG/rhodo-both.jpg
:figwidth: 80%
:figclass: align-center
Snapshots of the bulk Rhodopsin in lipid layer and water system (right)
and the generated slab geometry (left)
.. admonition:: Disclaimer
:class: note
The following workflow will work for many bulk systems, but not all.
Some systems cannot be converted (e.g. polymers with bonds to the
same molecule across periodic boundaries, sometimes called "infinite
polymers"). The amount of vacuum that needs to be added depends on
the length of the molecules where the system is split (the example
here splits where there is water with short molecules). In some
cases, the system may need to be re-centered in the box first using
the :doc:`displace_atoms command <displace_atoms>`. Also, the time
spent on strong thermalization and equilibration will depend on the
specific system and its thermodynamic conditions.
Below is a suggested workflow using the :doc:`Rhodopsin benchmark input
<Speed_bench>` for demonstration. The figure shows the state *before*
the procedure on the left (with unwrapped atoms that have diffused out
of the box) and *after* on the right (with the vacuum added above and
below). The procedure is implemented by modifying a copy of the
``in.rhodo`` input file. The first lines up to and including the
:doc:`read_data command <read_data>` remain unchanged. Then we insert
the following lines to add vacuum to the z direction above and below the
system:
.. code-block:: LAMMPS
variable delta index 10.0
reset_atoms image all
write_dump all custom rhodo-unwrap.lammpstrj id xu yu zu
change_box all z final $(zlo-2.0*v_delta) $(zhi+2.0*v_delta) &
boundary p p f
read_dump rhodo-unwrap.lammpstrj 0 x y z box no replace yes
kspace_modify slab 3.0
Specifically, the :doc:`variable delta <variable>` (set to 10.0)
represents a distance that determines the amount of vacuum added: we add
twice its value in each direction to the z-dimension; thus in total
:math:`40 \AA` get added. The :doc:`reset_atoms image all
<reset_atoms>` command shall reset any image flags to become either 0 or
:math:`\pm 1` and thus have the minimum distance from the center of the
simulation box, but the correct relative distance for bonded atoms.
The :doc:`write_dump command <write_dump>` then writes out the resulting
*unwrapped* coordinates of the system. After expanding the box,
coordinates that were outside the box should now be inside and the
unwrapped coordinates will become "wrapped", while atoms outside the
periodic boundaries will be wrapped back into the box and their image
flags in those directions restored.
The :doc:`change_box command <change_box>` adds the desired
distance to the low and high box boundary in z-direction and then changes
the :doc:`boundary to "p p f" <boundary>` which will force the image
flags in z-direction to zero and create an undesired displacement for
the atoms with non-zero image flags.
With the :doc:`read_dump command <read_dump>` we read back and replace
partially incorrect coordinates with the previously saved, unwrapped
coordinates. It is important to ignore the box dimensions stored in the
dump file. We want to preserve the expanded box. Finally, we turn on
the slab correction for the PPPM long-range solver with the
:doc:`kspace_modify command <kspace_modify>` as required when using a
long range Coulomb solver for non-periodic z-dimension.
Next we replace the :doc:`fix npt command <fix_nh>` with:
.. code-block:: LAMMPS
fix 2 nvt temp 300.0 300.0 10.0
We now have an open system and thus the adjustment of the cell in
z-direction is no longer required. Since splitting the bulk water
region where the vacuum is inserted, creates surface atoms with high
potential energy, we reduce the thermostat time constant from 100.0 to
10.0 to remove excess kinetic energy resulting from that change faster.
Also the high potential energy of the surface atoms can cause that some
of them are ejected from the slab. In order to suppress that, we add
soft harmonic walls to push back any atoms that want to leave the slab.
To determine the position of the wall, we first need to to determine the
extent of the atoms in z-direction and then place the harmonic walls
based on that information:
.. code-block:: LAMMPS
compute zmin all reduce min z
compute zmax all reduce max z
thermo_style custom zlo c_zmin zhi c_zmax
run 0 post no
fix 3 all wall/harmonic zhi $(c_zmax+v_delta) 10.0 0.0 ${delta} &
zlo $(c_zmin-v_delta) 10.0 0.0 ${delta}
The two :doc:`compute reduce <compute_reduce>` command determine the
minimum and maximum z-coordinate across all atoms. In order to trigger
the execution of the compute commands we need to "consume" them. This
is done with the :doc:`thermo_style custom <thermo_style>` command
followed by the :doc:`run 0 <run>` command. This avoids and error
accessing the min/max values determined by the compute commands to
compute the location of the wall in lower and upper direction. This
uses the previously defined *delta* variable to determine the distance
of the wall from the extent of the system and the cutoff for the wall
interaction. This way only atoms that move beyond the min/max values in
z-direction will experience a restoring force, nudging them back to the
slab. The force constant of :math:`10.0 \frac{\mathrm{kcal/mol}}{\AA}`
was determined empirically.
Adding these "restoring" soft walls assist in making the free surfaces
above and below the slab flat, instead of having rugged or ondulated
surfaces. The impact of the walls can be changed by adjusting the force
constant, cutoff, and position of the wall.
Finally, we replace the :doc:`run 100 <run>` of the original input with:
.. code-block:: LAMMPS
run 1000 post no
unfix 3
fix 2 all nvt temp 300.0 300.0 100.0
run 1000 post no
write_data data.rhodo-slab
This runs the system converted to a slab first for 1000 MD steps using
the walls and stronger Nose-Hoover thermostat. Then the walls are
removed with :doc:`unfix 3 <unfix>` and the thermostat time constant
reset to 100.0 and the system run for another 1000 steps. Finally the
resulting slab geometry is written to a new data file
``data.rhodo-slab`` with a :doc:`write_data command <write_data>`. The
number of MD steps required to reach a proper equilibrium state is very
likely larger. The number of 1000 steps (corresponding to 2
picoseconds) was chosen for demonstration purposes, so that the
procedure can be easily and quickly tested.

6
doc/src/Howto_github.rst
View File

@ -487,10 +487,10 @@ updates are back-ported from the *develop* branch to the *maintenance*
branch and occasionally merged to *stable* as an update release.
Furthermore, the naming of the release tags now follow the pattern
"patch_<Day><Month><Year>" to simplify comparisons between releases.
For stable releases additional "stable_<Day><Month><Year>" tags are
"patch\_<Day><Month><Year>" to simplify comparisons between releases.
For stable releases additional "stable\_<Day><Month><Year>" tags are
applied and update releases are tagged with
"stable_<Day><Month><Year>_update<Number>", Finally, all releases and
"stable\_<Day><Month><Year>\_update<Number>", Finally, all releases and
submissions are subject to automatic testing and code checks to make
sure they compile with a variety of compilers and popular operating
systems. Some unit and regression testing is applied as well.

7
doc/src/Howto_lammps_gui.rst
View File

@ -64,13 +64,18 @@ simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
since you only need to learn how to use a single program for most tasks
and thus time can be saved and people can focus on learning LAMMPS.
The tutorials at https://lammpstutorials.github.io/ are specifically
updated for use with LAMMPS-GUI.
updated for use with LAMMPS-GUI and can their tutorial materials can
be downloaded and loaded directly from the GUI.
Another design goal is to keep the barrier low when replacing part of
the functionality of LAMMPS-GUI with external tools. That said, LAMMPS-GUI
has some unique functionality that is not found elsewhere:
- auto-adapting to features available in the integrated LAMMPS library
- auto-completion for LAMMPS commands and options
- context-sensitive online help
- start and stop of simulations via mouse or keyboard
- monitoring of simulation progress
- interactive visualization using the :doc:`dump image <dump_image>`
command with the option to copy-paste the resulting settings
- automatic slide show generation from dump image out at runtime

