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Merge branch 'bosonic-pimd-langevin' of https://github.com/yotamfe/lammps into bosonic-pimd-langevin

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ofirblumer
2025-01-15 10:59:43 +02:00
parent 7f6cfd364d 274525ca25
commit 1b79f34b22
3035 changed files with 397377 additions and 147993 deletions
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30
.github/CODEOWNERS vendored
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@ -38,6 +38,7 @@ src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde
src/ML-UF3/* @monk-04
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
@ -49,6 +50,7 @@ src/PTM/* @pmla
src/QMMM/* @akohlmey
src/REACTION/* @jrgissing
src/REAXFF/* @hasanmetin @stanmoore1
src/RHEO/* @jtclemm
src/SCAFACOS/* @rhalver
src/SNAP/* @athomps
src/SPIN/* @julient31
@ -58,11 +60,15 @@ src/VTK/* @rbberger
# individual files in packages
src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane @stanmoore1
src/KOSSOS/pair_pod_kokkos.* @exapde @stanmoore1
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMMAND/geturl.* @akohlmey
src/EXTRA-COMMAND/group_ndx.* @akohlmey
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
@ -72,6 +78,8 @@ src/MC/fix_sgcmc.* @athomps
src/REAXFF/compute_reaxff_atom.* @rbberger
src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger
src/REPLICA/fix_pimd_langevin.* @Yi-FanLi
src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
# core LAMMPS classes
src/lammps.* @sjplimp
@ -83,7 +91,7 @@ src/bond.* @sjplimp
src/comm*.* @sjplimp
src/compute.* @sjplimp
src/dihedral.* @sjplimp
src/domain.* @sjplimp
src/domain.* @sjplimp @stanmoore1
src/dump*.* @sjplimp
src/error.* @sjplimp
src/finish.* @sjplimp
@ -91,9 +99,11 @@ src/fix.* @sjplimp
src/force.* @sjplimp
src/group.* @sjplimp
src/improper.* @sjplimp
src/info.* @akohlmey
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/library.* @sjplimp
src/lmptype.h @sjplimp
src/label_map.* @jrgissing @akohlmey
src/library.* @sjplimp @akohlmey
src/main.cpp @sjplimp
src/min_*.* @sjplimp
src/memory.* @sjplimp
@ -101,12 +111,12 @@ src/modify.* @sjplimp @stanmoore1
src/molecule.* @sjplimp
src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp
src/npair*.* @sjplimp
src/ntopo*.* @sjplimp
src/nstencil*.* @sjplimp
src/neighbor.* @sjplimp
src/nbin*.* @sjplimp
src/neigh_*.* @sjplimp
src/npair*.* @sjplimp @jtclemm
src/ntopo*.* @sjplimp @jtclemm
src/nstencil*.* @sjplimp @jtclemm
src/neighbor.* @sjplimp @jtclemm
src/nbin*.* @sjplimp @jtclemm
src/neigh_*.* @sjplimp @jtclemm
src/output.* @sjplimp
src/pair.* @sjplimp
src/rcb.* @sjplimp

