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Axel Kohlmeyer
2025-03-25 14:22:55 -04:00
parent c36e1a9c8e 9e241df062
commit bafd2a8d6b
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.github/CODEOWNERS vendored
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@ -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
@ -101,7 +103,8 @@ src/group.* @sjplimp
src/improper.* @sjplimp
src/info.* @akohlmey
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/lmptype.h @sjplimp
src/label_map.* @jrgissing @akohlmey
src/library.* @sjplimp @akohlmey
src/main.cpp @sjplimp
src/min_*.* @sjplimp

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# LAMMPS Release Steps
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.
### Preparing a 'next\_release' branch
Create a 'next\_release' branch off 'develop' and make the following changes:
- set the LAMMPS\_VERSION define to the planned release date in
src/version.h in the format "D Mmm YYYY" or "DD Mmm YYYY"
- remove the LAMMPS\_UPDATE define in src/version.h
- update the release date in doc/lammps.1
- update all TBD arguments for ..versionadded::, ..versionchanged::
..deprecated:: to the planned release date in the format "DMmmYYYY" or
"DDMmmYYYY"
- check release notes for merged new features and check if
..versionadded:: or ..versionchanged:: are missing and need to be
added
Submit this pull request. 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'.
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
git pull
git checkout release
git pull
git merge --ff-only develop
git tag -s -m "LAMMPS feature release 4 February 2025" patch_4Feb2025
git push git@github.com:lammps/lammps.git --tags develop release
```
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.
### Prepare pre-compiled packages, update packages to GitHub
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.
#### 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=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
cmake --build build-release --target all
cmake --build build-release --target install
/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
exit # fedora 41 container
cd ..
```
The resulting tar archive can be uploaded to the GitHub release page with:
``` sh
gh release upload patch_4Feb2025 lammps-linux-x86_64-4Feb2025.tar.gz
```
#### Linux x86_64 Flatpak bundle with GUI included
Make sure you have the `flatpak` and `flatpak-builder` packages
installed locally (they require binaries that run with elevated
privileges and thus cannot be used from the container) and build a
LAMMPS and LAMMPS-GUI flatpak bundle in the `release-packages` folder
with:
``` sh
cd release-packages
flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
flatpak-builder --force-clean --verbose --repo=$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.
### Prerequesites
Before making a stable release all remaining backported bugfixes shall
be released as a (final) stable update release (see below).
A LAMMPS stable release process starts like a feature release (see
above), only that this feature release is called a "Stable Release
Candidate" and no assets are uploaded to GitHub.
### Synchronize 'maintenance' branch with 'release'
The state of the 'release' branch is then transferred to the
'maintenance' branch (which will have diverged significantly from
'release' due to the selectively backported bug fixes).
### Fast-forward merge of 'maintenance' into 'stable' and apply tag
At this point it should be possible to do a fast-forward merge of
'maintenance' to 'stable' and then apply the stable\_DMmmYYYY tag.
### Push branches and tags
## LAMMPS Stable Update Release
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.

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# GitHub action to build LAMMPS on Linux with gcc and C++23
name: "Check for C++23 Compatibility"
on:
push:
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build with C++23 support enabled
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
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 \
mpi-default-bin \
mpi-default-dev \
ninja-build \
python3-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-cpp23-ccache-${{ github.sha }}
restore-keys: linux-cpp23-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/most.cmake \
-C cmake/presets/kokkos-openmp.cmake \
-D CMAKE_CXX_STANDARD=23 \
-D CMAKE_CXX_COMPILER=g++ \
-D CMAKE_C_COMPILER=gcc \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D CMAKE_BUILD_TYPE=Debug \
-D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
-D DOWNLOAD_POTENTIALS=off \
-D BUILD_MPI=on \
-D BUILD_SHARED_LIBS=on \
-D BUILD_TOOLS=off \
-D ENABLE_TESTING=off \
-D MLIAP_ENABLE_ACE=on \
-D MLIAP_ENABLE_PYTHON=off \
-D PKG_AWPMD=on \
-D PKG_GPU=on \
-D GPU_API=opencl \
-D PKG_KOKKOS=on \
-D PKG_LATBOLTZ=on \
-D PKG_MDI=on \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=off \
-D PKG_MOLFILE=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

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@ -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 \

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

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# GitHub action to build LAMMPS on Linux and run selected regression tests
name: "Kokkos OpenMP Regression Test"
on:
push:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build LAMMPS with Kokkos OpenMP
# restrict to official LAMMPS repository
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 6
matrix:
idx: [ 'pair-0', 'pair-1', 'fix-0', 'fix-1', 'compute', 'misc' ]
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
show-progress: false
- name: Install extra packages
run: |
sudo apt-get update
sudo apt-get install -y ccache ninja-build libeigen3-dev \
libcurl4-openssl-dev python3-dev \
mpi-default-bin mpi-default-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-kokkos-ccache-${{ github.sha }}
restore-keys: linux-kokkos-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install numpy pyyaml junit_xml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/basic.cmake \
-C cmake/presets/kokkos-openmp.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=off \
-D DOWNLOAD_POTENTIALS=off \
-D PKG_AMOEBA=on \
-D PKG_ASPHERE=on \
-D PKG_BROWNIAN=on \
-D PKG_CLASS2=on \
-D PKG_COLLOID=on \
-D PKG_CORESHELL=on \
-D PKG_DIPOLE=on \
-D PKG_DPD-BASIC=on \
-D PKG_EXTRA-COMPUTE=on \
-D PKG_EXTRA-FIX=on \
-D PKG_EXTRA-MOLECULE=on \
-D PKG_EXTRA-PAIR=on \
-D PKG_GRANULAR=on \
-D PKG_LEPTON=on \
-D PKG_MC=on \
-D PKG_MEAM=on \
-D PKG_POEMS=on \
-D PKG_PYTHON=on \
-D PKG_QEQ=on \
-D PKG_REAXFF=on \
-D PKG_REPLICA=on \
-D PKG_SRD=on \
-D PKG_SPH=on \
-D PKG_VORONOI=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Regression Tests for Selected Examples
shell: bash
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/get_kokkos_input.py \
--examples-top-level=examples --batch-size=50 \
--filter-out="balance;fire;gcmc;granregion;hyper;mc;mdi;mliap;neb;pace;prd;pour;python;rigid;snap;streitz;shear;ttm"
export OMP_PROC_BIND=false
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_kokkos_openmp.yaml \
--list-input=input-list-${{ matrix.idx }}-kk.txt \
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log \
--quick-max=100
tar -cvf kokkos-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
- name: Upload artifacts
uses: actions/upload-artifact@v4
with:
name: kokkos-regression-test-artifact-${{ matrix.idx }}
path: kokkos-regression-test-${{ matrix.idx }}.tar
merge:
runs-on: ubuntu-latest
needs: build
steps:
- name: Merge Artifacts
uses: actions/upload-artifact/merge@v4
with:
name: merged-kokkos-regresssion-artifact
pattern: kokkos-regression-test-artifact-*

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# 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

83
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)
@ -118,7 +121,7 @@ endif()
# silence excessive warnings for new Intel Compilers
if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
set(CMAKE_TUNE_DEFAULT "-fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
endif()
# silence excessive warnings for PGI/NVHPC compilers
@ -141,19 +144,31 @@ endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
endif()
# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
# we *require* C++11 without extensions but prefer C++17.
# Kokkos requires at least C++17 (currently)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
set(CMAKE_CXX_STANDARD 17)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(CMAKE_CXX_STANDARD LESS 17)
message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
# turn off C++17 check in lmptype.h
if(LAMMPS_CXX11)
add_compile_definitions(LAMMPS_CXX11)
endif()
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
@ -165,6 +180,7 @@ if(MSVC)
add_compile_options(/wd4267)
add_compile_options(/wd4250)
add_compile_options(/EHsc)
add_compile_options(/utf-8)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
@ -193,7 +209,7 @@ endif()
########################################################################
# User input options #
########################################################################
# backward compatibility with CMake before 3.12 and older LAMMPS documentation
# backward compatibility with older LAMMPS documentation
if (PYTHON_EXECUTABLE)
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
endif()
@ -209,6 +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)
@ -346,6 +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
######################################################
@ -398,8 +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 ${LAMMPS_SIZES} LAMMPS_SIZES)
@ -578,6 +611,16 @@ foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE
endif()
endforeach()
# settings for misc packages and styles
if(PKG_MISC)
option(LAMMPS_ASYNC_IMD "Asynchronous IMD processing" OFF)
mark_as_advanced(LAMMPS_ASYNC_IMD)
if(LAMMPS_ASYNC_IMD)
target_compile_definitions(lammps PRIVATE -DLAMMPS_ASYNC_IMD)
message(STATUS "Using IMD in asynchronous mode")
endif()
endif()
# optionally enable building script wrappers using swig
option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
if(WITH_SWIG)
@ -587,13 +630,8 @@ endif()
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
separate_arguments(CMAKE_TUNE_FLAGS)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
target_compile_options(lammps PRIVATE ${_FLAG})
# skip these flags when linking the main executable
if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma"))))
target_compile_options(lmp PRIVATE ${_FLAG})
endif()
endforeach()
target_compile_options(lammps PRIVATE ${CMAKE_TUNE_FLAGS})
target_compile_options(lmp PRIVATE ${CMAKE_TUNE_FLAGS})
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
@ -822,9 +860,15 @@ foreach(_DEF ${LAMMPS_DEFINES})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
endforeach()
if(BUILD_SHARED_LIBS)
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(TARGETS lammps EXPORT LAMMPS_Targets
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
if(NOT BUILD_MPI)
install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(TARGETS mpi_stubs EXPORT LAMMPS_Targets
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
endif()
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
@ -892,7 +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
@ -1076,12 +1120,15 @@ if(BUILD_TOOLS)
message(STATUS "<<< Building Tools >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
message(STATUS "<<< Building LAMMPS-GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)
message(STATUS "Loading LAMMPS library as plugin at run time")
else()
message(STATUS "Linking LAMMPS library at compile time")
endif()
if(BUILD_WHAM)
message(STATUS "<<< Building WHAM >>>")
endif()
endif()
if(ENABLE_TESTING)
message(STATUS "<<< Building Unit Tests >>>")

120
cmake/Modules/CodeCoverage.cmake
View File

@ -7,76 +7,76 @@
# For Python coverage the coverage package needs to be installed
###############################################################################
if(ENABLE_COVERAGE)
find_program(GCOVR_BINARY gcovr)
find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
find_program(GCOVR_BINARY gcovr)
find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
find_program(COVERAGE_BINARY coverage)
find_package_handle_standard_args(COVERAGE DEFAULT_MSG COVERAGE_BINARY)
find_program(COVERAGE_BINARY coverage)
find_package_handle_standard_args(COVERAGE DEFAULT_MSG COVERAGE_BINARY)
if(GCOVR_FOUND)
get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
if(GCOVR_FOUND)
get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
add_custom_target(
gen_coverage_xml
COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating XML coverage report..."
)
add_custom_target(
gen_coverage_xml
COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating XML coverage report..."
)
set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
add_custom_target(coverage_html_folder
COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
add_custom_target(coverage_html_folder
COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
add_custom_target(
gen_coverage_html
COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating HTML coverage report..."
)
add_dependencies(gen_coverage_html coverage_html_folder)
add_custom_target(
gen_coverage_html
COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Generating HTML coverage report..."
)
add_dependencies(gen_coverage_html coverage_html_folder)
add_custom_target(clean_coverage_html
${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
COMMENT "Deleting HTML coverage report..."
)
add_custom_target(clean_coverage_html
${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
COMMENT "Deleting HTML coverage report..."
)
add_custom_target(reset_coverage
${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
*/*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Deleting coverage data files..."
)
add_dependencies(reset_coverage clean_coverage_html)
endif()
add_custom_target(reset_coverage
${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
*/*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
*/*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
COMMENT "Deleting coverage data files..."
)
add_dependencies(reset_coverage clean_coverage_html)
endif()
if(COVERAGE_FOUND)
set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
if(COVERAGE_FOUND)
set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
add_custom_command(
OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
COMMAND ${COVERAGE_BINARY} combine
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Combine Python coverage files..."
)
add_custom_command(
OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
COMMAND ${COVERAGE_BINARY} combine
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Combine Python coverage files..."
)
add_custom_target(
gen_python_coverage_html
COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating HTML Python coverage report..."
)
add_custom_target(
gen_python_coverage_html
COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating HTML Python coverage report..."
)
add_custom_target(
gen_python_coverage_xml
COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating XML Python coverage report..."
)
endif()
add_custom_target(
gen_python_coverage_xml
COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
COMMENT "Generating XML Python coverage report..."