270
doc/src/Howto_moltemplate.rst
View File

@ -2,14 +2,18 @@ Moltemplate Tutorial
====================
In this tutorial, we are going to use the tool :ref:`Moltemplate
<moltemplate>` to set up a classical molecular dynamic simulation using
the :ref:`OPLS-AA force field <OPLSAA96>`. The first
task is to describe an organic compound and create a complete input deck
for LAMMPS. The second task is to map the OPLS-AA force field to a
molecular sample created with an external tool, e.g. PACKMOL, and
exported as a PDB file. The files used in this tutorial can be found
in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS
source code distribution.
<Moltemplate1>` from https://moltemplate.org/ to set up a classical
molecular dynamic simulation using the :ref:`OPLS-AA force field
<oplsaa2024>`. The first task is to describe an organic compound and
create a complete input deck for LAMMPS. The second task is to use
moltemplate to build a polymer. The third task is to map the OPLS-AA
force field to a molecular sample created with an external tool,
e.g. PACKMOL, and exported as a PDB file. The files used in this
tutorial can be found in the ``tools/moltemplate/tutorial-files`` folder
of the LAMMPS source code distribution.
Many more examples can be found here: https://moltemplate.org/examples.html
Simulating an organic solvent
"""""""""""""""""""""""""""""
@ -17,14 +21,13 @@ Simulating an organic solvent
This example aims to create a cubic box of the organic solvent
formamide.
The first step is to create a molecular topology in the
LAMMPS-template (LT) file format representing a single molecule, which
will be stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
The first step is to create a molecular topology in the LAMMPS-template
(LT) file format representing a single molecule, which will be
stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
This command states that the object ``_FAM`` is based on an existing
object called ``OPLSAA``, which contains OPLS-AA parameters, atom type
definitions, partial charges, masses and bond-angle rules for many organic
and biological compounds.
The atomic structure is the starting point to populate the command
``write('Data Atoms') {}``, which will write the ``Atoms`` section in the
LAMMPS data file. The OPLS-AA force field uses the ``atom_style full``,
@ -36,21 +39,23 @@ to the ``molID``, except that the same variable is used for the whole
molecule. The atom types are assigned using ``@``-type variables. The
assignment of atom types (e.g. ``@atom:177``, ``@atom:178``) is done using
the OPLS-AA atom types defined in the "In Charges" section of the file
``oplsaa.lt``, looking for a reasonable match with the description of the atom.
``oplsaa2024.lt``, looking for a reasonable match with the description of the atom.
The resulting file (``formamide.lt``) follows:
.. code-block:: bash
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt # defines OPLSAA
_FAM inherits OPLSAA {
# atomID molID atomType charge coordX coordY coordZ
write('Data Atoms') {
$atom:C00 $mol @atom:177 0.00 0.100 0.490 0.0
$atom:O01 $mol @atom:178 0.00 1.091 -0.250 0.0
$atom:N02 $mol @atom:179 0.00 -1.121 -0.181 0.0
$atom:H03 $mol @atom:182 0.00 -2.013 0.272 0.0
$atom:H04 $mol @atom:182 0.00 -1.056 -1.190 0.0
$atom:H05 $mol @atom:221 0.00 0.144 1.570 0.0
$atom:C00 $mol @atom:235 0.00 0.100 0.490 0.0
$atom:O01 $mol @atom:236 0.00 1.091 -0.250 0.0
$atom:N02 $mol @atom:237 0.00 -1.121 -0.181 0.0
$atom:H03 $mol @atom:240 0.00 -2.013 0.272 0.0
$atom:H04 $mol @atom:240 0.00 -1.056 -1.190 0.0
$atom:H05 $mol @atom:279 0.00 0.144 1.570 0.0
}
# A list of the bonds in the molecule:
@ -64,16 +69,17 @@ The resulting file (``formamide.lt``) follows:
}
}
You don't have to specify the charge in this example because they will
be assigned according to the atom type. Analogously, only a
"Data Bond List" section is needed as the atom type will determine the
bond type. The other bonded interactions (e.g. angles,
dihedrals, and impropers) will be automatically generated by
You don't have to specify the charge in this example because the OPLSAA
force-field assigns charge according to the atom type. (This is not true
when using other force fields.) A "Data Bond List" section is needed as
the atom type will determine the bond type. The other bonded interactions
(e.g. angles, dihedrals, and impropers) will be automatically generated by
Moltemplate.
If the simulation is non-neutral, or Moltemplate complains that you have
missing bond, angle, or dihedral types, this means at least one of your
atom types is incorrect.
If the simulation is not charge-neutral, or Moltemplate complains that
you have missing bond, angle, or dihedral types, this probably means that
at least one of your atom types is incorrect (or that perhaps there is no
suitable atom type currently defined in the ``oplsaa2024.lt`` file).
The second step is to create a master file with instructions to build a
starting structure and the LAMMPS commands to run an NPT simulation. The
@ -81,11 +87,9 @@ master file (``solv_01.lt``) follows:
.. code-block:: bash
# Import the force field.
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
import formamide.lt # after oplsaa.lt, as it depends on it.
import formamide.lt # Defines "_FAM" and OPLSAA
# Create the input sample.
# Distribute the molecules on a 5x5x5 cubic grid with spacing 4.6
solv = new _FAM [5].move( 4.6, 0, 0)
[5].move( 0, 4.6, 0)
[5].move( 0, 0, 4.6)
@ -98,8 +102,11 @@ master file (``solv_01.lt``) follows:
-11.5 11.5 zlo zhi
}
# Note: The lines below in the "In Run" section are often omitted.
write_once("In Run"){
# Create an input deck for LAMMPS.
write_once("In Init"){
# Run an NPT simulation.
# Input variables.
variable run string solv_01 # output name
variable ts equal 1 # timestep
@ -109,12 +116,6 @@ master file (``solv_01.lt``) follows:
variable equi equal 5000 # Equilibration steps
variable prod equal 30000 # Production steps
# PBC (set them before the creation of the box).
boundary p p p
}
# Run an NPT simulation.
write_once("In Run"){
# Derived variables.
variable tcouple equal \$\{ts\}*100
variable pcouple equal \$\{ts\}*1000
@ -143,7 +144,7 @@ master file (``solv_01.lt``) follows:
unfix NPT
}
The first two commands insert the content of files ``oplsaa.lt`` and
The first two commands insert the content of files ``oplsaa2024.lt`` and
``formamide.lt`` into the master file. At this point, we can use the
command ``solv = new _FAM [N]`` to create N copies of a molecule of type
``_FAM``. In this case, we create an array of 5*5*5 molecules on a cubic
@ -153,21 +154,37 @@ the sample was created from scratch, we also specify the simulation box
size in the "Data Boundary" section.
The LAMMPS setting for the force field are specified in the file
``oplsaa.lt`` and are written automatically in the input deck. We also
``oplsaa2024.lt`` and are written automatically in the input deck. We also
specify the boundary conditions and a set of variables in
the "In Init" section. The remaining commands to run an NPT simulation
the "In Init" section.
The remaining commands to run an NPT simulation
are written in the "In Run" section. Note that in this script, LAMMPS
variables are protected with the escape character ``\`` to distinguish
them from Moltemplate variables, e.g. ``\$\{run\}`` is a LAMMPS
variable that is written in the input deck as ``${run}``.
(Note: Moltemplate can be slow to run, so you need to change you run
settings frequently, I recommended moving those commands (from "In Run")
out of your .lt files and into a separate file. Moltemplate creates a
file named ``run.in.EXAMPLE`` for this purpose. You can put your run
settings and fixes that file and then invoke LAMMPS using
``mpirun -np 4 lmp -in run.in.EXAMPLE`` instead.)
Compile the master file with:
.. code-block:: bash
moltemplate.sh -overlay-all solv_01.lt
moltemplate.sh solv_01.lt
cleanup_moltemplate.sh # <-- optional: see below
And execute the simulation with the following:
(Note: The optional "cleanup_moltemplate.sh" command deletes
unused atom types, which sometimes makes LAMMPS run faster.
But it does not work with many-body pair styles or dreiding-style h-bonds.
Fortunately most force fields, including OPLSAA, don't use those features.)
Then execute the simulation with the following:
.. code-block:: bash
@ -180,15 +197,116 @@ And execute the simulation with the following:
Snapshot of the sample at the beginning and end of the simulation.
Rendered with Ovito.
Building a simple polymer
"""""""""""""""""""""""""
Moltemplate is particularly useful for building polymers (and other molecules
with sub-units). As an simple example, consider butane:
.. figure:: JPG/butane.jpg
The ``butane.lt`` file below defines Butane as a polymer containing
4 monomers (of type ``CH3``, ``CH2``, ``CH2``, ``CH3``).
.. code-block:: bash
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt # defines OPLSAA
CH3 inherits OPLSAA {
# atomID molID atomType charge coordX coordY coordZ
write("Data Atoms") {
$atom:c $mol:... @atom:54 0.0 0.000000 0.4431163 0.000000
$atom:h1 $mol:... @atom:60 0.0 0.000000 1.0741603 0.892431
$atom:h2 $mol:... @atom:60 0.0 0.000000 1.0741603 -0.892431
$atom:h3 $mol:... @atom:60 0.0 -0.892431 -0.1879277 0.000000
}
# (Using "$mol:..." indicates this object ("CH3") is part of a larger
# molecule. Moltemplate will share the molecule-ID with that molecule.)
# A list of the bonds within the "CH3" molecular sub-unit:
# BondID AtomID1 AtomID2
write('Data Bond List') {
$bond:ch1 $atom:c $atom:h1
$bond:ch2 $atom:c $atom:h2
$bond:ch3 $atom:c $atom:h3
}
}
CH2 inherits OPLSAA {
# atomID molID atomType charge coordX coordY coordZ
write("Data Atoms") {
$atom:c $mol:... @atom:57 0.0 0.000000 0.4431163 0.000000
$atom:h1 $mol:... @atom:60 0.0 0.000000 1.0741603 0.892431
$atom:h2 $mol:... @atom:60 0.0 0.000000 1.0741603 -0.892431
}
# A list of the bonds within the "CH2" molecular sub-unit:
# BondID AtomID1 AtomID2
write('Data Bond List') {
$bond:ch1 $atom:c $atom:h1
$bond:ch2 $atom:c $atom:h2
}
}
Butane inherits OPLSAA {
create_var {$mol} # optional:force all monomers to share the same molecule-ID
# - Create 4 monomers
# - Move them along the X axis using ".move()",
# - Rotate them 180 degrees with respect to the previous monomer
monomer1 = new CH3
monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0)
monomer3 = new CH2.move(2.5066446,0,0)
monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0)
# A list of the bonds connecting different monomers together:
write('Data Bond List') {
$bond:b1 $atom:monomer1/c $atom:monomer2/c
$bond:b2 $atom:monomer2/c $atom:monomer3/c
$bond:b3 $atom:monomer3/c $atom:monomer4/c
}
}
Again, you don't have to specify the charge in this example because OPLSAA
assigns charges according to the atom type.
This ``Butane`` object is a molecule which can be used anywhere other molecules
can be used. (You can arrange ``Butane`` molecules on a lattice, as we did previously.
You can also modify individual butane molecules by adding or deleting atoms or bonds.
You can add bonds between specific butane molecules or use ``Butane`` as a
subunit to define even larger molecules. See the moltemplate manual for details.)
How to build a complex polymer
""""""""""""""""""""""""""""""""""""""""""
A similar procedure can be used to create more complicated polymers,
such as the NIPAM polymer example shown below. For details, see:
https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/NIPAM_polymer+water+ions
Mapping an existing structure
"""""""""""""""""""""""""""""
Another helpful way to use Moltemplate is mapping an existing molecular
sample to a force field. This is useful when a complex sample is
assembled from different simulations or created with specialized
software (e.g. PACKMOL). As in the previous example, all molecular
species in the sample must be defined using single-molecule Moltemplate
objects. For this example, we use a short polymer in a box containing
sample to a force field. This is useful when a complex sample is assembled
from different simulations or created with specialized software (e.g. PACKMOL).
(Note: The previous link shows how to build this entire system from scratch
using only moltemplate. However here we will assume instead that we obtained
a PDB file for this system using PACKMOL.)
As in the previous examples, all molecular species in the sample
are defined using single-molecule Moltemplate objects.
For this example, we use a short polymer in a box containing
water molecules and ions in the PDB file ``model.pdb``.
It is essential to understand that the order of atoms in the PDB file
@ -246,25 +364,25 @@ The resulting master LT file defining short annealing at a fixed volume
.. code-block:: bash
# Use the OPLS-AA force field for all species.
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
import PolyNIPAM.lt
# Define the SPC water and ions as in the OPLS-AA
Ca inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:354 0.0 0.00000 0.00000 0.000000
$atom:a1 $mol:. @atom:412 0.0 0.00000 0.00000 0.000000
}
}
Cl inherits OPLSAA {
write("Data Atoms"){
$atom:a1 $mol:. @atom:344 0.0 0.00000 0.00000 0.000000
$atom:a1 $mol:. @atom:401 0.0 0.00000 0.00000 0.000000
}
}
SPC inherits OPLSAA {
write("Data Atoms"){
$atom:O $mol:. @atom:76 0. 0.0000000 0.00000 0.000000
$atom:H1 $mol:. @atom:77 0. 0.8164904 0.00000 0.5773590
$atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
$atom:O $mol:. @atom:9991 0. 0.0000000 0.00000 0.0000000
$atom:H1 $mol:. @atom:9990 0. 0.8164904 0.00000 0.5773590
$atom:H2 $mol:. @atom:9990 0. -0.8164904 0.00000 0.5773590
}
write("Data Bond List") {
$bond:OH1 $atom:O $atom:H1
@ -285,8 +403,15 @@ The resulting master LT file defining short annealing at a fixed volume
0 26 zlo zhi
}
# Define the input variables.
write_once("In Init"){
boundary p p p # "p p p" is the default. This line is optional.
neighbor 3 bin # (This line is also optional in this example.)
}
# Note: The lines below in the "In Run" section are often omitted.
# Run an NVT simulation.
write_once("In Run"){
# Input variables.
variable run string sample01 # output name
variable ts equal 2 # timestep
@ -294,13 +419,6 @@ The resulting master LT file defining short annealing at a fixed volume
variable p equal 1. # equilibrium pressure
variable equi equal 30000 # equilibration steps
# PBC (set them before the creation of the box).
boundary p p p
neighbor 3 bin
}
# Run an NVT simulation.
write_once("In Run"){
# Set the output.
thermo 1000
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
@ -314,8 +432,8 @@ The resulting master LT file defining short annealing at a fixed volume
write_data \$\{run\}.min
# Set the constrains.
group watergroup type @atom:76 @atom:77
fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043
group watergroup type @atom:9991 @atom:9990
fix 0 watergroup shake 0.0001 10 0 b @bond:spcO_spcH a @angle:spcH_spcO_spcH
# Short annealing.
timestep \$\{ts\}
@ -327,7 +445,7 @@ The resulting master LT file defining short annealing at a fixed volume
In this example, the water model is SPC and it is defined in the
``oplsaa.lt`` file with atom types ``@atom:76`` and ``@atom:77``. For
``oplsaa2024.lt`` file with atom types ``@atom:9991`` and ``@atom:9990``. For
water we also use the ``group`` and ``fix shake`` commands with
Moltemplate ``@``-type variables, to ensure consistency with the
numerical values assigned during compilation. To identify the bond and
@ -336,19 +454,20 @@ are:
.. code-block:: bash
replace{ @atom:76 @atom:76_b042_a042_d042_i042 }
replace{ @atom:77 @atom:77_b043_a043_d043_i043 }
replace{ @atom:9991 @atom:9991_bspcO_aspcO_dspcO_ispcO }
replace{ @atom:9990 @atom:9990_bspcH_aspcH_dspcH_ispcH }
From which we can identify the following "Data Bonds By Type":
``@bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i*`` and
"Data Angles By Type": ``@angle:043_042_043 @atom:*_b*_a043*_d*_i*
@atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i*``
``@bond:spcO_spcH @atom:*_bspcO*_a*_d*_i* @atom:*_bspcH*_a*_d*_i*``
and "Data Angles By Type":
``@angle:spcH_spcO_spcH @atom:*_b*_aspcH*_d*_i* @atom:*_b*_aspcO*_d*_i* @atom:*_b*_aspcH*_d*_i*``
Compile the master file with:
.. code-block:: bash
moltemplate.sh -overlay-all -pdb model.pdb sample01.lt
moltemplate.sh -pdb model.pdb sample01.lt
cleanup_moltemplate.sh
And execute the simulation with the following:
@ -363,8 +482,13 @@ And execute the simulation with the following:
Sample visualized with Ovito loading the trajectory into the DATA
file written after minimization.
------------
.. _OPLSAA96:
.. _oplsaa2024:
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
**(OPLS-AA)** Jorgensen, W.L., Ghahremanpour, M.M., Saar, A., Tirado-Rives, J., J. Phys. Chem. B, 128(1), 250-262 (2024).
.. _Moltemplate1:
**(Moltemplate)** Jewett et al., J. Mol. Biol., 433(11), 166841 (2021)

8
doc/src/Howto_peri.rst
View File

@ -197,7 +197,7 @@ The LPS model has a force scalar state
.. math::
\underline{t} = \frac{3K\theta}{m}\underline{\omega}\,\underline{x} +
\alpha \underline{\omega}\,\underline{e}^{\rm d}, \qquad\qquad\textrm{(3)}
\alpha \underline{\omega}\,\underline{e}^\mathrm{d}, \qquad\qquad\textrm{(3)}
with :math:`K` the bulk modulus and :math:`\alpha` related to the shear
modulus :math:`G` as
@ -242,14 +242,14 @@ scalar state are defined, respectively, as
.. math::
\underline{e}^{\rm i}=\frac{\theta \underline{x}}{3}, \qquad
\underline{e}^{\rm d} = \underline{e}- \underline{e}^{\rm i},
\underline{e}^\mathrm{i}=\frac{\theta \underline{x}}{3}, \qquad
\underline{e}^\mathrm{d} = \underline{e}- \underline{e}^\mathrm{i},
where the arguments of the state functions and the vectors on which they
operate are omitted for simplicity. We note that the LPS model is linear
in the dilatation :math:`\theta`, and in the deviatoric part of the
extension :math:`\underline{e}^{\rm d}`.
extension :math:`\underline{e}^\mathrm{d}`.
.. note::