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.github/release_steps.md vendored Normal file
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@ -0,0 +1,108 @@
# LAMMPS Release Steps
The following notes chronicle the current steps for preparing and publishing LAMMPS releases. For
definitions of LAMMPS versions and releases mean, please refer to [the corresponding section in the
LAMMPS manual](https://docs.lammps.org/Manual_version.html).
## 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, rebase if needed. This is the last pull request merged for the release
and should not contain any other changes. (Exceptions: this document, last minute trivial(!) changes).
This PR shall not be merged before **all** pending tests have completed and cleared. If needed, a
bugfix pull request should be created and merged to clear all tests.
### 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 'develop' locally, pull the latest changes, merge them into 'release', apply a suitable
release tag (for historical reasons the tag starts with "patch_" followed by the date, and finally
push everything back to GitHub. Example:
```
git checkout develop
git pull
git checkout release
git pull
git merge --ff-only develop
git tag -s -m "LAMMPS feature release 19 November 2024" patch_19Nov2024
git push git@github.com:lammps/lammps.git --tags develop release
```
Go to https://github.com/lammps/lammps/releases and create a new (draft) release page or check the
existing draft for any necessary changes from pull requests that were merged but are not listed.
Then select the applied tag for the release in the "Choose a tag" dropdown list. Go to the bottom of
the list and select the "Set as pre-release" checkbox. The "Set as the latest release" button is
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.
### Update download website, prepare pre-compiled packages, update packages to GitHub
Publishing the release on GitHub will trigger the Temple Jenkins cluster to update
the https://docs.lammps.org/ website with the documentation for the new feature release
and it will create a tarball for download (which contains the translated manual).
Build a fully static LAMMPS installation using a musl-libc cross-compiler, install into a
lammps-static folder, and create a tarball called lammps-linux-x86_64-19Nov2024.tar.gz (or using a
corresponding date with a future release) from the lammps-static folder and upload it to GitHub
with:
```
gh release upload patch_19Nov2024 ~/Downloads/lammps-linux-x86_64-19Nov2024.tar.gz
```
## 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

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@ -0,0 +1,92 @@
# 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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@ -0,0 +1,89 @@
# GitHub action to build LAMMPS on Linux with gcc and -Werror=vla
name: "Check for Variable Length Arrays"
on:
push:
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build with -Werror=vla
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: ${{ env.CCACHE_DIR }}
key: linux-vla-ccache-${{ github.sha }}
restore-keys: linux-vla-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 \
-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 -Werror=vla" \
-D DOWNLOAD_POTENTIALS=off \
-D BUILD_MPI=on \
-D BUILD_SHARED_LIBS=off \
-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_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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@ -1,5 +1,5 @@
# GitHub action to build LAMMPS on Windows with Visual C++
name: "Native Windows Compilation and Unit Tests"
# GitHub action to test LAMMPS on Windows with Visual C++
name: "Windows Unit Tests"
on:
push:
@ -11,11 +11,17 @@ on:
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Windows Compilation Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: windows-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
@ -23,36 +29,41 @@ jobs:
with:
fetch-depth: 2
- name: Enable MSVC++
uses: lammps/setup-msvc-dev@v3
with:
arch: x64
- name: Install Ccache
run: |
choco install ccache ninja -y
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: win-unit-ccache-${{ github.sha }}
restore-keys: win-unit-ccache-
- name: Select Python version
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m pip install numpy
python3 -m pip install pyyaml
nuget install MSMPIsdk
nuget install MSMPIDIST
cmake -C cmake/presets/windows.cmake \
-D DOWNLOAD_POTENTIALS=off \
-D PKG_PYTHON=on \
-D WITH_PNG=off \
-D WITH_JPEG=off \
-S cmake -B build \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on \
-D ENABLE_TESTING=on
cmake --build build --config Release --parallel 2
cmake -C cmake\presets\windows.cmake -D CMAKE_CXX_COMPILER=cl -D CMAKE_CXX_COMPILER_LAUNCHER=ccache -D CMAKE_C_COMPILER=cl -D CMAKE_C_COMPILER_LAUNCHER=ccache -D CMAKE_Fortran_COMPILER="" -D DOWNLOAD_POTENTIALS=off -D PKG_PYTHON=on -D WITH_PNG=off -D WITH_JPEG=off -S cmake -B build -D BUILD_SHARED_LIBS=on -D ENABLE_TESTING=on -D CMAKE_BUILD_TYPE=Release -G Ninja
cmake --build build
ccache -s
- name: Run LAMMPS executable
shell: bash
run: |
./build/Release/lmp.exe -h
./build/Release/lmp.exe -in bench/in.lj
build\lmp.exe -h
build\lmp.exe -in bench\in.lj
- name: Run Unit Tests
working-directory: build
shell: bash
run: ctest -V -C Release -E FixTimestep:python_move_nve
run: ctest -V -E FixTimestep:python_move_nve