)
endif()
endif()

67
cmake/Modules/CodingStandard.cmake
View File

@ -1,40 +1,39 @@
# 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 .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for permission errors")
add_custom_target(
fix-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix permission errors")
endif()
add_custom_target(
check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for whitespace errors")
add_custom_target(
check-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for homepage URL errors")
add_custom_target(
check-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Check for permission errors")
add_custom_target(
fix-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix whitespace errors")
add_custom_target(
fix-homepage
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix homepage URL errors")
add_custom_target(
fix-permissions
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix permission errors")
endif()

7
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)
@ -110,6 +110,7 @@ if(BUILD_DOC)
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} ${DOCENV_DEPS} ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
COMMAND ${Python3_EXECUTABLE} ${LAMMPS_DOC_DIR}/utils/make-globbed-tocs.py -d ${LAMMPS_DOC_DIR}/src
COMMAND Sphinx::sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF

6
cmake/Modules/FindVORO.cmake
View File

@ -21,9 +21,9 @@ if(VORO_FOUND)
set(VORO_LIBRARIES ${VORO_LIBRARY})
set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
if(NOT TARGET VORO::VORO)
add_library(VORO::VORO UNKNOWN IMPORTED)
set_target_properties(VORO::VORO PROPERTIES
if(NOT TARGET VORO::voro++)
add_library(VORO::voro++ UNKNOWN IMPORTED)
set_target_properties(VORO::voro++ PROPERTIES
IMPORTED_LOCATION "${VORO_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${VORO_INCLUDE_DIR}")
endif()

26
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -34,8 +34,26 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# C++11 is required
set(CMAKE_CXX_STANDARD 11)
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)

2
cmake/Modules/Packages/H5MD.cmake
View File

@ -3,7 +3,7 @@ enable_language(C)
# we don't use the parallel i/o interface.
set(HDF5_PREFER_PARALLEL FALSE)
find_package(HDF5 REQUIRED)
find_package(HDF5 COMPONENTS C REQUIRED)
# parallel HDF5 will import incompatible MPI headers with a serial build
if((NOT BUILD_MPI) AND HDF5_IS_PARALLEL)

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})

24
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -7,10 +7,13 @@ endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
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()
# Adding OpenMP compiler flags without the checks done for
# BUILD_OMP can result in compile failures. Enforce consistency.
if(Kokkos_ENABLE_OPENMP)
@ -18,6 +21,15 @@ if(Kokkos_ENABLE_OPENMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
endif()
endif()
if(Kokkos_ENABLE_SERIAL)
if(NOT (Kokkos_ENABLE_OPENMP OR Kokkos_ENABLE_THREADS OR
Kokkos_ENABLE_CUDA OR Kokkos_ENABLE_HIP OR Kokkos_ENABLE_SYCL
OR Kokkos_ENABLE_OPENMPTARGET))
option(Kokkos_ENABLE_ATOMICS_BYPASS "Disable atomics for Kokkos Serial Backend" ON)
mark_as_advanced(Kokkos_ENABLE_ATOMICS_BYPASS)
endif()
endif()
########################################################################
option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
@ -45,8 +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/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" 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)
@ -71,7 +83,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.3.01 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)

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)

98
cmake/Modules/Packages/ML-PACE.cmake
View File

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

2
cmake/Modules/Packages/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()

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

@ -54,5 +54,5 @@ else()
if(NOT VORO_FOUND)
message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
endif()
target_link_libraries(lammps PRIVATE VORO::VORO)
target_link_libraries(lammps PRIVATE VORO::voro++)
endif()

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

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

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)

15
cmake/presets/kokkos-sycl-intel.cmake
View File

@ -6,13 +6,24 @@ set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SYCL ON CACHE BOOL "" FORCE)
set(FFT "MKL" CACHE STRING "" FORCE)
set(FFT_KOKKOS "MKL_GPU" CACHE STRING "" FORCE)
unset(USE_INTERNAL_LINALG)
unset(USE_INTERNAL_LINALG CACHE)
set(BLAS_VENDOR "Intel10_64_dyn")
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
set(CMAKE_CXX_COMPILER icpx CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER icx CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
# Silence everything
set(CMAKE_CXX_FLAGS "-w" CACHE STRING "" FORCE)
set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-max-parallel-link-jobs=32 -fsycl-targets=spir64_gen -Xsycl-target-backend \"-device 12.60.7\" " CACHE STRING "" FORCE)
set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)
#set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-targets=spir64_gen " CACHE STRING "" FORCE)
#set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)
set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code " CACHE STRING "" FORCE)
set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel " CACHE STRING "" FORCE)

21
cmake/presets/oneapi.cmake
View File

@ -3,26 +3,9 @@
set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_CXX "icpx" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "icx" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
# force using internal BLAS/LAPCK since external ones may not be ABI compatible
set(USE_INTERNAL_LINALG ON CACHE BOOL "" FORCE)

7
doc/.gitignore vendored
View File

@ -17,3 +17,10 @@
*.el
/utils/sphinx-config/_static/mathjax
/utils/sphinx-config/_static/polyfill.js
/src/pairs.rst
/src/bonds.rst
/src/angles.rst
/src/dihedrals.rst
/src/impropers.rst
/src/computes.rst
/src/fixes.rst

54
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 $$?), 0)
HAS_PYTHON3 = YES
@ -31,10 +33,14 @@ endif
ifeq ($(shell type pdflatex >/dev/null 2>&1; echo $$?), 0)
ifeq ($(shell type latexmk >/dev/null 2>&1; echo $$?), 0)
HAS_PDFLATEX = YES
HAS_PDFLATEX = YES
endif
endif
ifeq ($(shell type pandoc >/dev/null 2>&1; echo $$?), 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:
@ -83,7 +90,10 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
-e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
-e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
globbed-tocs:
$(PYTHON) $(BUILDDIR)/utils/make-globbed-tocs.py -d $(RSTDIR)
html: 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
@(\
@ -113,26 +123,24 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@rm -rf html/PDF/.[sg]*
@echo "Build finished. The HTML pages are in doc/html."
fasthtml: xmlgen $(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."
spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
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
@(\
. $(VENV)/bin/activate ; \
@ -143,7 +151,7 @@ spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives
)
@echo "Spell check finished."
epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@if [ "$(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 epub/JPG
@ -166,7 +174,7 @@ mobi: epub
@ebook-convert LAMMPS.epub LAMMPS.mobi
@echo "Conversion finished. The MOBI manual file is created."
pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@$(MAKE) $(MFLAGS) -C graphviz all
@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi

20
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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.