564
doc/src/Howto_pylammps.rst
View File

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

464
doc/src/Howto_python.rst Normal file
View File

@ -0,0 +1,464 @@
LAMMPS Python Tutorial
======================
.. contents::
-----
Overview
--------
The :py:class:`lammps <lammps.lammps>` Python module is a wrapper class for the
LAMMPS :ref:`C language library interface API <lammps_c_api>` which is written using
`Python ctypes <ctypes_>`_. The design choice of this wrapper class is to
follow the C language API closely with only small changes related to Python
specific requirements and to better accommodate object oriented programming.
In addition to this flat `ctypes <ctypes_>`_ interface, the
:py:class:`lammps <lammps.lammps>` wrapper class exposes a discoverable
API that doesn't require as much knowledge of the underlying C language
library interface or LAMMPS C++ code implementation.
Finally, the API exposes some additional features for `IPython integration
<ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for embedded
visualization output from :doc:`dump style image <dump_image>`.
.. _ctypes: https://docs.python.org/3/library/ctypes.html
.. _ipython: https://ipython.org/
.. _jupyter: https://jupyter.org/
-----
Quick Start
-----------
System-wide or User Installation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step 1: Building LAMMPS as a shared library
"""""""""""""""""""""""""""""""""""""""""""
To use LAMMPS inside of Python it has to be compiled as shared library.
This library is then loaded by the Python interface. In this example we
enable the :ref:`MOLECULE package <PKG-MOLECULE>` and compile LAMMPS
with :ref:`PNG, JPEG and FFMPEG output support <graphics>` enabled.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
mkdir $LAMMPS_DIR/build-shared
cd $LAMMPS_DIR/build-shared
# MPI, PNG, Jpeg, FFMPEG are auto-detected
cmake ../cmake -DPKG_MOLECULE=yes -DPKG_PYTHON=on -DBUILD_SHARED_LIBS=yes
make
.. tab:: Traditional make
.. code-block:: bash
cd $LAMMPS_DIR/src
# add LAMMPS packages if necessary
make yes-MOLECULE
make yes-PYTHON
# compile shared library using Makefile
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
Step 2: Installing the LAMMPS Python module
"""""""""""""""""""""""""""""""""""""""""""
Next install the LAMMPS Python module into your current Python installation with:
.. code-block:: bash
make install-python
This will create a so-called `"wheel"
<https://packaging.python.org/en/latest/discussions/package-formats/#what-is-a-wheel>`_
and then install the LAMMPS Python module from that "wheel" into either
into a system folder (provided the command is executed with root
privileges) or into your personal Python module folder.
.. note::
Recompiling the shared library requires re-installing the Python
package.
.. _externally_managed:
.. admonition:: Handling an "externally-managed-environment" Error
:class: Hint
Some Python installations made through Linux distributions
(e.g. Ubuntu 24.04LTS or later) will prevent installing the LAMMPS
Python module into a system folder or a corresponding folder of the
individual user as attempted by ``make install-python`` with an error
stating that an *externally managed* python installation must be only
managed by the same package package management tool. This is an
optional setting, so not all Linux distributions follow it currently
(Spring 2025). The reasoning and explanations for this error can be
found in the `Python Packaging User Guide
<https://packaging.python.org/en/latest/specifications/externally-managed-environments/>`_
These guidelines suggest to create a virtual environment and install
the LAMMPS Python module there (see below). This is generally a good
idea and the LAMMPS developers recommend this, too. If, however, you
want to proceed and install the LAMMPS Python module regardless, you
can install the "wheel" file (see above) manually with the ``pip``
command by adding the ``--break-system-packages`` flag.
Installation inside of a virtual environment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can use virtual environments to create a custom Python environment
specifically tuned for your workflow.
Benefits of using a virtualenv
""""""""""""""""""""""""""""""
* isolation of your system Python installation from your development installation
* installation can happen in your user directory without root access (useful for HPC clusters)
* installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
* you can even install specific old versions of a package if necessary
**Prerequisite (e.g. on Ubuntu)**
.. code-block:: bash
apt-get install python-venv
Creating a virtualenv with lammps installed
"""""""""""""""""""""""""""""""""""""""""""
.. code-block:: bash
# create virtual envrionment named 'testing'
python3 -m venv $HOME/python/testing
# activate 'testing' environment
source $HOME/python/testing/bin/activate
Now configure and compile the LAMMPS shared library as outlined above.
When using CMake and the shared library has already been build, you
need to re-run CMake to update the location of the python executable
to the location in the virtual environment with:
.. code-block:: bash
cmake . -DPython_EXECUTABLE=$(which python)
# install LAMMPS package in virtualenv
(testing) make install-python
# install other useful packages
(testing) pip install matplotlib jupyter mpi4py pandas
...
# return to original shell
(testing) deactivate
-------
Creating a new lammps instance
------------------------------
To create a lammps object you need to first import the class from the lammps
module. By using the default constructor, a new :py:class:`lammps
<lammps.lammps>` instance is created.
.. code-block:: python
from lammps import lammps
L = lammps()
See the :doc:`LAMMPS Python documentation <Python_create>` for how to customize
the instance creation with optional arguments.
-----
Commands
--------
Sending a LAMMPS command with the library interface is done using
the ``command`` method of the lammps object.
For instance, let's take the following LAMMPS command:
.. code-block:: LAMMPS
region box block 0 10 0 5 -0.5 0.5
This command can be executed with the following Python code if ``L`` is a ``lammps``
instance:
.. code-block:: python
L.command("region box block 0 10 0 5 -0.5 0.5")
For convenience, the ``lammps`` class also provides a command wrapper ``cmd``
that turns any LAMMPS command into a regular function call:
.. code-block:: python
L.cmd.region("box block", 0, 10, 0, 5, -0.5, 0.5)
Note that each parameter is set as Python number literal. With
the wrapper each command takes an arbitrary parameter list and transparently
merges it to a single command string, separating individual parameters by
white-space.
The benefit of this approach is avoiding redundant command calls and easier
parameterization. With the ``command`` function each call needs to be assembled
manually using formatted strings.
.. code-block:: python
L.command(f"region box block {xlo} {xhi} {ylo} {yhi} {zlo} {zhi}")
The wrapper accepts parameters directly and will convert
them automatically to a final command string.
.. code-block:: python
L.cmd.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
.. note::
When running in IPython you can use Tab-completion after ``L.cmd.`` to see
all available LAMMPS commands.
-----
Accessing atom data
-------------------
All per-atom properties that are part of the :doc:`atom style
<atom_style>` in the current simulation can be accessed using the
:py:meth:`extract_atoms() <lammps.lammps.extract_atoms()>` method. This
can be retrieved as ctypes objects or as NumPy arrays through the
lammps.numpy module. Those represent the *local* atoms of the
individual sub-domain for the current MPI process and may contain
information for the local ghost atoms or not depending on the property.
Both can be accessed as lists, but for the ctypes list object the size
is not known and hast to be retrieved first to avoid out-of-bounds
accesses.
.. code-block:: python
nlocal = L.extract_setting("nlocal")
nall = L.extract_setting("nall")
print("Number of local atoms ", nlocal, " Number of local and ghost atoms ", nall);
# access via ctypes directly
atom_id = L.extract_atom("id")
print("Atom IDs", atom_id[0:nlocal])
# access through numpy wrapper
atom_type = L.numpy.extract_atom("type")
print("Atom types", atom_type)
x = L.numpy.extract_atom("x")
v = L.numpy.extract_atom("v")
print("positions array shape", x.shape)
print("velocity array shape", v.shape)
# turn on communicating velocities to ghost atoms
L.cmd.comm_modify("vel", "yes")
v = L.numpy.extract_atom('v')
print("velocity array shape", v.shape)
Some properties can also be set from Python since internally the
data of the C++ code is accessed directly:
.. code-block:: python
# set position in 2D simulation
x[0] = (1.0, 0.0)
# set position in 3D simulation
x[0] = (1.0, 0.0, 1.)
------
Retrieving the values of thermodynamic data and variables
---------------------------------------------------------
To access thermodynamic data from the last completed timestep,
you can use the :py:meth:`get_thermo() <lammps.lammps.get_thermo>`
method, and to extract the value of (compatible) variables, you
can use the :py:meth:`extract_variable() <lammps.lammps.extract_variable>`
method.
.. code-block:: python
result = L.get_thermo("ke") # kinetic energy
result = L.get_thermo("pe") # potential energy
result = L.extract_variable("t") / 2.0
Error handling
--------------
We are using C++ exceptions in LAMMPS for errors and the C language
library interface captures and records them. This allows checking
whether errors have happened in Python during a call into LAMMPS and
then re-throw the error as a Python exception. This way you can handle
LAMMPS errors in the conventional way through the Python exception
handling mechanism.
.. warning::
Capturing a LAMMPS exception in Python can still mean that the
current LAMMPS process is in an illegal state and must be
terminated. It is advised to save your data and terminate the Python
instance as quickly as possible.
Using LAMMPS in IPython notebooks and Jupyter
---------------------------------------------
If the LAMMPS Python package is installed for the same Python
interpreter as IPython, you can use LAMMPS directly inside of an IPython
notebook inside of Jupyter. Jupyter is a powerful integrated development
environment (IDE) for many dynamic languages like Python, Julia and
others, which operates inside of any web browser. Besides
auto-completion and syntax highlighting it allows you to create
formatted documents using Markup, mathematical formulas, graphics and
animations intermixed with executable Python code. It is a great format
for tutorials and showcasing your latest research.
To launch an instance of Jupyter simply run the following command inside your
Python environment (this assumes you followed the Quick Start instructions):
.. code-block:: bash
jupyter notebook
Interactive Python Examples
---------------------------
Examples of IPython notebooks can be found in the ``python/examples/ipython``
subdirectory. To open these notebooks launch ``jupyter notebook`` inside this
directory and navigate to one of them. If you compiled and installed
a LAMMPS shared library with PNG, JPEG and FFMPEG support
you should be able to rerun all of these notebooks.
Validating a dihedral potential
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
This example showcases how an IPython Notebook can be used to compare a simple
LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
Four atoms are placed in the simulation and the dihedral potential is applied on
them using a datafile. Then one of the atoms is rotated along the central axis by
setting its position from Python, which changes the dihedral angle.
.. code-block:: python
phi = [d \* math.pi / 180 for d in range(360)]
pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]
x = L.numpy.extract_atom("x")
pe = []
for p in pos:
x[3] = p
L.cmd.run(0, "post", "no")
pe.append(L.get_thermo("pe"))
By evaluating the potential energy for each position we can verify that
trajectory with the analytical formula. To compare both solutions, we plot
both trajectories over each other using matplotlib, which embeds the generated
plot inside the IPython notebook.
.. image:: JPG/pylammps_dihedral.jpg
:align: center
Running a Monte Carlo relaxation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
This second example shows how to use the `lammps` Python interface to create a
2D Monte Carlo Relaxation simulation, computing and plotting energy terms and
even embedding video output.
Initially, a 2D system is created in a state with minimal energy.
.. image:: JPG/pylammps_mc_minimum.jpg
:align: center
It is then disordered by moving each atom by a random delta.
.. code-block:: python
random.seed(27848)
deltaperturb = 0.2
x = L.numpy.extract_atom("x")
natoms = x.shape[0]
for i in range(natoms):
dx = deltaperturb \* random.uniform(-1, 1)
dy = deltaperturb \* random.uniform(-1, 1)
x[i][0] += dx
x[i][1] += dy
L.cmd.run(0, "post", "no")
.. image:: JPG/pylammps_mc_disordered.jpg
:align: center
Finally, the Monte Carlo algorithm is implemented in Python. It continuously
moves random atoms by a random delta and only accepts certain moves.
.. code-block:: python
estart = L.get_thermo("pe")
elast = estart
naccept = 0
energies = [estart]
niterations = 3000
deltamove = 0.1
kT = 0.05
for i in range(niterations):
x = L.numpy.extract_atom("x")
natoms = x.shape[0]
iatom = random.randrange(0, natoms)
current_atom = x[iatom]
x0 = current_atom[0]
y0 = current_atom[1]
dx = deltamove \* random.uniform(-1, 1)
dy = deltamove \* random.uniform(-1, 1)
current_atom[0] = x0 + dx
current_atom[1] = y0 + dy
L.cmd.run(1, "pre no post no")
e = L.get_thermo("pe")
energies.append(e)
if e <= elast:
naccept += 1
elast = e
elif random.random() <= math.exp(natoms\*(elast-e)/kT):
naccept += 1
elast = e
else:
current_atom[0] = x0
current_atom[1] = y0
The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
.. image:: JPG/pylammps_mc_energies_plot.jpg
:align: center
The IPython notebook also shows how to use dump commands and embed video files
inside of the IPython notebook.