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@ -0,0 +1,109 @@
# GitHub action to build LAMMPS on Linux and run regression tests
name: "Full Regression Test"
on:
push:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build LAMMPS
# restrict to official LAMMPS repository
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 8
matrix:
idx: [ 0, 1, 2, 3, 4, 5, 6, 7 ]
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: ${{ env.CCACHE_DIR }}
key: linux-full-ccache-${{ github.sha }}
restore-keys: linux-full-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/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=off \
-D DOWNLOAD_POTENTIALS=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 Full Regression Tests
shell: bash
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_serial.yaml \
--examples-top-level=examples --analyze --num-workers=8
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_serial.yaml \
--list-input=input-list-${{ matrix.idx }}.txt \
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log
tar -cvf full-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: full-regression-test-artifact-${{ matrix.idx }}
path: full-regression-test-${{ matrix.idx }}.tar
merge:
runs-on: ubuntu-latest
needs: build
steps:
- name: Merge Artifacts
uses: actions/upload-artifact/merge@v4
with:
name: merged-full-regresssion-artifact
pattern: full-regression-test-artifact-*

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@ -0,0 +1,126 @@
# 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-*

118
.github/workflows/quick-regression.yml vendored Normal file
View File

@ -0,0 +1,118 @@
# GitHub action to build LAMMPS on Linux and run selected regression tests
name: "Quick Regression Test"
on:
pull_request:
branches:
- develop
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Build LAMMPS
# restrict to official LAMMPS repository
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 4
matrix:
idx: [ 0, 1, 2, 3 ]
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 0
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: ${{ env.CCACHE_DIR }}
key: linux-quick-ccache-${{ github.sha }}
restore-keys: linux-quick-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/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=off \
-D DOWNLOAD_POTENTIALS=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 Regression Tests for Modified Styles
shell: bash
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_quick.yaml \
--examples-top-level=examples \
--quick-reference=tools/regression-tests/reference.yaml \
--quick --quick-branch=origin/develop --quick-max=100 --num-workers=4
if [ -f input-list-${{ matrix.idx }}.txt ]
then \
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_quick.yaml \
--list-input=input-list-${{ matrix.idx }}.txt \
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log
fi
tar -cvf quick-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
- name: Upload artifacts
uses: actions/upload-artifact@v4
with:
name: quick-regression-test-artifact-${{ matrix.idx }}
path: quick-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-quick-regresssion-artifact
pattern: quick-regression-test-artifact-*

37
.github/workflows/style-check.yml vendored Normal file
View File

@ -0,0 +1,37 @@
# GitHub action to run checks from tools/coding_standard
name: "Check for Programming Style Conformance"
on:
push:
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Programming Style Conformance
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: Run Tests
working-directory: src
shell: bash
run: |
make check-whitespace
make check-permissions
make check-homepage
make check-errordocs

86
.github/workflows/unittest-linux.yml vendored Normal file
View File

@ -0,0 +1,86 @@
# GitHub action to build LAMMPS on Linux and run standard unit tests
name: "Unittest for Linux /w LAMMPS_BIGBIG"
on:
push:
branches:
- develop
pull_request:
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 Unit Test
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 \
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 LAMMPS_SIZES=bigbig \
-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

8
.github/workflows/unittest-macos.yml vendored
View File

@ -11,11 +11,15 @@ on:
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
runs-on: macos-13
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
@ -43,6 +47,8 @@ jobs:
working-directory: build
run: |
ccache -z
python3 -m venv macosenv
source macosenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -C ../cmake/presets/clang.cmake \

11
.gitignore vendored
View File

@ -43,12 +43,12 @@ Thumbs.db
#cmake
/build*
/CMakeCache.txt
/CMakeFiles/
/Testing
CMakeCache.txt
CMakeFiles
/Makefile
/Testing
/cmake_install.cmake
Testing
Temporary
cmake_install.cmake
/lmp
out/Debug
out/RelWithDebInfo
@ -60,3 +60,4 @@ src/Makefile.package.settings-e
/cmake/build/x64-Debug-Clang
/install/x64-GUI-MSVC
/install
.Rhistory