9
doc/documentation_conventions.md
View File

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

2
doc/doxygen/Doxyfile.in
View File

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

15
doc/github-development-workflow.md
View File

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

6
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "29 August 2024" "2024-08-29"
.TH LAMMPS "1" "4 February 2025" "2025-02-04"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 29 August 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

41
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@ -160,7 +160,7 @@ with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility
with compiler versions in use. If compilation with OpenMP enabled fails
because of your compiler requiring strict OpenMP 4.0 semantics, you can
change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the
``LMP_INC`` variable in your makefile, or add it to the command line
``LMP_INC`` variable in your makefile, or add it to the command-line flags
while configuring with CMake. LAMMPS will auto-detect a suitable setting
for most GNU, Clang, and Intel compilers.
@ -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
@ -321,15 +328,23 @@ LAMMPS.
you would have to install a newer compiler that supports C++11;
either as a binary package or through compiling from source.
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
achieve optimal performance. You need to include these in the
``CCFLAGS`` and ``LINKFLAGS`` settings above. For details, see the
documentation for the individual packages listed on the
:doc:`Speed_packages` page. Or examine these files in the
``src/MAKE/OPTIONS`` directory. They correspond to each of the 5
accelerator packages and their hardware variants:
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
achieve optimal performance. You need to include these in the
``CCFLAGS`` and ``LINKFLAGS`` settings above. For details, see the
documentation for the individual packages listed on the
:doc:`Speed_packages` page. Or examine these files in the
``src/MAKE/OPTIONS`` directory. They correspond to each of the 5
accelerator packages and their hardware variants:
.. code-block:: bash
@ -502,6 +517,8 @@ using CMake or Make.
# chain.x, micelle2d.x, msi2lmp, phana,
# stl_bin2txt
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build LAMMPS-GUI
-D BUILD_WHAM=value # yes (default). Download and build WHAM;
# only available for BUILD_LAMMPS_GUI=yes
The generated binaries will also become part of the LAMMPS installation
(see below).

41
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@ -8,7 +8,7 @@ packages. Links to those pages on the :doc:`Build overview <Build>`
page.
The following text assumes some familiarity with CMake and focuses on
using the command line tool ``cmake`` and what settings are supported
using the command-line tool ``cmake`` and what settings are supported
for building LAMMPS. A more detailed tutorial on how to use CMake
itself, the text mode or graphical user interface, to change the
generated output files for different build tools and development
@ -16,7 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
.. note::
LAMMPS currently requires that CMake version 3.16 or later is available.
LAMMPS currently requires that CMake version 3.20 or later is available.
.. warning::
@ -32,29 +32,29 @@ environments is on a :doc:`separate page <Howto_cmake>`.
Advantages of using CMake
^^^^^^^^^^^^^^^^^^^^^^^^^
CMake is an alternative to compiling LAMMPS in the traditional way
through :doc:`(manually customized) makefiles <Build_make>`. Using
CMake has multiple advantages that are specifically helpful for
people with limited experience in compiling software or for people
that want to modify or extend LAMMPS.
CMake is the preferred way of compiling LAMMPS in contrast to the legacy
build system based on GNU make and through :doc:`(manually customized)
makefiles <Build_make>`. Using CMake has multiple advantages that are
specifically helpful for people with limited experience in compiling
software or for people that want to modify or extend LAMMPS.
- CMake can detect available hardware, tools, features, and libraries
and adapt the LAMMPS default build configuration accordingly.
- CMake can generate files for different build tools and integrated
development environments (IDE).
- CMake supports customization of settings with a command line, text
- CMake supports customization of settings with a command-line, text
mode, or graphical user interface. No manual editing of files,
knowledge of file formats or complex command line syntax is required.
knowledge of file formats or complex command-line syntax is required.
- All enabled components are compiled in a single build operation.
- Automated dependency tracking for all files and configuration options.
- Support for true out-of-source compilation. Multiple configurations
- Support for true out-of-source compilation. Multiple configurations
and settings with different choices of LAMMPS packages, settings, or
compilers can be configured and built concurrently from the same
source tree.
- 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:
@ -68,7 +68,7 @@ that purpose you can use either the command-line utility ``cmake`` (or
graphical utility ``cmake-gui``, or use them interchangeably. The
second step is then the compilation and linking of all objects,
libraries, and executables using the selected build tool. Here is a
minimal example using the command line version of CMake to build LAMMPS
minimal example using the command-line version of CMake to build LAMMPS
with no add-on packages enabled and no customization:
.. code-block:: bash
@ -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
@ -131,7 +138,7 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
configuration step. The cache file contains all current CMake settings.
To modify settings, enable or disable features, you need to set
*variables* with either the ``-D`` command line flag (``-D
*variables* with either the ``-D`` command-line flag (``-D
VARIABLE1_NAME=value``) or change them in the text mode of the graphical
user interface. The ``-D`` flag can be used several times in one command.
@ -141,11 +148,11 @@ a different compiler tool chain. Those are loaded with the ``-C`` flag
(``-C ../cmake/presets/basic.cmake``). This step would only be needed
once, as the settings from the preset files are stored in the
``CMakeCache.txt`` file. It is also possible to customize the build
by adding one or more ``-D`` flags to the CMake command line.
by adding one or more ``-D`` flags to the CMake command.
Generating files for alternate build tools (e.g. Ninja) and project files
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
command line flag. A list of available generator settings for your
command-line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
.. _cmake_multiconfig:

10
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View File

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

169
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@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
* :ref:`LEPTON <lepton>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MISC <misc>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
@ -209,7 +210,7 @@ necessary for ``hipcc`` and the linker to work correctly.
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero back ends. To use
CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
command-line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne.
@ -232,7 +233,7 @@ option in preparations to run on Aurora system at Argonne.
.. code:: bash
# CUDA target (not recommended, use GPU_ARCH=cuda)
# CUDA target (not recommended, use GPU_API=cuda)
# !!! DO NOT set CMAKE_CXX_COMPILER !!!
export HIP_PLATFORM=nvcc
export HIP_PATH=/path/to/HIP/install
@ -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``
@ -421,9 +421,10 @@ minutes to hours) to build. Of course you only need to do that once.)
cmake build system. The ``lib/kim/Install.py`` script supports a
``CMAKE`` environment variable if the cmake executable is named other
than ``cmake`` on your system. Additional environment variables may be
provided on the command line for use by cmake. For example, to use the
``cmake3`` executable and tell it to use the gnu version 11 compilers
to build KIM, one could use the following command line.
set with the ``make`` command for use by cmake. For example, to use the
``cmake3`` executable and tell it to use the GNU version 11 compilers
called ``g++-11``, ``gcc-11`` and ``gfortran-11`` to build KIM, one
could use the following command.
.. code-block:: bash
@ -546,16 +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
@ -571,105 +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
@ -678,7 +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
@ -701,7 +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::
@ -1125,11 +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::
@ -1145,7 +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
@ -2018,7 +2030,7 @@ TBB and MKL.