24
doc/src/Howto_triclinic.rst
View File

@ -249,23 +249,23 @@ as follows:
.. math::
a = & {\rm lx} \\
b^2 = & {\rm ly}^2 + {\rm xy}^2 \\
c^2 = & {\rm lz}^2 + {\rm xz}^2 + {\rm yz}^2 \\
\cos{\alpha} = & \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
\cos{\beta} = & \frac{\rm xz}{c} \\
\cos{\gamma} = & \frac{\rm xy}{b} \\
a = & \mathrm{lx} \\
b^2 = & \mathrm{ly}^2 + \mathrm{xy}^2 \\
c^2 = & \mathrm{lz}^2 + \mathrm{xz}^2 + \mathrm{yz}^2 \\
\cos{\alpha} = & \frac{\mathrm{xy}*\mathrm{xz} + \mathrm{ly}*\mathrm{yz}}{b*c} \\
\cos{\beta} = & \frac{\mathrm{xz}}{c} \\
\cos{\gamma} = & \frac{\mathrm{xy}}{b} \\
The inverse relationship can be written as follows:
.. math::
{\rm lx} = & a \\
{\rm xy} = & b \cos{\gamma} \\
{\rm xz} = & c \cos{\beta}\\
{\rm ly}^2 = & b^2 - {\rm xy}^2 \\
{\rm yz} = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
{\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\
\mathrm{lx} = & a \\
\mathrm{xy} = & b \cos{\gamma} \\
\mathrm{xz} = & c \cos{\beta}\\
\mathrm{ly}^2 = & b^2 - \mathrm{xy}^2 \\
\mathrm{yz} = & \frac{b*c \cos{\alpha} - \mathrm{xy}*\mathrm{xz}}{\mathrm{ly}} \\
\mathrm{lz}^2 = & c^2 - \mathrm{xz}^2 - \mathrm{yz}^2 \\
The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
:math:`\gamma` can be printed out or accessed by computes using the

1
doc/src/Install_git.rst
View File

@ -52,6 +52,7 @@ your machine and "release" is one of the 3 branches listed above.
between them at any time using "git checkout <branch name>".)
.. admonition:: Saving time and disk space when using ``git clone``
:class: note
The complete git history of the LAMMPS project is quite large because
it contains the entire commit history of the project since fall 2006,

3
doc/src/Install_mac.rst
View File

@ -5,8 +5,7 @@ LAMMPS can be downloaded, built, and configured for macOS with `Homebrew
<homebrew_>`_. (Alternatively, see the installation instructions for
:doc:`downloading an executable via Conda <Install_conda>`.) The
following LAMMPS packages are unavailable at this time because of
additional requirements not yet met: GPU, KOKKOS, MSCG, POEMS,
VORONOI.
additional requirements not yet met: GPU, KOKKOS.
After installing Homebrew, you can install LAMMPS on your system with
the following commands:

14
doc/src/Intro_portability.rst
View File

@ -13,10 +13,14 @@ Programming language standards
Most of the C++ code currently requires a compiler compatible with the
C++11 standard, the KOKKOS package currently requires C++17. Most of
the Python code is written to be compatible with Python 3.5 or later or
Python 2.7. Some Python scripts *require* Python 3 and a few others
still need to be ported from Python 2 to Python 3.
the Python code is written to be compatible with Python 3.6 or later.
.. deprecated:: TBD
Python 2.x is no longer supported and trying to use it, e.g. for the
LAMMPS Python module should result in an error. If you come across
some part of the LAMMPS distribution that is not (yet) compatible with
Python 3, please notify the LAMMPS developers.
Build systems
^^^^^^^^^^^^^
@ -24,8 +28,8 @@ Build systems
LAMMPS can be compiled from source code using a (traditional) build
system based on shell scripts, a few shell utilities (grep, sed, cat,
tr) and the GNU make program. This requires running within a Bourne
shell (``/bin/sh``). Alternatively, a build system with different back ends
can be created using CMake. CMake must be at least version 3.16.
shell (``/bin/sh``). Alternatively, a build system with different back
ends can be created using CMake. CMake must be at least version 3.16.
Operating systems
^^^^^^^^^^^^^^^^^

BIN
doc/src/JPG/PolyNIPAM.jpg
View File

Binary file not shown.
Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 40 KiB

After

Width:  |  Height:  |  Size: 94 KiB

BIN
doc/src/JPG/butane.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 22 KiB

BIN
doc/src/JPG/rhodo-both.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 568 KiB

7
doc/src/Library.rst
View File

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

6
doc/src/Library_add.rst
View File

@ -19,9 +19,9 @@ there are now a few requirements for including new changes or extensions.
be added.
- New features should also be implemented and documented not just
for the C interface, but also the Python and Fortran interfaces.
- All additions should work and be compatible with ``-DLAMMPS_BIGBIG``,
``-DLAMMPS_SMALLBIG``, ``-DLAMMPS_SMALLSMALL`` as well as when
compiling with and without MPI support.
- All additions should work and be compatible with
``-DLAMMPS_BIGBIG``, ``-DLAMMPS_SMALLBIG`` as well as when compiling
with and without MPI support.
- The ``library.h`` file should be kept compatible to C code at
a level similar to C89. Its interfaces may not reference any
custom data types (e.g. ``bigint``, ``tagint``, and so on) that

6
doc/src/Library_execute.rst
View File

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

28
doc/src/Library_objects.rst
View File

@ -1,5 +1,5 @@
Compute, fixes, variables
=========================
Computes, fixes, variables
==========================
This section documents accessing or modifying data stored by computes,
fixes, or variables in LAMMPS using the following functions:
@ -12,6 +12,10 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_set_string_variable`
- :cpp:func:`lammps_set_internal_variable`
- :cpp:func:`lammps_variable_info`
- :cpp:func:`lammps_eval`
- :cpp:func:`lammps_clearstep_compute`
- :cpp:func:`lammps_addstep_compute_all`
- :cpp:func:`lammps_addstep_compute`
-----------------------
@ -55,6 +59,26 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_eval
:project: progguide
-----------------------
.. doxygenfunction:: lammps_clearstep_compute
:project: progguide
-----------------------
.. doxygenfunction:: lammps_addstep_compute_all
:project: progguide
-----------------------
.. doxygenfunction:: lammps_addstep_compute
:project: progguide
-----------------------
.. doxygenenum:: _LMP_DATATYPE_CONST
.. doxygenenum:: _LMP_STYLE_CONST

6
doc/src/Library_utility.rst
View File

@ -20,6 +20,7 @@ functions. They do not directly call the LAMMPS library.
- :cpp:func:`lammps_force_timeout`
- :cpp:func:`lammps_has_error`
- :cpp:func:`lammps_get_last_error_message`
- :cpp:func:`lammps_set_show_error`
- :cpp:func:`lammps_python_api_version`
The :cpp:func:`lammps_free` function is a clean-up function to free
@ -110,6 +111,11 @@ where such memory buffers were allocated that require the use of
-----------------------
.. doxygenfunction:: lammps_set_show_error
:project: progguide
-----------------------
.. doxygenfunction:: lammps_python_api_version
:project: progguide

2
doc/src/Modify_compute.rst
View File

@ -45,6 +45,8 @@ class. See compute.h for details.
+-----------------------+------------------------------------------------------------------+
| pair_tally_callback | callback function for *tally*\ -style computes (optional). |
+-----------------------+------------------------------------------------------------------+
| modify_param | called when a compute_modify request is executed (optional) |
+-----------------------+------------------------------------------------------------------+
| memory_usage | tally memory usage (optional) |
+-----------------------+------------------------------------------------------------------+

23
doc/src/Modify_requirements.rst
View File

@ -189,10 +189,8 @@ of the contribution. As of January 2023, all previously included
Fortran code for the LAMMPS executable has been replaced by equivalent
C++ code.
Python code must be compatible with Python 3.5 and later. Large parts
of LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
compatible with Python 2.7. Compatibility with Python 2.7 is desirable,
but compatibility with Python 3.5 is **required**.
Python code currently must be compatible with Python 3.6. If a later
version or Python is required, it needs to be documented.
Compatibility with older programming language standards is very
important to maintain portability and availability of LAMMPS on many
@ -208,20 +206,21 @@ Build system (strict)
LAMMPS currently supports two build systems: one that is based on
:doc:`traditional Makefiles <Build_make>` and one that is based on
:doc:`CMake <Build_cmake>`. Therefore, your contribution must be
compatible with and support both build systems.
:doc:`CMake <Build_cmake>`. As of fall 2024, it is no longer required
to support the traditional make build system. New packages may choose
to only support building with CMake. Additions to existing packages
must follow the requirements set by that package.
For a single pair of header and implementation files that are an
independent feature, it is usually only required to add them to
``src/.gitignore``.
For traditional make, if your contributed files or package depend on
other LAMMPS style files or packages also being installed
(e.g. because your file is a derived class from the other LAMMPS
class), then an ``Install.sh`` file is also needed to check for those
dependencies and modifications to ``src/Depend.sh`` to trigger the checks.
See other README and Install.sh files in other directories as
examples.
other LAMMPS style files or packages also being installed (e.g. because
your file is a derived class from the other LAMMPS class), then an
``Install.sh`` file is also needed to check for those dependencies and
modifications to ``src/Depend.sh`` to trigger the checks. See other
README and Install.sh files in other directories as examples.
Similarly, for CMake support, changes may need to be made to
``cmake/CMakeLists.txt``, some of the files in ``cmake/presets``, and

3
doc/src/Packages_details.rst
View File

@ -994,6 +994,7 @@ Additional pair styles that are less commonly used.
* ``src/EXTRA-PAIR``: filenames -> commands
* :doc:`pair_style <pair_style>`
* ``examples/PACKAGES/dispersion``
----------
@ -2427,7 +2428,7 @@ ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python development
environment (headers and libraries) available on your system, which needs
to be either Python version 2.7 or Python 3.5 and later.
to be Python version 3.6 or later.
**Install:**

58
doc/src/Python_atoms.rst
View File

@ -2,14 +2,8 @@ Per-atom properties
===================
Similar to what is described in :doc:`Library_atoms`, the instances of
:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`, or
:py:class:`IPyLammps <lammps.IPyLammps>` can be used to extract atom quantities
and modify some of them. The main difference between the interfaces is how the information
is exposed.
While the :py:class:`lammps <lammps.lammps>` is just a thin layer that wraps C API calls,
:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps <lammps.IPyLammps>` expose
information as objects and properties.
:py:class:`lammps <lammps.lammps>` can be used to extract atom quantities
and modify some of them.
In some cases the data returned is a direct reference to the original data
inside LAMMPS cast to ``ctypes`` pointers. Where possible, the wrappers will
@ -25,10 +19,6 @@ against invalid accesses.
accordingly. These arrays can change sizes and order at every neighbor list
rebuild and atom sort event as atoms are migrating between subdomains.
.. tabs::
.. tab:: lammps API
.. code-block:: python
from lammps import lammps
@ -36,14 +26,30 @@ against invalid accesses.
lmp = lammps()
lmp.file("in.sysinit")
# Read/Write access via ctypes
nlocal = lmp.extract_global("nlocal")
x = lmp.extract_atom("x")
for i in range(nlocal):
print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
# Read/Write access via NumPy arrays
atom_id = L.numpy.extract_atom("id")
atom_type = L.numpy.extract_atom("type")
x = L.numpy.extract_atom("x")
v = L.numpy.extract_atom("v")
f = L.numpy.extract_atom("f")
# set position in 2D simulation
x[0] = (1.0, 0.0)
# set position in 3D simulation
x[0] = (1.0, 0.0, 1.)
lmp.close()
**Methods**:
* :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
@ -51,31 +57,3 @@ against invalid accesses.
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
.. tab:: PyLammps/IPyLammps API
All atoms in the current simulation can be accessed by using the :py:attr:`PyLammps.atoms <lammps.PyLammps.atoms>` property.
Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
these objects provide access to their data (id, type, position, velocity, force, etc.):
.. code-block:: python
# access first atom
L.atoms[0].id
L.atoms[0].type
# access second atom
L.atoms[1].position
L.atoms[1].velocity
L.atoms[1].force
Some attributes can be changed:
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)
# set position in 3D simulation
L.atoms[0].position = (1.0, 0.0, 1.0)

96
doc/src/Python_create.rst
View File

@ -6,11 +6,10 @@ Creating or deleting a LAMMPS object
====================================
With the Python interface the creation of a :cpp:class:`LAMMPS
<LAMMPS_NS::LAMMPS>` instance is included in the constructors for the
:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`,
and :py:class:`IPyLammps <lammps.IPyLammps>` classes.
Internally it will call either :cpp:func:`lammps_open` or :cpp:func:`lammps_open_no_mpi` from the C
library API to create the class instance.
<LAMMPS_NS::LAMMPS>` instance is included in the constructor for the
:py:class:`lammps <lammps.lammps>` class. Internally it will call either
:cpp:func:`lammps_open` or :cpp:func:`lammps_open_no_mpi` from the C library
API to create the class instance.
All arguments are optional. The *name* argument allows loading a
LAMMPS shared library that is named ``liblammps_machine.so`` instead of
@ -26,11 +25,7 @@ to run the Python module like the library interface on a subset of the
MPI ranks after splitting the communicator.
Here are simple examples using all three Python interfaces:
.. tabs::
.. tab:: lammps API
Here is a simple example using the LAMMPS Python interface:
.. code-block:: python
@ -48,86 +43,7 @@ Here are simple examples using all three Python interfaces:
# explicitly close and delete LAMMPS instance (optional)
lmp.close()
.. tab:: PyLammps API
The :py:class:`PyLammps <lammps.PyLammps>` class is a wrapper around the
:py:class:`lammps <lammps.lammps>` class and all of its lower level functions.
By default, it will create a new instance of :py:class:`lammps <lammps.lammps>` passing
along all arguments to the constructor of :py:class:`lammps <lammps.lammps>`.
.. code-block:: python
from lammps import PyLammps
# NOTE: argv[0] is set by the lammps class constructor
args = ["-log", "none"]
# create LAMMPS instance
L = PyLammps(cmdargs=args)
# get and print numerical version code
print("LAMMPS Version: ", L.version())
# explicitly close and delete LAMMPS instance (optional)
L.close()
:py:class:`PyLammps <lammps.PyLammps>` objects can also be created on top of an existing
:py:class:`lammps <lammps.lammps>` object:
.. code-block:: python
from lammps import lammps, PyLammps
...
# create LAMMPS instance
lmp = lammps(cmdargs=args)
# create PyLammps instance using previously created LAMMPS instance
L = PyLammps(ptr=lmp)
This is useful if you have to create the :py:class:`lammps <lammps.lammps>`
instance is a specific way, but want to take advantage of the
:py:class:`PyLammps <lammps.PyLammps>` interface.
.. tab:: IPyLammps API
The :py:class:`IPyLammps <lammps.IPyLammps>` class is an extension of the
:py:class:`PyLammps <lammps.PyLammps>` class. It has the same construction behavior. By
default, it will create a new instance of :py:class:`lammps` passing
along all arguments to the constructor of :py:class:`lammps`.
.. code-block:: python
from lammps import IPyLammps
# NOTE: argv[0] is set by the lammps class constructor
args = ["-log", "none"]
# create LAMMPS instance
L = IPyLammps(cmdargs=args)
# get and print numerical version code
print("LAMMPS Version: ", L.version())
# explicitly close and delete LAMMPS instance (optional)
L.close()
You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object:
.. code-block:: python
from lammps import lammps, IPyLammps
...
# create LAMMPS instance
lmp = lammps(cmdargs=args)
# create PyLammps instance using previously created LAMMPS instance
L = PyLammps(ptr=lmp)
This is useful if you have to create the :py:class:`lammps <lammps.lammps>`
instance is a specific way, but want to take advantage of the
:py:class:`IPyLammps <lammps.IPyLammps>` interface.
In all of the above cases, same as with the :ref:`C library API <lammps_c_api>`, this will use the
Same as with the :ref:`C library API <lammps_c_api>`, this will use the
``MPI_COMM_WORLD`` communicator for the MPI library that LAMMPS was
compiled with.