88
cmake/CMakeLists.txt
View File

@ -12,6 +12,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about requiring execute permission for find_program
# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
@ -23,6 +28,7 @@ project(lammps CXX)
set(SOVERSION 0)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
include(GNUInstallDirs)
get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
# collect all executables and shared libs in the top level build folder
@ -112,7 +118,7 @@ endif()
# silence excessive warnings for new Intel Compilers
if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
set(CMAKE_TUNE_DEFAULT "-fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
endif()
# silence excessive warnings for PGI/NVHPC compilers
@ -135,7 +141,7 @@ endif()
# silence nvcc warnings
if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
set(CMAKE_TUNE_DEFAULT "${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)
@ -159,10 +165,27 @@ 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()
# warn about potentially problematic GCC compiler versions
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
endif()
endif()
if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
endif()
endif()
endif()
# export all symbols when building a .dll file on windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@ -197,18 +220,17 @@ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
option(BUILD_SHARED_LIBS "Build shared library" OFF)
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
# Support using clang-tidy for C++ files with selected options
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
else()
unset(CMAKE_CXX_CLANG_TIDY CACHE)
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@ -256,6 +278,7 @@ set(STANDARD_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -281,10 +304,11 @@ set(STANDARD_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP
ML-POD
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -303,6 +327,7 @@ set(STANDARD_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK
@ -407,6 +432,7 @@ pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
pkg_depends(MESONT MOLECULE)
pkg_depends(RHEO BPM)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -449,13 +475,13 @@ if(BUILD_OMP)
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
endif()
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
endif()
endif()
endif()
@ -472,7 +498,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
PROPERTIES COMPILE_OPTIONS "-std=c++14")
endif()
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
@ -547,7 +573,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -562,13 +588,8 @@ 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 ${CMAKE_TUNE_FLAGS})
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
@ -689,7 +710,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -797,9 +818,15 @@ 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)
@ -867,7 +894,7 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
find_package(ClangFormat 8.0)
find_package(ClangFormat 11.0)
if(ClangFormat_FOUND)
add_custom_target(format-src
@ -937,8 +964,12 @@ message(STATUS "<<< Compilers and Flags: >>>
-- C++ Compiler: ${CMAKE_CXX_COMPILER}
Type: ${CMAKE_CXX_COMPILER_ID}
Version: ${CMAKE_CXX_COMPILER_VERSION}
C++ Standard: ${CMAKE_CXX_STANDARD}
C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines: ${DEFINES}")
if(CMAKE_CXX_COMPILER_LAUNCHER)
message(STATUS " Launcher: ${CMAKE_CXX_COMPILER_LAUNCHER}")
endif()
get_target_property(OPTIONS lammps COMPILE_OPTIONS)
if(OPTIONS)
message(" Options: ${OPTIONS}")
@ -957,6 +988,9 @@ if(_index GREATER -1)
Type: ${CMAKE_C_COMPILER_ID}
Version: ${CMAKE_C_COMPILER_VERSION}
C Flags: ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
if(CMAKE_C_COMPILER_LAUNCHER)
message(STATUS " Launcher: ${CMAKE_C_COMPILER_LAUNCHER}")
endif()
endif()
message(STATUS "<<< Linker flags: >>>")
message(STATUS "Executable name: ${LAMMPS_BINARY}")
@ -1043,16 +1077,16 @@ endif()
if(BUILD_TOOLS)
message(STATUS "<<< Building Tools >>>")
endif()
if(BUILD_LAMMPS_SHELL)
message(STATUS "<<< Building LAMMPS Shell >>>")
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 >>>")