.. _mdi:
MDI package
-----------------------------
-----------
.. tabs::
@ -2045,6 +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
@ -2191,7 +2234,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
from the sources in the *lib* folder (including the essential
libqmmm.a) are not included in the static LAMMPS library and
(currently) not installed, while their code is included in the
shared LAMMPS library. Thus a typical command line to configure
shared LAMMPS library. Thus a typical command to configure
building LAMMPS for QMMM would be:
.. code-block:: bash

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
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@ -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 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.
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

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

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

1
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@ -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>`

13
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@ -43,7 +43,7 @@ OPT.
* :doc:`brownian/asphere <fix_brownian>`
* :doc:`brownian/sphere <fix_brownian>`
* :doc:`charge/regulation <fix_charge_regulation>`
* :doc:`cmap <fix_cmap>`
* :doc:`cmap (k) <fix_cmap>`
* :doc:`colvars <fix_colvars>`
* :doc:`controller <fix_controller>`
* :doc:`damping/cundall <fix_damping_cundall>`
@ -58,6 +58,7 @@ OPT.
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield (k) <fix_efield>`
* :doc:`efield/lepton <fix_efield_lepton>`
* :doc:`efield/tip4p <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode>`
@ -134,7 +135,7 @@ OPT.
* :doc:`nve/dot <fix_nve_dot>`
* :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
* :doc:`nve/eff <fix_nve_eff>`
* :doc:`nve/limit <fix_nve_limit>`
* :doc:`nve/limit (k) <fix_nve_limit>`
* :doc:`nve/line <fix_nve_line>`
* :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
* :doc:`nve/noforce <fix_nve_noforce>`
@ -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>`
@ -178,6 +181,7 @@ OPT.
* :doc:`python/move <fix_python_move>`
* :doc:`qbmsst <fix_qbmsst>`
* :doc:`qeq/comb (o) <fix_qeq_comb>`
* :doc:`qeq/ctip <fix_qeq>`
* :doc:`qeq/dynamic <fix_qeq>`
* :doc:`qeq/fire <fix_qeq>`
* :doc:`qeq/point <fix_qeq>`
@ -186,10 +190,11 @@ OPT.
* :doc:`qeq/slater <fix_qeq>`
* :doc:`qmmm <fix_qmmm>`
* :doc:`qtb <fix_qtb>`
* :doc:`qtpie/reaxff <fix_qtpie_reaxff>`
* :doc:`rattle <fix_shake>`
* :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`recenter (k) <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rheo <fix_rheo>`
* :doc:`rheo/oxidation <fix_rheo_oxidation>`
@ -267,7 +272,7 @@ OPT.
* :doc:`wall/piston <fix_wall_piston>`
* :doc:`wall/reflect (k) <fix_wall_reflect>`
* :doc:`wall/reflect/stochastic <fix_wall_reflect_stochastic>`
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region (k) <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
* :doc:`wall/table <fix_wall>`

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

6
doc/src/Commands_pair.rst
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@ -44,7 +44,7 @@ OPT.
* :doc:`born/coul/wolf/cs (g) <pair_cs>`
* :doc:`born/gauss <pair_born_gauss>`
* :doc:`bpm/spring <pair_bpm_spring>`
* :doc:`brownian (o) <pair_brownian>`
* :doc:`brownian (ko) <pair_brownian>`
* :doc:`brownian/poly (o) <pair_brownian>`
* :doc:`buck (giko) <pair_buck>`
* :doc:`buck/coul/cut (giko) <pair_buck>`
@ -59,6 +59,7 @@ OPT.
* :doc:`comb (o) <pair_comb>`
* :doc:`comb3 <pair_comb>`
* :doc:`cosine/squared <pair_cosine_squared>`
* :doc:`coul/ctip <pair_coul>`
* :doc:`coul/cut (gko) <pair_coul>`
* :doc:`coul/cut/dielectric <pair_dielectric>`
* :doc:`coul/cut/global (o) <pair_coul>`
@ -79,6 +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>`
@ -113,7 +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
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@ -1,6 +1,10 @@
Removed commands and packages
=============================
.. contents::
------
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or
replacements. LAMMPS has special dummy styles implemented, that will
@ -8,94 +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
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@ -24,4 +24,5 @@ of time and requests from the LAMMPS user community.
Classes
Developer_platform
Developer_utils
Developer_internal
Developer_grid

41
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@ -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
==================================

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

2
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@ -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
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@ -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

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@ -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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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

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

15
doc/src/Developer_utils.rst
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@ -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

4
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View File

@ -96,8 +96,8 @@ 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",
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
utils::print(screen, "{}, {}, {}\n",
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
}
}

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

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

823
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@ -4,9 +4,237 @@ Error and warning 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.
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.
.. 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:
@ -34,8 +262,8 @@ 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:
@ -45,12 +273,589 @@ 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
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 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, 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 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, or improper) 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 - simulation unstable
---------------------------------------------
This error usually occurs due to issues with system geometry or the potential in
use. See :ref:`Pressure, forces, positions becoming NaN or Inf <hint07>` above in the
general troubleshooting section.
.. _err0007:
Non-numeric pressure - simulation unstable
------------------------------------------
This error usually occurs due to issues with system geometry or the potential in
use. See :ref:`Pressure, forces, positions becoming NaN or Inf <hint07>` above in the
general troubleshooting section.
.. _err0008:
Lost atoms ...
--------------
A simulation stopping with an error due to lost atoms can have multiple
causes. In the majority of cases, lost atoms are unexpected and a result
of extremely high velocities causing instabilities in the system, and
those 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 resolved
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 has become too large relative to the size of a
neighbor bin and LAMMPS is unable to store the needed number of
bins. This typically implies the simulation box has expanded too far.
This can happen 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.
.. _err0010:
Unrecognized pair 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 pair 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 to enable
the package, but to forget to run commands to rebuild (e.g., to run the final
``make`` or ``cmake`` command).
If this error is occurring 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.
.. _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
:doc:`Section 5.2. 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. Nevertheless, 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.

7
doc/src/Errors_messages.rst
View File

@ -6233,8 +6233,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Atom IDs must be positive integers.
*One or more atom IDs is too big*
The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
setting in your LAMMPS build. See the :doc:`Build settings <Build_settings>` page for more info.
The limit on atom IDs is set by the SMALLBIG, BIGBIG
setting in your LAMMPS build. See the
:doc:`Build settings <Build_settings>` page for more info.
*One or more atom IDs is zero*
Either all atoms IDs must be zero or none of them.
@ -7774,7 +7775,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Too few values in body section of molecule file*
Self-explanatory.