74
doc/src/Python_execute.rst
View File

@ -1,24 +1,17 @@
Executing commands
==================
Once an instance of the :py:class:`lammps <lammps.lammps>`,
:py:class:`PyLammps <lammps.PyLammps>`, or
:py:class:`IPyLammps <lammps.IPyLammps>` class is created, there are
Once an instance of the :py:class:`lammps <lammps.lammps>` class is created, there are
multiple ways to "feed" it commands. In a way that is not very different from
running a LAMMPS input script, except that Python has many more facilities
for structured programming than the LAMMPS input script syntax. Furthermore
it is possible to "compute" what the next LAMMPS command should be.
.. tabs::
.. tab:: lammps API
Same as in the equivalent
:doc:`C library functions <Library_execute>`, commands can be read from a file, a
single string, a list of strings and a block of commands in a single
multi-line string. They are processed under the same boundary conditions
as the C library counterparts. The example below demonstrates the use
of :py:func:`lammps.file()`, :py:func:`lammps.command()`,
Same as in the equivalent :doc:`C library functions <Library_execute>`,
commands can be read from a file, a single string, a list of strings and a
block of commands in a single multi-line string. They are processed under the
same boundary conditions as the C library counterparts. The example below
demonstrates the use of :py:func:`lammps.file()`, :py:func:`lammps.command()`,
:py:func:`lammps.commands_list()`, and :py:func:`lammps.commands_string()`:
.. code-block:: python
@ -33,7 +26,7 @@ it is possible to "compute" what the next LAMMPS command should be.
lmp.command('variable zpos index 1.0')
# create 10 groups with 10 atoms each
cmds = ["group g{} id {}:{}".format(i,10*i+1,10*(i+1)) for i in range(10)]
cmds = [f"group g{i} id {10*i+1}:{10*(i+1)}" for i in range(10)]
lmp.commands_list(cmds)
# run commands from a multi-line string
@ -45,11 +38,9 @@ it is possible to "compute" what the next LAMMPS command should be.
"""
lmp.commands_string(block)
.. tab:: PyLammps/IPyLammps API
Unlike the lammps API, the PyLammps/IPyLammps APIs allow running LAMMPS
commands by calling equivalent member functions of :py:class:`PyLammps <lammps.PyLammps>`
and :py:class:`IPyLammps <lammps.IPyLammps>` instances.
For convenience, the :py:class:`lammps <lammps.lammps>` class also provides a
command wrapper ``cmd`` that turns any LAMMPS command into a regular function
call.
For instance, the following LAMMPS command
@ -57,8 +48,7 @@ it is possible to "compute" what the next LAMMPS command should be.
region box block 0 10 0 5 -0.5 0.5
can be executed using with the lammps API with the following Python code if ``lmp`` is an
instance of :py:class:`lammps <lammps.lammps>`:
would normally be executed with the following Python code:
.. code-block:: python
@ -67,7 +57,7 @@ it is possible to "compute" what the next LAMMPS command should be.
lmp = lammps()
lmp.command("region box block 0 10 0 5 -0.5 0.5")
With the PyLammps interface, any LAMMPS command can be split up into arbitrary parts.
With the ``cmd`` wrapper, any LAMMPS command can be split up into arbitrary parts.
These parts are then passed to a member function with the name of the :doc:`command <Commands_all>`.
For the :doc:`region <region>` command that means the :code:`region()` method can be called.
The arguments of the command can be passed as one string, or
@ -75,53 +65,59 @@ it is possible to "compute" what the next LAMMPS command should be.
.. code-block:: python
from lammps import PyLammps
from lammps import lammps
L = PyLammps()
L = lammps()
# pass command parameters as one string
L.region("box block 0 10 0 5 -0.5 0.5")
L.cmd.region("box block 0 10 0 5 -0.5 0.5")
# OR pass them individually
L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
L.cmd.region("box block", 0, 10, 0, 5, -0.5, 0.5)
In the latter example, all parameters except the first are Python floating-point literals. The
member function takes the entire parameter list and transparently merges it to a single command
string.
The benefit of this approach is avoiding redundant command calls and easier
parameterization. In the lammps API parameterization needed to be done
manually by creating formatted command strings.
parameterization. With `command`, `commands_list`, and `commands_string` the
parameterization needed to be done manually by creating formatted command
strings.
.. code-block:: python
lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
In contrast, methods of PyLammps accept parameters directly and will convert
In contrast, methods of the `cmd` wrapper accept parameters directly and will convert
them automatically to a final command string.
.. code-block:: python
L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
L.cmd.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
Using these facilities, the example shown for the lammps API can be rewritten as follows:
.. note::
When running in IPython you can use Tab-completion after ``L.cmd.`` to see
all available LAMMPS commands.
Using these facilities, the previous example shown above can be rewritten as follows:
.. code-block:: python
from lammps import PyLammps
L = PyLammps()
from lammps import lammps
L = lammps()
# read commands from file 'in.melt'
L.file('in.melt')
# issue a single command
L.variable('zpos', 'index', 1.0)
L.cmd.variable('zpos', 'index', 1.0)
# create 10 groups with 10 atoms each
for i in range(10):
L.group(f"g{i}", "id", f"{10*i+1}:{10*(i+1)}")
L.cmd.group(f"g{i}", "id", f"{10*i+1}:{10*(i+1)}")
L.clear()
L.region("box block", 0, 2, 0, 2, 0, 2)
L.create_box(1, "box")
L.create_atoms(1, "single", 1.0, 1.0, "${zpos}")
L.cmd.clear()
L.cmd.region("box block", 0, 2, 0, 2, 0, 2)
L.cmd.create_box(1, "box")
L.cmd.create_atoms(1, "single", 1.0, 1.0, "${zpos}")

1
doc/src/Python_head.rst
View File

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

32
doc/src/Python_install.rst
View File

@ -7,6 +7,10 @@ LAMMPS shared library through the Python `ctypes <ctypes_>`_
module. Because of the dynamic loading, it is required that LAMMPS is
compiled in :ref:`"shared" mode <exe>`.
.. versionchanged:: TBD
LAMMPS currently only supports Python version 3.6 or later.
Two components are necessary for Python to be able to invoke LAMMPS code:
* The LAMMPS Python Package (``lammps``) from the ``python`` folder
@ -106,13 +110,16 @@ folder that the dynamic loader searches or inside of the installed
.. code-block:: bash
python install.py -p <python package> -l <shared library> -v <version.h file> [-n]
python install.py -p <python package> -l <shared library> -v <version.h file> [-n] [-f]
* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
* the ``-l`` flag points to the LAMMPS shared library file to be installed,
* the ``-v`` flag points to the LAMMPS version header file to extract the version date,
* and the optional ``-n`` instructs the script to only build a wheel file
but not attempt to install it.
* the optional ``-n`` instructs the script to only build a wheel file but not attempt
to install it,
* and the optional ``-f`` argument instructs the script to force installation even if
pip would otherwise refuse installation with an
:ref:`error about externally managed environments <externally_managed>`.
.. tab:: Virtual environment
@ -136,11 +143,6 @@ folder that the dynamic loader searches or inside of the installed
# create virtual environment in folder $HOME/myenv
python3 -m venv $HOME/myenv
For Python versions prior 3.3 you can use `virtualenv
<https://packaging.python.org/en/latest/key_projects/#virtualenv>`_
command instead of "python3 -m venv". This step has to be done
only once.
To activate the virtual environment type:
.. code-block:: bash
@ -199,6 +201,10 @@ folder that the dynamic loader searches or inside of the installed
The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package!
In case you run into an "externally-managed-environment" error when
trying to install the LAMMPS Python module, please refer to
:ref:`corresponding paragraph <externally_managed>` in the Python HOWTO
page to learn about options for handling this error.
To verify if LAMMPS can be successfully started from Python, start the
Python interpreter, load the ``lammps`` Python module and create a
@ -245,14 +251,14 @@ make MPI calls directly from Python in your script, if you desire.
We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
(aka mpi4py) and you will find installation instruction for it below.
Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
Installation of mpi4py (version 4.0.1 as of Feb 2025) can be done as
follows:
- Via ``pip`` into a local user folder with:
.. code-block:: bash
pip install --user mpi4py
python3 -m pip install --user mpi4py
- Via ``dnf`` into a system folder for RedHat/Fedora systems:
@ -261,20 +267,20 @@ follows:
# for use with OpenMPI
sudo dnf install python3-mpi4py-openmpi
# for use with MPICH
sudo dnf install python3-mpi4py-openmpi
sudo dnf install python3-mpi4py-mpich
- Via ``pip`` into a virtual environment (see above):
.. code-block:: console
$ source $HOME/myenv/activate
(myenv)$ pip install mpi4py
(myenv)$ python -m pip install mpi4py
- Via ``pip`` into a system folder (not recommended):
.. code-block:: bash
sudo pip install mpi4py
sudo python3 -m pip install mpi4py
For more detailed installation instructions and additional options,
please see the `mpi4py installation <https://mpi4py.readthedocs.io/en/stable/install.html>`_ page.

45
doc/src/Python_jupyter.rst Normal file
View File

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

53
doc/src/Python_module.rst
View File

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

43
doc/src/Python_objects.rst
View File

@ -4,10 +4,6 @@ Compute, fixes, variables
This section documents accessing or modifying data from objects like
computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
.. tabs::
.. tab:: lammps API
For :py:meth:`lammps.extract_compute() <lammps.lammps.extract_compute()>` and
:py:meth:`lammps.extract_fix() <lammps.lammps.extract_fix()>`, the global, per-atom,
or local data calculated by the compute or fix can be accessed. What is returned
@ -57,42 +53,3 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
.. tab:: PyLammps/IPyLammps API
PyLammps and IPyLammps classes currently do not add any additional ways of
retrieving information out of computes and fixes. This information can still be accessed by using the lammps API:
.. code-block:: python
L.lmp.extract_compute(...)
L.lmp.extract_fix(...)
# OR
L.lmp.numpy.extract_compute(...)
L.lmp.numpy.extract_fix(...)
LAMMPS variables can be both defined and accessed via the :py:class:`PyLammps <lammps.PyLammps>` interface.
To define a variable you can use the :doc:`variable <variable>` command:
.. code-block:: python
L.variable("a index 2")
A dictionary of all variables is returned by the :py:attr:`PyLammps.variables <lammps.PyLammps.variables>` property:
you can access an individual variable by retrieving a variable object from the
``L.variables`` dictionary by name
.. code-block:: python
a = L.variables['a']
The variable value can then be easily read and written by accessing the value
property of this object.
.. code-block:: python
print(a.value)
a.value = 4

33
doc/src/Python_overview.rst
View File

@ -44,19 +44,15 @@ Below is an example output for Python version 3.8.5.
.. warning::
The options described in this section of the manual for using Python
with LAMMPS currently support either Python 2 or 3. Specifically
version 2.7 or later and 3.6 or later. Since the Python community no
longer maintains Python 2 (see `this notice
<https://www.python.org/doc/sunset-python-2/>`_), we recommend use of
Python 3 with LAMMPS. While Python 2 code should continue to work,
that is not something we can guarantee long-term. If you notice
Python code in the LAMMPS distribution that is not compatible with
Python 3, please contact the LAMMPS developers or submit `and issue
on GitHub <https://github.com/lammps/lammps/issues>`_
with LAMMPS support only Python 3.6 or later. For use with Python
2.x you will need to use an older LAMMPS version like 29 Aug 2024
or older. If you notice Python code in the LAMMPS distribution that
is not compatible with Python 3, please contact the LAMMPS developers
or submit `and issue on GitHub <https://github.com/lammps/lammps/issues>`_
---------
LAMMPS can work together with Python in three ways. First, Python can
LAMMPS can work together with Python in two ways. First, Python can
wrap LAMMPS through the its :doc:`library interface <Library>`, so
that a Python script can create one or more instances of LAMMPS and
launch one or more simulations. In Python terms, this is referred to as
@ -67,22 +63,7 @@ launch one or more simulations. In Python terms, this is referred to as
Launching LAMMPS via Python
Second, the lower-level Python interface in the :py:class:`lammps Python
class <lammps.lammps>` can be used indirectly through the provided
:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps
<lammps.IPyLammps>` wrapper classes, also written in Python. These
wrappers try to simplify the usage of LAMMPS in Python by providing a
more object-based interface to common LAMMPS functionality. They also
reduce the amount of code necessary to parameterize LAMMPS scripts
through Python and make variables and computes directly accessible.
.. figure:: JPG/pylammps-invoke-lammps.png
:figclass: align-center
Using the PyLammps / IPyLammps wrappers
Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
script or styles can invoke Python code directly, and pass information
back-and-forth between the input script and Python functions you write.
This Python code can also call back to LAMMPS to query or change its