49
cmake/Modules/Documentation.cmake
View File

@ -4,6 +4,8 @@
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
option(BUILD_DOC_VENV "Build LAMMPS documentation virtual environment" ON)
mark_as_advanced(BUILD_DOC_VENV)
# Current Sphinx versions require at least Python 3.8
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
@ -18,14 +20,6 @@ if(BUILD_DOC)
find_package(Doxygen 1.8.10 REQUIRED)
file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
add_custom_command(
OUTPUT docenv
COMMAND ${VIRTUALENV} docenv
)
set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
set(SPHINX_STATIC_DIR ${SPHINX_CONFIG_DIR}/_static)
@ -44,14 +38,32 @@ if(BUILD_DOC)
# configure paths in conf.py, since relative paths change when file is copied
configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
add_custom_command(
OUTPUT ${DOC_BUILD_DIR}/requirements.txt
DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
)
if(BUILD_DOC_VENV)
add_custom_command(
OUTPUT docenv
COMMAND ${VIRTUALENV} docenv
)
set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
add_custom_command(
OUTPUT ${DOC_BUILD_DIR}/requirements.txt
DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
)
set(DOCENV_DEPS docenv ${DOC_BUILD_DIR}/requirements.txt)
if(NOT TARGET Sphinx::sphinx-build)
add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${DOCENV_BINARY_DIR}/sphinx-build")
endif()
else()
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")
@ -97,8 +109,9 @@ if(BUILD_DOC)
endif()
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/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
COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp

3
cmake/Modules/FindClangFormat.cmake
View File

@ -1,5 +1,8 @@
# Find clang-format
find_program(ClangFormat_EXECUTABLE NAMES clang-format
clang-format-20.0
clang-format-19.0
clang-format-18.0
clang-format-17.0
clang-format-16.0
clang-format-15.0

29
cmake/Modules/FindSphinx.cmake Normal file
View File

@ -0,0 +1,29 @@
# Find sphinx-build
find_program(Sphinx_EXECUTABLE NAMES sphinx-build
PATH_SUFFIXES bin
DOC "Sphinx documenation build executable")
mark_as_advanced(Sphinx_EXECUTABLE)
if(Sphinx_EXECUTABLE)
execute_process(COMMAND ${Sphinx_EXECUTABLE} --version
OUTPUT_VARIABLE sphinx_version
OUTPUT_STRIP_TRAILING_WHITESPACE
RESULT_VARIABLE _sphinx_version_result)
if(_sphinx_version_result)
message(WARNING "Unable to determine sphinx-build verison: ${_sphinx_version_result}")
else()
string(REGEX REPLACE "sphinx-build ([0-9.]+).*"
"\\1"
Sphinx_VERSION
"${sphinx_version}")
endif()
if(NOT TARGET Sphinx::sphinx-build)
add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${Sphinx_EXECUTABLE}")
endif()
endif()
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(Sphinx REQUIRED_VARS Sphinx_EXECUTABLE VERSION_VAR Sphinx_VERSION)

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()

8
cmake/Modules/LAMMPSUtils.cmake
View File

@ -32,7 +32,13 @@ function(check_omp_h_include)
set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
check_include_file_cxx(omp.h _have_omp_h)
# there are all kinds of problems with finding omp.h
# for Clang and derived compilers so we pretend it is there.
if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
set(_have_omp_h TRUE)
else()
check_include_file_cxx(omp.h _have_omp_h)
endif()
else()
set(_have_omp_h FALSE)
endif()

4
cmake/Modules/OpenCLLoader.cmake
View File

@ -1,6 +1,6 @@
message(STATUS "Downloading and building OpenCL loader library")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.02.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "f3573cf9daa3558ba46fd5866517f38f" CACHE STRING "MD5 checksum of OpenCL loader tarball")
set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
mark_as_advanced(OPENCL_LOADER_MD5)

6
cmake/Modules/Packages/COLVARS.cmake
View File

@ -24,6 +24,12 @@ target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
target_link_libraries(lammps PRIVATE colvars)
if(BUILD_OMP)
# Enable OpenMP for Colvars as well
target_compile_options(colvars PRIVATE ${OpenMP_CXX_FLAGS})
target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
endif()
if(COLVARS_DEBUG)
# Need to export the define publicly to be valid in interface code
target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

9
cmake/Modules/Packages/DPD-BASIC.cmake Normal file
View File

@ -0,0 +1,9 @@
# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
if(NOT PKG_KSPACE)
get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