*Too many -pk arguments in command line*
*Too many -pk arguments in command-line*
The string formed by concatenating the arguments is too long. Use a
package command in the input script instead.

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 |

79
doc/src/Fortran.rst
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@ -16,7 +16,7 @@ compiled alongside the code using it from the source code in
``fortran/lammps.f90`` *and* with the same compiler used to build the
rest of the Fortran code that interfaces to LAMMPS. When linking, you
also need to :doc:`link to the LAMMPS library <Build_link>`. A typical
command line for a simple program using the Fortran interface would be:
command for a simple program using the Fortran interface would be:
.. code-block:: bash
@ -91,12 +91,12 @@ function and triggered with the optional logical argument set to
CALL lmp%close(.TRUE.)
END PROGRAM testlib
It is also possible to pass command line flags from Fortran to C/C++ and
It is also possible to pass command-line flags from Fortran to C/C++ and
thus make the resulting executable behave similarly to the standalone
executable (it will ignore the `-in/-i` flag, though). This allows
using the command line to configure accelerator and suffix settings,
using the command-line to configure accelerator and suffix settings,
configure screen and logfile output, or to set index style variables
from the command line and more. Here is a correspondingly adapted
from the command-line and more. Here is a correspondingly adapted
version of the previous example:
.. code-block:: fortran
@ -108,7 +108,7 @@ version of the previous example:
CHARACTER(LEN=128), ALLOCATABLE :: command_args(:)
INTEGER :: i, argc
! copy command line flags to `command_args()`
! copy command-line flags to `command_args()`
argc = COMMAND_ARGUMENT_COUNT()
ALLOCATE(command_args(0:argc))
DO i=0, argc
@ -321,6 +321,14 @@ 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`
@ -448,7 +456,7 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
compiled with MPI support, it will also initialize MPI, if it has
not already been initialized before.
The *args* argument with the list of command line parameters is
The *args* argument with the list of command-line parameters is
optional and so it the *comm* argument with the MPI communicator.
If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For
more details please see the documentation of :cpp:func:`lammps_open`.
@ -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

1
doc/src/Howto.rst
View File

@ -103,6 +103,7 @@ Tutorials howto
Howto_github
Howto_lammps_gui
Howto_moltemplate
Howto_python
Howto_pylammps
Howto_wsl

15
doc/src/Howto_barostat.rst
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@ -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

41
doc/src/Howto_bioFF.rst
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@ -1,5 +1,5 @@
CHARMM, AMBER, COMPASS, and DREIDING force fields
=================================================
CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields
=======================================================
A compact summary of the concepts, definitions, and properties of
force fields with explicit bonded interactions (like the ones discussed
@ -236,6 +236,40 @@ documentation for the formula it computes.
* :doc:`special_bonds <special_bonds>` dreiding
OPLS
----
OPLS (Optimized Potentials for Liquid Simulations) is a general force
field for atomistic simulation of organic molecules in solvent. It was
developed by the `Jorgensen group
<https://traken.chem.yale.edu/oplsaam.html>`_ at Purdue University and
later at Yale University. Multiple versions of the OPLS parameters
exist for united atom representations (OPLS-UA) and for all-atom
representations (OPLS-AA).
This force field is based on atom types mapped to specific functional
groups in organic and biological molecules. Each atom includes a
static, partial atomic charge reflecting the oxidation state of the
element derived from its bonded neighbors :ref:`(Jorgensen)
<howto-jorgensen>` and computed based on increments determined by the
atom type of the atoms bond to it.
The interaction styles listed below compute force field formulas that
are fully or in part consistent with the OPLS style force fields. See
each command's documentation for the formula it computes. Some are only
compatible with a subset of OPLS interactions.
* :doc:`bond_style <bond_harmonic>` harmonic
* :doc:`angle_style <angle_harmonic>` harmonic
* :doc:`dihedral_style <dihedral_opls>` opls
* :doc:`improper_style <improper_cvff>` cvff
* :doc:`improper_style <improper_fourier>` fourier
* :doc:`improper_style <improper_harmonic>` harmonic
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
* :doc:`pair_modify <pair_modify>` geometric
* :doc:`special_bonds <special_bonds>` lj/coul 0.0 0.0 0.5
----------
.. _Typelabel2:
@ -266,3 +300,6 @@ documentation for the formula it computes.
**(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010
.. _howto-Jorgensen:
**(Jorgensen)** Jorgensen, Tirado-Rives (1988). J Am Chem Soc, 110, 1657-1666. https://doi.org/10.1021/ja00214a001

18
doc/src/Howto_bpm.rst
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@ -5,7 +5,11 @@ The BPM package implements bonded particle models which can be used to
simulate mesoscale solids. Solids are constructed as a collection of
particles, which each represent a coarse-grained region of space much
larger than the atomistic scale. Particles within a solid region are
then connected by a network of bonds to provide solid elasticity.
then connected by a network of bonds to model solid elasticity.
There are many names for methods that are based on similar (or
equivalent) capabilities to those in this package, including, but not
limited to, cohesive beam models, bonded DEMs, lattice spring models,
mass spring models, and lattice particle methods.
Unlike traditional bonds in molecular dynamics, the equilibrium bond
length can vary between bonds. Bonds store the reference state. This
@ -38,11 +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. Alternatively, the second bond style, :doc:`bond bpm/rotational
network. An optional multibody term can be used to adjust the network's
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
@ -55,8 +62,9 @@ orientation similar to :doc:`fix nve/asphere <fix_nve_asphere>`.
In addition to bond styles, a new pair style :doc:`pair bpm/spring
<pair_bpm_spring>` was added to accompany the bpm/spring bond
style. This pair style is simply a hookean repulsion with similar
velocity damping as its sister bond style.
style. By default, this pair style is simply a hookean repulsion with
similar velocity damping as its sister bond style, but optional
arguments can be used to modify the force.
----------

67
doc/src/Howto_chunk.rst
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@ -58,28 +58,30 @@ chunk ID for an individual atom can also be static (e.g. a molecule
ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
Note that this compute allows the per-atom output of other
:doc:`computes <compute>`, :doc:`fixes <fix>`, and
:doc:`variables <variable>` to be used to define chunk IDs for each
atom. This means you can write your own compute or fix to output a
per-atom quantity to use as chunk ID. See the :doc:`Modify <Modify>`
doc pages for info on how to do this. You can also define a :doc:`per-atom variable <variable>` in the input script that uses a formula to
generate a chunk ID for each atom.
:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`variables
<variable>` to be used to define chunk IDs for each atom. This means
you can write your own compute or fix to output a per-atom quantity to
use as chunk ID. See the :doc:`Modify <Modify>` doc pages for info on
how to do this. You can also define a :doc:`per-atom variable
<variable>` in the input script that uses a formula to generate a chunk
ID for each atom.
Fix ave/chunk command:
----------------------
This fix takes the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. For each chunk,
it then sums one or more specified per-atom values over the atoms in
each chunk. The per-atom values can be any atom property, such as
velocity, force, charge, potential energy, kinetic energy, stress,
etc. Additional keywords are defined for per-chunk properties like
density and temperature. More generally any per-atom value generated
by other :doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom variables <variable>`, can be summed over atoms in each chunk.
This fix takes the ID of a :doc:`compute chunk/atom
<compute_chunk_atom>` command as input. For each chunk, it then sums
one or more specified per-atom values over the atoms in each chunk. The
per-atom values can be any atom property, such as velocity, force,
charge, potential energy, kinetic energy, stress, etc. Additional
keywords are defined for per-chunk properties like density and
temperature. More generally any per-atom value generated by other
:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom
variables <variable>`, can be summed over atoms in each chunk.
Similar to other averaging fixes, this fix allows the summed per-chunk
values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
fix produces a global array as output with one row of values per chunk.
Compute \*/chunk commands:
--------------------------
@ -97,17 +99,20 @@ category:
* :doc:`compute torque/chunk <compute_vcm_chunk>`
* :doc:`compute vcm/chunk <compute_vcm_chunk>`
They each take the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input. As their names
indicate, they calculate the center-of-mass, radius of gyration,
moments of inertia, mean-squared displacement, temperature, torque,
and velocity of center-of-mass for each chunk of atoms. The :doc:`compute property/chunk <compute_property_chunk>` command can tally the
count of atoms in each chunk and extract other per-chunk properties.
They each take the ID of a :doc:`compute chunk/atom
<compute_chunk_atom>` command as input. As their names indicate, they
calculate the center-of-mass, radius of gyration, moments of inertia,
mean-squared displacement, temperature, torque, and velocity of
center-of-mass for each chunk of atoms. The :doc:`compute
property/chunk <compute_property_chunk>` command can tally the count of
atoms in each chunk and extract other per-chunk properties.
The reason these various calculations are not part of the :doc:`fix ave/chunk command <fix_ave_chunk>`, is that each requires a more
The reason these various calculations are not part of the :doc:`fix
ave/chunk command <fix_ave_chunk>`, is that each requires a more
complicated operation than simply summing and averaging over per-atom
values in each chunk. For example, many of them require calculation
of a center of mass, which requires summing mass\*position over the
atoms and then dividing by summed mass.
values in each chunk. For example, many of them require calculation of
a center of mass, which requires summing mass\*position over the atoms
and then dividing by summed mass.
All of these computes produce a global vector or global array as
output, with one or more values per chunk. The output can be used in
@ -118,9 +123,10 @@ various ways:
* As input to the :doc:`fix ave/histo <fix_ave_histo>` command to
histogram values across chunks. E.g. a histogram of cluster sizes or
molecule diffusion rates.
* As input to special functions of :doc:`equal-style variables <variable>`, like sum() and max() and ave(). E.g. to
find the largest cluster or fastest diffusing molecule or average
radius-of-gyration of a set of molecules (chunks).
* As input to special functions of :doc:`equal-style variables
<variable>`, like sum() and max() and ave(). E.g. to find the largest
cluster or fastest diffusing molecule or average radius-of-gyration of
a set of molecules (chunks).
Other chunk commands:
---------------------
@ -138,9 +144,10 @@ spatially average per-chunk values calculated by a per-chunk compute.
The :doc:`compute reduce/chunk <compute_reduce_chunk>` command reduces a
peratom value across the atoms in each chunk to produce a value per
chunk. When used with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can
create peratom values that induce a new set of chunks with a second
:doc:`compute chunk/atom <compute_chunk_atom>` command.
chunk. When used with the :doc:`compute chunk/spread/atom
<compute_chunk_spread_atom>` command it can create peratom values that
induce a new set of chunks with a second :doc:`compute chunk/atom
<compute_chunk_atom>` command.
Example calculations with chunks
--------------------------------

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

8
doc/src/Howto_github.rst
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@ -163,7 +163,7 @@ After everything is done, add the files to the branch and commit them:
*git rm*, *git mv* for adding, removing, renaming individual files,
respectively, and then *git commit* to finalize the commit.
Carefully check all pending changes with *git status* before
committing them. If you find doing this on the command line too
committing them. If you find doing this on the command-line too
tedious, consider using a GUI, for example the one included in git
distributions written in Tk, i.e. use *git gui* (on some Linux
distributions it may be required to install an additional package to
@ -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.

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

272
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@ -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
}
# Create an input deck for LAMMPS.
write_once("In Init"){
# Note: The lines below in the "In Run" section are often omitted.
write_once("In Run"){
# Create an input deck for LAMMPS.
# 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)

12
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::
@ -738,8 +738,8 @@ command.
This can be done, for example, by using the built-in visualizer of the
:doc:`dump image or dump movie <dump_image>` command to create snapshot
images or a movie. Below are example command lines for using dump image
with the :ref:`example listed below <periexample>` and a set of images
images or a movie. Below are example command for using dump image with
the :ref:`example listed below <periexample>` and a set of images
created for steps 300, 600, and 2000 this way.
.. code-block:: LAMMPS

564
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.

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

24
doc/src/Howto_triclinic.rst
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@ -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

2
doc/src/Howto_wsl.rst
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@ -260,7 +260,7 @@ Switch into the :code:`examples/melt` folder:
cd ../examples/melt
To run this example in serial, use the following command line:
To run this example in serial, use the following command:
.. code-block::

3
doc/src/Install_git.rst
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@ -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,
@ -60,7 +61,7 @@ between them at any time using "git checkout <branch name>".)
files (mostly by accident). If you do not need access to the entire
commit history (most people don't), you can speed up the "cloning"
process and reduce local disk space requirements by using the
``--depth`` git command line flag. That will create a "shallow clone"
``--depth`` git command-line flag. That will create a "shallow clone"
of the repository, which contains only a subset of the git history.
Using a depth of 1000 is usually sufficient to include the head
commits of the *develop*, the *release*, and the *maintenance*

4
doc/src/Intro_authors.rst
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@ -8,6 +8,8 @@ send an email to all of them at this address: "developers at
lammps.org". General questions about LAMMPS should be posted in the
`LAMMPS forum on MatSci <https://matsci.org/lammps/>`_.