85
doc/src/Python_properties.rst
View File

@ -2,14 +2,8 @@ System properties
=================
Similar to what is described in :doc:`Library_properties`, the instances of
:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`, or
:py:class:`IPyLammps <lammps.IPyLammps>` can be used to extract different kinds
of information about the active LAMMPS instance and also to modify some of it. The
main difference between the interfaces is how the information is exposed.
While the :py:class:`lammps <lammps.lammps>` is just a thin layer that wraps C API calls,
:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps <lammps.IPyLammps>` expose
information as objects and properties.
:py:class:`lammps <lammps.lammps>` can be used to extract different kinds
of information about the active LAMMPS instance and also to modify some of it.
In some cases the data returned is a direct reference to the original data
inside LAMMPS cast to ``ctypes`` pointers. Where possible, the wrappers will
@ -25,10 +19,6 @@ against invalid accesses.
accordingly. These arrays can change sizes and order at every neighbor list
rebuild and atom sort event as atoms are migrating between subdomains.
.. tabs::
.. tab:: lammps API
.. code-block:: python
from lammps import lammps
@ -64,74 +54,3 @@ against invalid accesses.
**Properties**:
* :py:attr:`last_thermo_step <lammps.lammps.last_thermo_step>`: the last timestep thermodynamic output was computed
.. tab:: PyLammps/IPyLammps API
In addition to the functions provided by :py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>` objects
have several properties which allow you to query the system state:
L.system
Is a dictionary describing the system such as the bounding box or number of atoms
L.system.xlo, L.system.xhi
bounding box limits along x-axis
L.system.ylo, L.system.yhi
bounding box limits along y-axis
L.system.zlo, L.system.zhi
bounding box limits along z-axis
L.communication
configuration of communication subsystem, such as the number of threads or processors
L.communication.nthreads
number of threads used by each LAMMPS process
L.communication.nprocs
number of MPI processes used by LAMMPS
L.fixes
List of fixes in the current system
L.computes
List of active computes in the current system
L.dump
List of active dumps in the current system
L.groups
List of groups present in the current system
**Retrieving the value of an arbitrary LAMMPS expressions**
LAMMPS expressions can be immediately evaluated by using the ``eval`` method. The
passed string parameter can be any expression containing global :doc:`thermo` values,
variables, compute or fix data (see :doc:`Howto_output`):
.. code-block:: python
result = L.eval("ke") # kinetic energy
result = L.eval("pe") # potential energy
result = L.eval("v_t/2.0")
**Example**
.. code-block:: python
from lammps import PyLammps
L = PyLammps()
L.file("in.sysinit")
print(f"running simulation with {L.system.natoms} atoms")
L.run(1000, "post no");
for i in range(10):
L.run(100, "pre no post no")
pe = L.eval("pe")
ke = L.eval("ke")
print(f"PE = {pe}\nKE = {ke}")

416
doc/src/Run_formats.rst Normal file
View File

@ -0,0 +1,416 @@
File formats used by LAMMPS
===========================
This page provides a general overview of the kinds of files and file
formats that LAMMPS is reading and writing.
.. contents:: On this page
:depth: 2
:backlinks: top
-------------------
Character Encoding
^^^^^^^^^^^^^^^^^^
For processing text files, the LAMMPS source code assumes `ASCII
character encoding <https://en.wikipedia.org/wiki/ASCII>`_ which
represents the digits 0 to 9, the lower and upper case letters a to z,
some common punctuation and other symbols and a few whitespace
characters including a regular "space character", "line feed", "carriage
return", "tabulator". These characters are all represented by single
bytes with a value smaller than 128 and only 95 of those 128 values
represent printable characters. This list is sufficient to represent
most English text, but misses accented characters or umlauts or Greek
symbols and more.
Modern text often uses `UTF-8 character encoding
<https://en.wikipedia.org/wiki/UTF-8>`_ instead. This encoding is a way
to represent many more different characters as defined by the Unicode
standard. UFT-8 is compatible with ASCII, since the first 128 values
are identical with the ASCII encoding. It is important to note,
however, that there are Unicode characters that *look* similar to ASCII
characters, but have a different binary representation. As a general
rule, these characters may not be correctly recognized by LAMMPS. For
some parts of LAMMPS' text processing, translation tables with known
"lookalike" characters are used. The tables are used to substitute
non-ASCII characters with their ASCII equivalents. Non-ASCII lookalike
characters are often used by web browsers or PDF viewers to improve the
readability of text. Thus, when using copy and paste to transfer text
from such an application to your input file, you may unintentionally
create text that is not exclusively using ASCII encoding and may cause
errors when LAMMPS is trying to read it.
Lines with non-printable and non-ASCII characters in text files can be
detected for example with a (Linux) command like the following:
.. code-block:: bash
env LC_ALL=C grep -n '[^ -~]' some_file.txt
Number Formatting
^^^^^^^^^^^^^^^^^
Different countries and languages have different conventions to format
numbers. While in some regions commas are used for fractions and points
to indicate thousand, million and so on, this is reversed in other
regions. Modern operating systems have facilities to adjust input and
output accordingly that are collectively referred to as "native language
support" (NLS). The exact rules are often applied according to the
value of the ``$LANG`` environment variable (e.g. "en_US.utf8" for
English text in UTF-8 encoding).
For the sake of simplicity of the implementation and transferability of
results, LAMMPS does not support this and instead expects numbers being
formatted in the generic or "C" locale. The "C" locale has no
punctuation for thousand, million and so on and uses a decimal point for
fractions. One thousand would be represented as "1000.0" and not as
"1,000.0" nor as "1.000,0". Having native language support enabled for
a locale other than "C" will result in different behavior when
converting or formatting numbers that can trigger unexpected errors.
LAMMPS also only accepts integer numbers when an integer is required, so
using floating point equivalents like "1.0" are not accepted; you *must*
use "1" instead.
For floating point numbers in scientific notation, the Fortran double
precision notation "1.1d3" is not accepted; you have to use "1100",
"1100.0" or "1.1e3".
Input file
^^^^^^^^^^
A LAMMPS input file is a text file with commands. It is read
line-by-line and each line is processed *immediately*. Before looking
for commands and executing them, there is a pre-processing step where
comments (non-quoted text starting with a pound sign '#') are removed,
``${variable}`` and ``$(expression)`` constructs are expanded or
evaluated, and lines that end in the ampersand character '&' are
combined with the next line (similar to Fortran 90 free-format source
code). After the pre-processing, lines are split into "words" and
evaluated. The first word must be a :doc:`command <Commands_all>` and
all following words are arguments. Below are some example lines:
.. code-block:: LAMMPS
# full line comment
# some global settings
units lj
atom_style atomic
# ^^ command ^^ argument(s)
variable x index 1 # may be overridden from command line with -var x <value>
variable xx equal 20*$x # variable "xx" is always 20 times "x"
lattice fcc 0.8442
# example of a command written across multiple lines
# the "region" command uses spacing from "lattice" command, unless "units box" is specified
region box block 0.0 ${xx} &
0.0 40.0 &
0.0 30.0
# create simulation box and fill with atoms according to lattice setting
create_box 1 box
create_atoms 1 box
# set force field and parameters
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
# run simulation
fix 1 all nve
run 1000
The pivotal command in this example input is the :doc:`create_box
command <create_box>`. It defines the simulation system and many
parameters that go with it: units, atom style, number of atom types (and
other types) and more. Those settings are *locked in* after the box is
created. Commands that change these kind of settings are only allowed
**before** a simulation box is created and many other commands are only
allowed **after** the simulation box is defined (e.g. :doc:`pair_coeff
<pair_coeff>`). Very few commands (e.g. :doc:`pair_style <pair_style>`)
may be used in either part of the input. The :doc:`read_data
<read_data>` and :doc:`read_restart <read_restart>` commands also create
the system box and thus have a similar pivotal function.
The LAMMPS input syntax has minimal support for conditionals and loops,
but if more complex operations are required, it is recommended to use
the library interface, e.g. :doc:`from Python using the LAMMPS Python
module <Python_run>`.
There is a frequent misconception about the :doc:`if command <if>`:
this is a command for conditional execution **outside** a run or
minimization. To trigger actions on specific conditions **during**
a run is a non-trivial operation that usually requires adopting one
of the available "fix" commands or creating a new "fix" command.
LAMMPS commands change the internal state and thus the order of commands
matters and reordering them can produce different results. For example,
the region defined by the :doc:`region command <region>` in the example
above depends on the :doc:`lattice setting <lattice>` and thus its
dimensions will be different depending on the order of the two commands.
Each line must have an "end-of-line" character (line feed or carriage
return plus line feed). Some text editors do not automatically insert
one which may cause LAMMPS to ignore the last command. It is thus
recommended to always have an empty line at the end of an input file.
The specific details describing how LAMMPS input is processed and parsed
are explained in :doc:`Commands_parse`.
Data file
^^^^^^^^^
A LAMMPS data file contains a description of a system suitable for
reading with the :doc:`read_data command <read_data>`. Data files are
commonly used for setting up complex molecular systems that can be
difficult to achieve with the commands :doc:`create_box <create_box>`
and :doc:`create_atoms <create_atoms>` alone. Also, data files can be
used as a portable alternatives to a :doc:`binary restart file
<restart>`. A restart file can be converted into a data file from the
:doc:`command line <Run_options>`.
Data files have a header section at the very beginning of the file and
multiple titled sections such as "Atoms", Masses", "Pair Coeffs", and so
on. Header keywords can only be used *before* the first title section.
The data file **always** starts with a "title" line, which will be
**ignored** by LAMMPS. Omitting the title line can lead to unexpected
behavior because a line of the header with an actual setting may be
ignored. In this case, the mistakenly ignored line often contains the
"atoms" keyword, which results in LAMMPS assuming that there are no
atoms in the data file and thus throwing an error on the contents of the
"Atoms" section. The title line may contain some keywords that can be
used by external programs to convey information about the system
(included as comments), that is not required and not read by LAMMPS.
The line following a section title is also **ignored**. An error will
occur if an empty line is not placed after a section title. The number
of lines in titled sections depends on header keywords, like the number
of atom types, the number of atoms, the number of bond types, the number
of bonds, and so on. The data in those sections has to be complete. A
special case are the "Pair Coeffs" and "PairIJ Coeffs" sections; the
former is for force fields and pair styles that use mixing of non-bonded
potential parameters, the latter for pair styles and force fields
requiring explicit coefficients. Thus with *N* being the number of atom
types, the "Pair Coeffs" section has *N* entries while "PairIJ Coeffs"
has :math:`N \cdot (N-1)` entries. Internally, these sections will be
converted to :doc:`pair_coeff <pair_coeff>` commands. Thus the
corresponding :doc:`pair style <pair_style>` must have been set *before*
the :doc:`read_data command <read_data>` reads the data file.
Data files may contain comments, which start with the pound sign '#'.
There must be at least one blank between a valid keyword and the pound
sign. Below is a simple example case of a data file for :doc:`atom style
full <atom_style>`.
.. code-block:: bash
LAMMPS Title line (ignored)
# full line comment
10 atoms # comment
4 atom types
-36.840194 64.211560 xlo xhi
-41.013691 68.385058 ylo yhi
-29.768095 57.139462 zlo zhi
Masses
1 12.0110
2 12.0110
3 15.9990
4 1.0080
Pair Coeffs # this section is optional
1 0.110000 3.563595 0.110000 3.563595
2 0.080000 3.670503 0.010000 3.385415
3 0.120000 3.029056 0.120000 2.494516
4 0.022000 2.351973 0.022000 2.351973
Atoms # full
1 1 1 0.560 43.99993 58.52678 36.78550 0 0 0
2 1 2 -0.270 45.10395 58.23499 35.86693 0 0 0
3 1 3 -0.510 43.81519 59.54928 37.43995 0 0 0
4 1 4 0.090 45.71714 57.34797 36.13434 0 0 0
5 1 4 0.090 45.72261 59.13657 35.67007 0 0 0
6 1 4 0.090 44.66624 58.09539 34.85538 0 0 0
7 1 3 -0.470 43.28193 57.47427 36.91953 0 0 0
8 1 4 0.070 42.07157 57.45486 37.62418 0 0 0
9 1 1 0.510 42.19985 57.57789 39.12163 0 0 0
10 1 1 0.510 41.88641 58.62251 39.70398 0 0 0
# ^^atomID ^^molID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord ^^image^^flags (optional)
Velocities # this section is optional
1 0.0050731 -0.00398928 0.00391473
2 -0.0175184 0.0173484 -0.00489207
3 0.00597225 -0.00202006 0.00166454
4 -0.010395 -0.0082582 0.00316419
5 -0.00390877 0.00470331 -0.00226911
6 -0.00111157 -0.00374545 -0.0169374
7 0.00209054 -0.00594936 -0.000124563
8 0.00635002 -0.0120093 -0.0110999
9 -0.004955 -0.0123375 0.000403422
10 0.00265028 -0.00189329 -0.00293198
The common problem is processing the "Atoms" section, since its format
depends on the :doc:`atom style <atom_style>` used, and that setting
must be done in the input file *before* reading the data file. To
assist with detecting incompatible data files, a comment is appended to
the "Atoms" title indicating the atom style used (or intended) when
*writing* the data file. For example, below is an "Atoms" section for
:doc:`atom style charge <atom_style>`, which omits the molecule ID
column.
.. code-block:: bash
Atoms # charge
1 1 0.560 43.99993 58.52678 36.78550
2 2 -0.270 45.10395 58.23499 35.86693
3 3 -0.510 43.81519 59.54928 37.43995
4 4 0.090 45.71714 57.34797 36.13434
5 4 0.090 45.72261 59.13657 35.67007
6 4 0.090 44.66624 58.09539 34.85538
7 3 -0.470 43.28193 57.47427 36.91953
8 4 0.070 42.07157 57.45486 37.62418
9 1 0.510 42.19985 57.57789 39.12163
10 1 0.510 41.88641 58.62251 39.70398
# ^^atomID ^^type ^^charge ^^xcoord ^^ycoord ^^ycoord
Another source of confusion about the "Atoms" section format is the
ordering of columns. The three atom style variants `atom_style full`,
`atom_style hybrid charge molecular`, and `atom_style hybrid molecular
charge` all carry the same per-atom information. However, in data files,
the Atoms section has the columns 'Atom-ID Molecule-ID Atom-type Charge
X Y Z' for atom style full, but for hybrid atom styles the first columns
are always 'Atom-ID Atom-type X Y Z' followed by any *additional* data
added by the hybrid styles, for example, 'Charge Molecule-ID' for the
first hybrid style and 'Molecule-ID Charge' in the second hybrid style
variant. Finally, an alternative to a hybrid atom style is to use fix
property/atom, e.g. to add molecule IDs to atom style charge. In this
case the "Atoms" section is formatted according to atom style charge and
a new section, "Molecules" is added that contains lines with 'Atom-ID
Molecule-ID', one for each atom in the system. For adding charges to
atom style molecular with fix property/atom, the "Atoms" section is now
formatted according to the atom style and a "Charges" section is added.
Molecule file
^^^^^^^^^^^^^
Molecule files for use with the :doc:`molecule command <molecule>` look
quite similar to data files but they do not have a compatible format,
i.e., one cannot use a data file as molecule file and vice versa. Below
is a simple example for a water molecule (SPC/E model). Same as a data
file, there is an ignored title line and you can use comments. However,
there is no information about the number of types or the box dimensions.
These parameters are set when the simulation box is created. Thus the
header only has the count of atoms, bonds, and so on.
Molecule files have a header followed by sections (just as in data
files), but the section names are different than those of a data file.
There is no "Atoms" section and the section formats in molecule files is
independent of the atom style. Its information is split across multiple
sections, like "Coords", "Types", and "Charges". Note that no "Masses"
section is needed here. The atom masses are by default tied to the atom
type and set with a data file or the :doc:`mass command <mass>`. A
"Masses" section would only be required for atom styles with per-atom
masses, e.g. atom style sphere, where in data files you would provide
the density and the diameter instead of the mass.
Since the entire file is a 'molecule', LAMMPS will assign a new
molecule-ID (if supported by the atom style) when atoms are instantiated
from a molecule file, e.g. with the :doc:`create_atoms command
<create_atoms>`. It is possible to include a "Molecules" section to
indicate that the atoms belong to multiple 'molecules'. Atom-IDs and
molecule-IDs in the molecule file are relative for the file
(i.e. starting from 1) and will be translated into actual atom-IDs also
when the atoms from the molecule are created.
.. code-block:: bash
# Water molecule. SPC/E model.
3 atoms
2 bonds
1 angles
Coords
1 1.12456 0.09298 1.27452
2 1.53683 0.75606 1.89928
3 0.49482 0.56390 0.65678
Types
1 1
2 2
3 2
Charges
1 -0.8472
2 0.4236
3 0.4236
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
There are also optional sections, e.g. about :doc:`SHAKE <fix_shake>`
and :doc:`special bonds <special_bonds>`. Those sections are only needed
if the molecule command is issued *before* the simulation box is
defined. Otherwise, the molecule command can derive the required
settings internally.
Restart file
^^^^^^^^^^^^
LAMMPS restart files are binary files and not available in text format.
They can be identified by the first few bytes that contain the (C-style)
string ``LammpS RestartT`` as `magic string
<https://en.wikipedia.org/wiki/Magic_string>`_. This string is followed
by a 16-bit integer of the number 1 used for detecting whether the
computer writing the restart has the same `endianness
<https://en.wikipedia.org/wiki/Endianness>`_ as the computer reading it.
If not, the file cannot be read correctly. This integer is followed by
a 32-bit integer indicating the file format revision (currently 3),
which can be used to implement backward compatibility for reading older
revisions.
This information has been added to the `Unix "file" command's
<https://www.darwinsys.com/file/>` "magic" file so that restart files
can be identified without opening them. If you have a fairly recent
version, it should already be included. If you have an older version,
the LAMMPS source package :ref:`contains a file with the necessary
additions <magic>`.
The rest of the file is organized in sections of a 32-bit signed integer
constant indicating the kind of content and the corresponding value (or
values). If those values are arrays (including C-style strings), then
the integer constant is followed by a 32-bit integer indicating the
length of the array. This mechanism will read the data regardless of
the ordering of the sections. Symbolic names of the section constants
are in the ``lmprestart.h`` header file.
LAMMPS restart files are not expected to be portable between platforms
or LAMMPS versions, but changes to the file format are rare.
.. Native Dump file
.. ^^^^^^^^^^^^^^^^
..
.. Potential files
.. ^^^^^^^^^^^^^^^