10
cmake/Modules/Packages/EXTRA-COMMAND.cmake Normal file
View File

@ -0,0 +1,10 @@
# the geturl command needs libcurl
find_package(CURL QUIET COMPONENTS HTTP HTTPS)
option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
if(WITH_CURL)
find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
target_link_libraries(lammps PRIVATE CURL::libcurl)
endif()

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)

53
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -8,8 +8,24 @@ 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)
option(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC "CUDA asynchronous malloc support" OFF)
mark_as_advanced(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
if(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
message(STATUS "KOKKOS: CUDA malloc async support enabled")
else()
message(STATUS "KOKKOS: CUDA malloc async support disabled")
endif()
endif()
if(Kokkos_ENABLE_HIP)
option(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS "Enable multiple kernel instantiations with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS)
option(Kokkos_ENABLE_ROCTHRUST "Use RoCThrust library" ON)
mark_as_advanced(Kokkos_ENABLE_ROCTHRUST)
if(Kokkos_ARCH_AMD_GFX942 OR Kokkos_ARCH_AMD_GFX940)
option(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY "Enable unified memory with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY)
endif()
endif()
# Adding OpenMP compiler flags without the checks done for
# BUILD_OMP can result in compile failures. Enforce consistency.
@ -18,6 +34,15 @@ 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 +70,8 @@ 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/4.2.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "16b9b09ae947d434dfb58fc5c87c2b76" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "de6ee80d00b6212b02bfb7f1e71a8392" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -71,7 +96,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.2.01 REQUIRED CONFIG)
find_package(Kokkos 4.4.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -105,6 +130,7 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/group_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
@ -127,7 +153,7 @@ if(PKG_KSPACE)
${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT)
set(FFT_KOKKOS_VALUES KISS FFTW3 MKL NVPL HIPFFT CUFFT MKL_GPU)
set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
@ -137,10 +163,8 @@ if(PKG_KSPACE)
message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
elseif(FFT_KOKKOS STREQUAL "KISS")
message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "CUFFT")
find_package(CUDAToolkit REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
target_link_libraries(lammps PRIVATE CUDA::cufft)
endif()
elseif(Kokkos_ENABLE_HIP)
@ -152,10 +176,21 @@ if(PKG_KSPACE)
elseif(FFT_KOKKOS STREQUAL "HIPFFT")
include(DetectHIPInstallation)
find_package(hipfft REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
target_link_libraries(lammps PRIVATE hip::hipfft)
endif()
elseif(FFT_KOKKOS STREQUAL "MKL_GPU")
if(NOT Kokkos_ENABLE_SYCL)
message(FATAL_ERROR "Using MKL_GPU FFT currently requires the SYCL backend of Kokkos.")
endif()
find_package(MKL REQUIRED)
target_link_libraries(lammps PRIVATE mkl_sycl_dft mkl_intel_ilp64 mkl_tbb_thread mkl_core tbb)
elseif(FFT_KOKKOS STREQUAL "MKL")
find_package(MKL REQUIRED)
elseif(FFT_KOKKOS STREQUAL "NVPL")
find_package(nvpl_fft REQUIRED)
target_link_libraries(lammps PRIVATE nvpl::fftw)
endif()
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_${FFT_KOKKOS})
endif()
if(PKG_ML-IAP)

6
cmake/Modules/Packages/KSPACE.cmake
View File

@ -10,7 +10,7 @@ if(${FFTW}_FOUND)
else()
set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
endif()
set(FFT_VALUES KISS FFTW3 MKL)
set(FFT_VALUES KISS FFTW3 MKL NVPL)
set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
validate_option(FFT FFT_VALUES)
string(TOUPPER ${FFT} FFT)
@ -41,6 +41,10 @@ elseif(FFT STREQUAL "MKL")
target_compile_definitions(lammps PRIVATE -DFFT_MKL_THREADS)
endif()
target_link_libraries(lammps PRIVATE MKL::MKL)
elseif(FFT STREQUAL "NVPL")
find_package(nvpl_fft REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_NVPL)
target_link_libraries(lammps PRIVATE nvpl::fftw)
else()
# last option is KISSFFT
target_compile_definitions(lammps PRIVATE -DFFT_KISS)