.. We need to keep this file in sync with https://www.lammps.org/authors.html
.. raw:: latex
\small
@ -27,7 +29,7 @@ lammps.org". General questions about LAMMPS should be posted in the
* - `Steve Plimpton <sjp_>`_
- SNL (retired)
- sjplimp at gmail.com
- MD kernels, parallel algorithms & scalability, code structure and design
- original author, MD kernels, parallel algorithms & scalability, code structure and design
* - `Aidan Thompson <at_>`_
- SNL
- athomps at sandia.gov

27
doc/src/Intro_portability.rst
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@ -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
^^^^^^^^^^^^^
@ -24,25 +28,26 @@ 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
^^^^^^^^^^^^^^^^^
The primary development platform for LAMMPS is Linux. Thus, the chances
for LAMMPS to compile without problems on Linux machines are the best.
for LAMMPS to compile without problems are the best on Linux machines.
Also, compilation and correct execution on macOS and Windows (using
Microsoft Visual C++) is checked automatically for largest part of the
source code. Some (optional) features are not compatible with all
Microsoft Visual C++) is checked automatically for the largest part of
the source code. Some (optional) features are not compatible with all
operating systems, either through limitations of the corresponding
LAMMPS source code or through source code or build system
incompatibilities of required libraries.
LAMMPS source code or through incompatibilities of source code or
build system of required external libraries or packages.
Executables for Windows may be created natively using either Cygwin or
Visual Studio or with a Linux to Windows MinGW cross-compiler.
Additionally, FreeBSD and Solaris have been tested successfully.
Additionally, FreeBSD and Solaris have been tested successfully to
run LAMMPS and produce results consistent with those on Linux.
Compilers
^^^^^^^^^

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

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

28
doc/src/Library_objects.rst
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@ -1,5 +1,5 @@
Compute, fixes, variables
=========================
Computes, fixes, variables
==========================
This section documents accessing or modifying data stored by computes,
fixes, or variables in LAMMPS using the following functions:
@ -12,6 +12,10 @@ 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

2
doc/src/Modify_compute.rst
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@ -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
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@ -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

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

37
doc/src/Packages_details.rst
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@ -880,7 +880,7 @@ groups of atoms that interact with the remaining atoms as electrolyte.
**Authors:** The ELECTRODE package is written and maintained by Ludwig
Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
Robert Meissner (TUHH, Hamburg, Germany).
Robert Meissner (Helmholtz-Zentrum Hereon, Geesthacht and TUHH, Hamburg, Germany).
.. versionadded:: 4May2022
@ -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``
----------
@ -2171,8 +2172,8 @@ the :doc:`Build extras <Build_extras>` page.
* ``src/OPENMP/README``
* :doc:`Accelerator packages <Speed_packages>`
* :doc:`OPENMP package <Speed_omp>`
* :doc:`Command line option -suffix/-sf omp <Run_options>`
* :doc:`Command line option -package/-pk omp <Run_options>`
* :doc:`Command-line option -suffix/-sf omp <Run_options>`
* :doc:`Command-line option -package/-pk omp <Run_options>`
* :doc:`package omp <package>`
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
@ -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:**
@ -2789,14 +2790,15 @@ implements smoothed particle hydrodynamics (SPH) for liquids. See the
related :ref:`MACHDYN package <PKG-MACHDYN>` package for smooth Mach dynamics
(SMD) for solids.
This package contains ideal gas, Lennard-Jones equation of states,
Tait, and full support for complete (i.e. internal-energy dependent)
equations of state. It allows for plain or Monaghans XSPH integration
of the equations of motion. It has options for density continuity or
density summation to propagate the density field. It has
:doc:`set <set>` command options to set the internal energy and density
of particles from the input script and allows the same quantities to
be output with thermodynamic output or to dump files via the :doc:`compute property/atom <compute_property_atom>` command.
This package contains ideal gas, Lennard-Jones equation of states, Tait,
and full support for complete (i.e. internal-energy dependent) equations
of state. It allows for plain or Monaghans XSPH integration of the
equations of motion. It has options for density continuity or density
summation to propagate the density field. It has :doc:`set <set>`
command options to set the internal energy and density of particles from
the input script and allows the same quantities to be output with
thermodynamic output or to dump files via the :doc:`compute
property/atom <compute_property_atom>` command.
**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
@ -2809,6 +2811,17 @@ Dynamics, Ernst Mach Institute, Germany).
* ``examples/PACKAGES/sph``
* https://www.lammps.org/movies.html#sph
.. note::
Please note that the SPH PDF guide file has not been updated for
many years and thus does not reflect the current *syntax* of the
SPH package commands. For that please refer to the LAMMPS manual.
.. note::
Please also note, that the :ref:`RHEO package <PKG-RHEO>` offers
similar functionality in a more modern and flexible implementation.
----------
.. _PKG-SPIN:

74
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
@ -25,57 +19,41 @@ against invalid accesses.
accordingly. These arrays can change sizes and order at every neighbor list
rebuild and atom sort event as atoms are migrating between subdomains.
.. tabs::
.. code-block:: python
.. tab:: lammps API
from lammps import lammps
.. code-block:: python
lmp = lammps()
lmp.file("in.sysinit")
from lammps import lammps
lmp = lammps()
lmp.file("in.sysinit")
# Read/Write access via ctypes
nlocal = lmp.extract_global("nlocal")
x = lmp.extract_atom("x")
nlocal = lmp.extract_global("nlocal")
x = lmp.extract_atom("x")
for i in range(nlocal):
print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
for i in range(nlocal):
print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
# Read/Write access via NumPy arrays
atom_id = L.numpy.extract_atom("id")
atom_type = L.numpy.extract_atom("type")
x = L.numpy.extract_atom("x")
v = L.numpy.extract_atom("v")
f = L.numpy.extract_atom("f")
lmp.close()
# set position in 2D simulation
x[0] = (1.0, 0.0)
**Methods**:
# set position in 3D simulation
x[0] = (1.0, 0.0, 1.)
* :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
lmp.close()
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
**Methods**:
.. tab:: PyLammps/IPyLammps API
* :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
All atoms in the current simulation can be accessed by using the :py:attr:`PyLammps.atoms <lammps.PyLammps.atoms>` property.
Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
these objects provide access to their data (id, type, position, velocity, force, etc.):
.. code-block:: python
# access first atom
L.atoms[0].id
L.atoms[0].type
# access second atom
L.atoms[1].position
L.atoms[1].velocity
L.atoms[1].force
Some attributes can be changed:
.. code-block:: python
# set position in 2D simulation
L.atoms[0].position = (1.0, 0.0)
# set position in 3D simulation
L.atoms[0].position = (1.0, 0.0, 1.0)
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array

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