10
doc/src/Run_head.rst
View File

@ -1,10 +1,11 @@
Run LAMMPS
**********
These pages explain how to run LAMMPS once you have :doc:`installed an executable <Install>` or :doc:`downloaded the source code <Install>`
and :doc:`built an executable <Build>`. The :doc:`Commands <Commands>`
doc page describes how input scripts are structured and the commands
they can contain.
These pages explain how to run LAMMPS once you have :doc:`installed an
executable <Install>` or :doc:`downloaded the source code <Install>` and
:doc:`built an executable <Build>`. The :doc:`Commands <Commands>` doc
page describes how input scripts are structured and the commands they
can contain.
.. toctree::
:maxdepth: 1
@ -12,4 +13,5 @@ they can contain.
Run_basics
Run_options
Run_output
Run_formats
Run_windows

82
doc/src/Run_output.rst
View File

@ -117,14 +117,19 @@ number of histogram counts is equal to the number of processors.
----------
The last section gives aggregate statistics (across all processors)
for pairwise neighbors and special neighbors that LAMMPS keeps track
of (see the :doc:`special_bonds <special_bonds>` command). The number
of times neighbor lists were rebuilt is tallied, as is the number of
potentially *dangerous* rebuilds. If atom movement triggered neighbor
list rebuilding (see the :doc:`neigh_modify <neigh_modify>` command),
then dangerous reneighborings are those that were triggered on the
first timestep atom movement was checked for. If this count is
The last section gives aggregate statistics (across all processors) for
pairwise neighbors and special neighbors that LAMMPS keeps track of (see
the :doc:`special_bonds <special_bonds>` command). This section will
not always contain data, for example when there has not been a neighbor
rebuild, or the neighbor list was constructed on the GPU or when a
hybrid pair style was used and LAMMPS cannot determine a suitable (base)
neighbor list to draw the statistics from.
The number of times neighbor lists were rebuilt is tallied, as is the
number of potentially *dangerous* rebuilds. If atom movement triggered
neighbor list rebuilding (see the :doc:`neigh_modify <neigh_modify>`
command), then dangerous reneighborings are those that were triggered on
the first timestep atom movement was checked for. If this count is
non-zero you may wish to reduce the delay factor to ensure no force
interactions are missed by atoms moving beyond the neighbor skin
distance before a rebuild takes place.
@ -178,3 +183,64 @@ with and without the communication and a Gflop rate is computed. The
3d rate is with communication; the 1d rate is without (just the 1d
FFTs). Thus you can estimate what fraction of your FFT time was spent
in communication, roughly 75% in the example above.
Error message output
====================
Depending on the error function arguments when it is called in the
source code, there will be one to four lines of error output.
A single line
^^^^^^^^^^^^^
The line starts with "ERROR: ", followed by the error message and
information about the location in the source where the error function
was called in parenthesis on the right (here: line 131 of the file
src/fix_print.cpp). Example:
.. parsed-literal::
ERROR: Fix print timestep variable nevery returned a bad timestep: 9900 (src/fix_print.cpp:131)
Two lines
^^^^^^^^^
In addition to the single line output, also the last line of the input
will be repeated. If a command is spread over multiple lines in the
input using the continuation character '&', then the error will print
the entire concatenated line. For readability all whitespace is
compressed to single blanks. Example:
.. parsed-literal::
ERROR: Unrecognized fix style 'printf' (src/modify.cpp:924)
Last input line: fix 0 all printf v_nevery "Step: $(step) ${step}"
Three lines
^^^^^^^^^^^
In addition to the two line output from above, a third line is added
that uses caret character markers '^' to indicate which "word" in the
input failed. Example:
.. parsed-literal::
ERROR: Illegal fix print nevery value -100; must be > 0 (src/fix_print.cpp:41)
Last input line: fix 0 all print -100 "Step: $(step) ${stepx}"
^^^^
Four lines
^^^^^^^^^^
The three line output is expanded to four lines, if the the input is
modified through input pre-processing, e.g. when substituting
variables. Now the last command is printed once in the original form and
a second time after substitutions are applied. The caret character
markers '^' are applied to the second version. Example:
.. parsed-literal::
ERROR: Illegal fix print nevery value -100; must be > 0 (src/fix_print.cpp:41)
Last input line: fix 0 all print ${nevery} 'Step: $(step) ${step}'
--> parsed line: fix 0 all print -100 "Step: $(step) ${step}"
^^^^

13
doc/src/Speed_compare.rst
View File

@ -44,11 +44,6 @@ section below for examples where this has been done.
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller.
* Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
etc) on the CPU. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster in these
cases.
* When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
performance depends to some extent on the available bandwidth between
the CPUs and the GPU. This can differ significantly based on the
@ -85,10 +80,10 @@ section below for examples where this has been done.
code (with a performance penalty due to having data transfers between
host and GPU).
* The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists, or a triclinic simulation box.
* The GPU package can be compiled for CUDA or OpenCL and thus supports
both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically
resulting in equal or better performance over OpenCL.
hybrid pair styles, exclusion lists, or a triclinic simulation box.
* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus supports
NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is
typically resulting in equal or better performance over OpenCL.
* OpenCL in the GPU package does theoretically also support Intel CPUs or
Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
is superior.

80
doc/src/Speed_kokkos.rst
View File

@ -67,6 +67,14 @@ version 23 November 2023 and Kokkos version 4.2.
To build with Kokkos support for AMD GPUs, the AMD ROCm toolkit
software version 5.2.0 or later must be installed on your system.
.. admonition:: Intel Data Center GPU support
:class: note
Support for Kokkos with Intel Data Center GPU accelerators (formerly
known under the code name "Ponte Vecchio") in LAMMPS is still a work
in progress. Only a subset of the functionality works correctly.
Please contact the LAMMPS developers if you run into problems.
.. admonition:: CUDA and MPI library compatibility
:class: note
@ -80,13 +88,15 @@ version 23 November 2023 and Kokkos version 4.2.
LAMMPS command-line or by using the command :doc:`package kokkos
gpu/aware off <package>` in the input file.
.. admonition:: Intel Data Center GPU support
.. admonition:: Using multiple MPI ranks per GPU
:class: note
Support for Kokkos with Intel Data Center GPU accelerators (formerly
known under the code name "Ponte Vecchio") in LAMMPS is still a work
in progress. Only a subset of the functionality works correctly.
Please contact the LAMMPS developers if you run into problems.
Unlike with the GPU package, there are limited benefits from using
multiple MPI processes per GPU with KOKKOS. But when doing this it
is **required** to enable CUDA MPS (`Multi-Process Service :: GPU
Deployment and Management Documentation
<https://docs.nvidia.com/deploy/mps/index.html>`_ ) to get acceptable
performance.
Building LAMMPS with the KOKKOS package
"""""""""""""""""""""""""""""""""""""""
@ -365,13 +375,13 @@ one or more nodes, each with two GPUs:
.. note::
When using a GPU, you will achieve the best performance if your
input script does not use fix or compute styles which are not yet
When using a GPU, you will achieve the best performance if your input
script does not use fix or compute styles which are not yet
Kokkos-enabled. This allows data to stay on the GPU for multiple
timesteps, without being copied back to the host CPU. Invoking a
non-Kokkos fix or compute, or performing I/O for
:doc:`thermo <thermo_style>` or :doc:`dump <dump>` output will cause data
to be copied back to the CPU incurring a performance penalty.
non-Kokkos fix or compute, or performing I/O for :doc:`thermo
<thermo_style>` or :doc:`dump <dump>` output will cause data to be
copied back to the CPU incurring a performance penalty.
.. note::
@ -379,6 +389,56 @@ one or more nodes, each with two GPUs:
kspace, etc., you must set the environment variable ``CUDA_LAUNCH_BLOCKING=1``.
However, this will reduce performance and is not recommended for production runs.
Troubleshooting segmentation faults on GPUs
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
As noted above, KOKKOS by default assumes that the MPI library is
GPU-aware. This is not always the case and can lead to segmentation
faults when using more than one MPI process. Normally, LAMMPS will
print a warning like "*Turning off GPU-aware MPI since it is not
detected*", or an error message like "*Kokkos with GPU-enabled backend
assumes GPU-aware MPI is available*", OR a **segmentation fault**. To
confirm that a segmentation fault is caused by this, you can turn off
the GPU-aware assumption via the :doc:`package kokkos command <package>`
or the corresponding command-line flag.
If you still get a segmentation fault, despite running with only one MPI
process or using the command-line flag to turn off expecting a GPU-aware
MPI library, then using the CMake compile setting
``-DKokkos_ENABLE_DEBUG=on`` or adding ``KOKKOS_DEBUG=yes`` to your
machine makefile for building with traditional make will generate useful
output that can be passed to the LAMMPS developers for further
debugging.
Troubleshooting memory allocation on GPUs
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
`Kokkos Tools <https://github.com/kokkos/kokkos-tools/>`_ provides a set
of lightweight profiling and debugging utilities, which interface with
instrumentation hooks (eg. `space-time-stack
<https://github.com/kokkos/kokkos-tools/tree/develop/profiling/space-time-stack>`_)
built directly into the Kokkos runtime. After compiling a dynamic LAMMPS
library, you then have to set the environment variable ``KOKKOS_TOOLS_LIBS``
before executing your LAMMPS Kokkos run. Example:
.. code-block:: bash
export KOKKOS_TOOLS_LIBS=${HOME}/kokkos-tools/src/tools/memory-events/kp_memory_event.so
mpirun -np 4 lmp_kokkos_cuda_openmpi -in in.lj -k on g 4 -sf kk
Starting with the NVIDIA Pascal GPU architecture, CUDA supports
`"Unified Virtual Memory" (UVM)
<https://developer.nvidia.com/blog/unified-memory-cuda-beginners/>`_
which enables allocating more memory than a GPU possesses by also using
memory on the host CPU and then CUDA will transparently move data
between CPU and GPU as needed. The resulting LAMMPS performance depends
on `memory access pattern, data residency, and GPU memory
oversubscription
<https://developer.nvidia.com/blog/improving-gpu-memory-oversubscription-performance/>`_
. The CMake option ``-DKokkos_ENABLE_CUDA_UVM=on`` or the makefile
setting ``KOKKOS_CUDA_OPTIONS=enable_lambda,force_uvm`` enables using
:ref:`UVM with Kokkos <kokkos>` when compiling LAMMPS.
Run with the KOKKOS package by editing an input script
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

2
doc/src/Tools.rst
View File

@ -930,7 +930,7 @@ dependencies and redirects the download to the local cache.
mkdir build
cd build
cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake -D DOWNLOAD_POTENTIALS=off ../cmake
make -j 8
deactivate_caches

94
doc/src/angle_mwlc.rst Normal file
View File

@ -0,0 +1,94 @@
.. index:: angle_style mwlc
angle_style mwlc command
==========================
Syntax
""""""
.. code-block:: LAMMPS
angle_style mwlc
Examples
""""""""
.. code-block:: LAMMPS
angle_style mwlc
angle_coeff * 25 1 10 1
Description
"""""""""""
.. versionadded:: 4Feb2025
The *mwlc* angle style models a meltable wormlike chain and can be used
to model non-linear bending elasticity of polymers, e.g. DNA. *mwlc*
uses a potential that is a canonical-ensemble superposition of a
non-melted and a melted state :ref:`(Farrell) <Farrell>`. The potential
is
.. math::
E = -k_{B}T\,\log [q + q^{m}] + E_{0},
where the non-melted and melted partition functions are
.. math::
q = \exp [-k_{1}(1+\cos{\theta})/k_{B}T]; \\
q^{m} = \exp [-(\mu+k_{2}(1+\cos{\theta}))/k_{B}T].
:math:`k_1` is the bending elastic constant of the non-melted state,
:math:`k_2` is the bending elastic constant of the melted state,
:math:`\mu` is the melting energy, and
:math:`T` is the reference temperature.
The reference energy,
.. math::
E_{0} = -k_{B}T\,\log [1 + \exp[-\mu/k_{B}T]],
ensures that E is zero for a fully extended chain.
This potential is a continuous version of the two-state potential
introduced by :ref:`(Yan) <Yan>`.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`k_1` (energy)
* :math:`k_2` (energy)
* :math:`\mu` (energy)
* :math:`T` (temperature)
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
doc page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none
----------
.. _Farrell:
**(Farrell)** `Farrell, Dobnikar, Podgornik, Curk, Phys Rev Lett, 133, 148101 (2024). <https://doi.org/10.1103/PhysRevLett.133.148101>`_
.. _Yan:
**(Yan)** `Yan, Marko, Phys Rev Lett, 93, 108108 (2004). <https://doi.org/10.1103/PhysRevLett.93.108108>`_

1
doc/src/angle_style.rst
View File

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

17
doc/src/bond_bpm_spring.rst
View File

@ -10,7 +10,7 @@ Syntax
bond_style bpm/spring keyword value attribute1 attribute2 ...
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* or *volume/factor*
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *normalize* or *break* or *volume/factor*
.. parsed-literal::
@ -123,7 +123,7 @@ heuristic maximum strain used by typical non-bpm bond styles. Similar behavior
to *break no* can also be attained by setting an arbitrarily high value of
:math:`\epsilon_c`. One cannot use *break no* with *smooth yes*.
.. versionadded:: TBD
.. versionadded:: 4Feb2025
The *volume/factor* keyword toggles whether an additional multibody
contribution is added to he force using the formulation in
@ -141,7 +141,8 @@ calculated using bond lengths squared and the cube root in the above equation
is accordingly replaced with a square root. This approximation assumes bonds
are evenly distributed on a spherical surface and neglects constant prefactors
which are irrelevant since only the ratio of volumes matters. This term may be
used to adjust the Poisson's ratio.
used to adjust the Poisson's ratio. See the simulation in the
``examples/bpm/poissons_ratio`` directory for a demonstration of this effect.
If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting
(or adding) that bond's contribution.
@ -214,11 +215,11 @@ for an overview of LAMMPS output options.
The vector or array will be floating point values that correspond to
the specified attribute.
The single() function of this bond style returns 0.0 for the energy
of a bonded interaction, since energy is not conserved in these
dissipative potentials. The single() function also calculates an
extra bond quantity, the initial distance :math:`r_0`. This
extra quantity can be accessed by the
The potential energy and the single() function of this bond style return
:math:`k (r - r_0)^2 / 2` as a proxy of the energy of a bonded interaction,
ignoring any volumetric/smoothing factors or dissipative forces. The single()
function also calculates an extra bond quantity, the initial distance
:math:`r_0`. This extra quantity can be accessed by the
:doc:`compute bond/local <compute_bond_local>` command as *b1*\ .
Restrictions

184
doc/src/bond_bpm_spring_plastic.rst Normal file
View File

@ -0,0 +1,184 @@
.. index:: bond_style bpm/spring/plastic
bond_style bpm/spring/plastic command
=====================================
Syntax
""""""
.. code-block:: LAMMPS
bond_style bpm/spring/plastic keyword value attribute1 attribute2 ...
* optional keyword = *overlay/pair* or *store/local* or *smooth* or *normalize* or *break*
.. parsed-literal::
*store/local* values = fix_ID N attributes ...
* fix_ID = ID of associated internal fix to store data
* N = prepare data for output every this many timesteps
* attributes = zero or more of the below attributes may be appended
*id1, id2* = IDs of two atoms in the bond
*time* = the timestep the bond broke
*x, y, z* = the center of mass position of the two atoms when the bond broke (distance units)
*x/ref, y/ref, z/ref* = the initial center of mass position of the two atoms (distance units)
*overlay/pair* value = *yes* or *no*
bonded particles will still interact with pair forces
*smooth* value = *yes* or *no*
smooths bond forces near the breaking point
*normalize* value = *yes* or *no*
normalizes bond forces by the reference length
*break* value = *yes* or *no*
indicates whether bonds break during a run
Examples
""""""""
.. code-block:: LAMMPS
bond_style bpm/spring/plastic
bond_coeff 1 1.0 0.05 0.1 0.02
bond_style bpm/spring/plastic myfix 1000 time id1 id2
dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
dump_modify 1 write_header no
Description
"""""""""""
.. versionadded:: TBD
The *bpm/spring/plastic* bond style computes forces based on
deviations from the initial reference state of the two atoms and the
strain history. The reference length of the bond :math:`r_0` is stored
by each bond when it is first computed in the setup of a run. Initially,
the equilibrium length of each bond :math:`r_\mathrm{eq}` is set equal
to :math:`r_0` but can evolve. data is then preserved across run commands
and is written to :doc:`binary restart files <restart>` such that restarting
the system will not modify either of these quantities.
This bond style only applies central-body forces which conserve the
translational and rotational degrees of freedom of a bonded set of
particles. The force has a magnitude of
.. math::
F = -k (r_\mathrm{eq} - r) w
where :math:`k` is a stiffness, :math:`r` is the current distance between
the two particles, and :math:`w` is an optional smoothing factor discussed
below. If the bond stretches beyond a strain of :math:`\epsilon_p` in compression
or extension, it will plastically activate and :math:`r_\mathrm{eq}` will evolve
to ensure :math:`|(r-r_\mathrm{eq})/r_\mathrm{eq}|` never exceeds :math:`\epsilon_p`.
Therefore, if a bond is continually loaded in either tension or compression, the
force will initially grow elastically before plateauing. See
:ref:`(Clemmer) <plastic-Clemmer>` for more details on these mechanics.
Bonds will break at a strain of :math:`\epsilon_c`. This is done by setting
the bond type to 0 such that forces are no longer computed.
An additional damping force is applied to the bonded
particles. This forces is proportional to the difference in the
normal velocity of particles:
.. math::
F_D = - \gamma w (\hat{r} \bullet \vec{v})
where :math:`\gamma` is the damping strength, :math:`\hat{r}` is the
radial normal vector, and :math:`\vec{v}` is the velocity difference
between the two particles.
The smoothing factor :math:`w` is constructed such that forces smoothly
go to zero, avoiding discontinuities, as bonds approach the critical
breaking strain
.. math::
w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data
<read_data>` or :doc:`read_restart <read_restart>` commands:
* :math:`k` (force/distance units)
* :math:`\epsilon_c` (unitless)
* :math:`\gamma` (force/velocity units)
* :math:`\epsilon_p` (unitless)
See the :doc:`bpm/spring doc page <bond_bpm_spring>` for information on
the *smooth*, *normalize*, *break*, *overlay/pair*, and *store/local*
keywords.
Note that when unbroken bonds are dumped to a file via the
:doc:`dump local <dump>` command, bonds with type 0 (broken bonds)
are not included.
The :doc:`delete_bonds <delete_bonds>` command can also be used to
query the status of broken bonds or permanently delete them, e.g.:
.. code-block:: LAMMPS
delete_bonds all stats
delete_bonds all bond 0 remove
----------
Restart and other info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This bond style writes the reference state and plastic history of each
bond to :doc:`binary restart files <restart>`. Loading a restart file
will properly restore bonds. However, the reference state is NOT written
to data files. Therefore reading a data file will not restore bonds and
will cause their reference states to be redefined.
The potential energy and the single() function of this bond style
returns zero. The single() function also calculates two extra bond
quantities, the initial distance :math:`r_0` and the current equilibrium
length :math:`r_eq`. These extra quantities can be accessed by the
:doc:`compute bond/local <compute_bond_local>` command as *b1* and *b2*,
respectively.
Restrictions
""""""""""""
This bond style is part of the BPM package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
By default if pair interactions between bonded atoms are to be disabled,
this bond style requires setting
.. code-block:: LAMMPS
special_bonds lj 0 1 1 coul 1 1 1
and :doc:`newton <newton>` must be set to bond off. If the *overlay/pair*
keyword is set to *yes*, this bond style alternatively requires setting
.. code-block:: LAMMPS
special_bonds lj/coul 1 1 1
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`bond bpm/spring <bond_bpm_spring>`
Default
"""""""
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
----------
.. _plastic-Clemmer:
**(Clemmer)** Clemmer and Lechman, Powder Technology (2025).

2
doc/src/bond_harmonic.rst
View File

@ -60,6 +60,8 @@ Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
:doc:`bond style harmonic/shift <bond_harmonic_shift>`,
:doc:`bond style harmonic/shift/cut <bond_harmonic_shift_cut>`
Default
"""""""

17
doc/src/bond_harmonic_shift.rst
View File

@ -31,9 +31,15 @@ the potential
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the
critical distance. The potential energy has the value
:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`. This
bond style differs from :doc:`bond_style harmonic <bond_harmonic>`
by the value of the potential energy.
The equivalent spring constant value *K* for use with :doc:`bond_style
harmonic <bond_harmonic>` can be computed using :math:`K =
U_{\text{min}} / [(r_0-r_c)^2]`.
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@ -41,9 +47,7 @@ the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* :math:`U_{\text{min}}` (energy)
* :math:`r_0` (distance)
* :math:`r_c` (distance)
----------
@ -63,7 +67,8 @@ Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`bond_harmonic <bond_harmonic>`
:doc:`bond style harmonic <bond_harmonic>`,
:doc:`bond style harmonic/shift/cut <bond_harmonic_shift_cut>`
Default
"""""""

11
doc/src/bond_harmonic_shift_cut.rst
View File

@ -31,9 +31,14 @@ uses the potential
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the
critical distance. The bond potential is zero and thus its force also
zero for distances :math:`r > r_c`. The potential energy has the value
:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`.
The equivalent spring constant value *K* for use with :doc:`bond_style
harmonic <bond_harmonic>` for :math:`r <= r_c`, can be computed using
:math:`K = U_{\text{min}} / [(r_0-r_c)^2]`
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in

3
doc/src/bond_style.rst
View File

@ -10,7 +10,7 @@ Syntax
bond_style style args
* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *bpm/spring/plastic* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/restrain* *harmonic/shift* or *harmonic/shift/cut* or *lepton* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
* args = none for any style except *hybrid*
@ -86,6 +86,7 @@ accelerated styles exist.
* :doc:`bpm/rotational <bond_bpm_rotational>` - breakable bond with forces and torques based on deviation from reference state
* :doc:`bpm/spring <bond_bpm_spring>` - breakable bond with forces based on deviation from reference length
* :doc:`bpm/spring/plastic <bond_bpm_spring_plastic>` - a similar breakable bond with plastic yield
* :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
* :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
* :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles

Some files were not shown because too many files have changed in this diff Show More