15
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -10,6 +10,14 @@ endif()
option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP
set(MLIAP_ENABLE_ACE_DEFAULT OFF)
if(PKG_ML-PACE)
set(MLIAP_ENABLE_ACE_DEFAULT ON)
endif()
option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT})
if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED)
find_package(Python COMPONENTS NumPy REQUIRED)
@ -36,3 +44,10 @@ if(MLIAP_ENABLE_PYTHON)
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
endif()
if(MLIAP_ENABLE_ACE)
if(NOT PKG_ML-PACE)
message(FATAL_ERROR "Must enable ML-PACE package for including ACE support in ML-IAP")
endif()
target_compile_definitions(lammps PRIVATE -DMLIAP_ACE)
endif()

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

@ -1,5 +1,11 @@
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")
# PACE library support for ML-PACE package
# 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)

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

@ -27,7 +27,7 @@ if(DOWNLOAD_QUIP)
else()
message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
endif()
set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
set(temp "${temp}MATH_LINKOPTS=")
foreach(flag ${BLAS_LIBRARIES})
set(temp "${temp} ${flag}")

35
cmake/Modules/Packages/PLUMED.cmake
View File

@ -1,5 +1,14 @@
# Plumed2 support for PLUMED package
# 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()
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
@ -21,9 +30,11 @@ else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
# 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"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
@ -75,6 +86,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
DEPENDS plumed_build
COMMENT "Copying Plumed files"
)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
endif()
else()
@ -149,21 +163,26 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
endif()
endif()
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

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)

4
cmake/Modules/Testing.cmake
View File

@ -102,9 +102,9 @@ endif()
#######################################
# select code sanitizer options
#######################################
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, hwaddress, leak, thread, undefined)")
mark_as_advanced(ENABLE_SANITIZER)
set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
set(ENABLE_SANITIZER_VALUES none address hwaddress leak thread undefined)
set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)

31
cmake/Modules/Tools.cmake
View File

@ -37,37 +37,6 @@ if(BUILD_TOOLS)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
find_package(PkgConfig QUIET)
if(BUILD_LAMMPS_SHELL)
if(NOT PkgConfig_FOUND)
message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
endif()
find_package(PkgConfig REQUIRED)
pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
# include resource compiler to embed icons into the executable on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
enable_language(RC)
set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
endif()
add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
# workaround for broken readline pkg-config file on FreeBSD
if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
target_include_directories(lammps-shell PRIVATE /usr/local/include)
endif()
if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
endif()
install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
endif()
if(BUILD_LAMMPS_GUI)
get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)

BIN
cmake/packaging/LAMMPS_DMG_Background.xcf Normal file
View File

Binary file not shown.

7
cmake/packaging/build_linux_tgz.sh
View File

@ -2,9 +2,10 @@
APP_NAME=lammps-gui
DESTDIR=${PWD}/../LAMMPS_GUI
VERSION="$1"
echo "Delete old files, if they exist"
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
@ -59,17 +60,19 @@ done
echo "Set up wrapper script"
MYDIR=$(dirname "$0")
cp ${MYDIR}/xdg-open ${DESTDIR}/bin
cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
for s in ${DESTDIR}/bin/*
do \
EXE=$(basename $s)
test ${EXE} = linux_wrapper.sh && continue
test ${EXE} = qt.conf && continue
test ${EXE} = xdg-open && continue
ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
done
pushd ..
tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI
tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
popd
echo "Cleanup dir"

9
cmake/packaging/build_macos_dmg.sh
View File

@ -1,9 +1,10 @@
#!/bin/bash
APP_NAME=lammps-gui
VERSION="$1"
echo "Delete old files, if they exist"
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch.dmg
rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch*.dmg
echo "Create initial dmg file with macdeployqt"
macdeployqt lammps-gui.app -dmg
@ -96,12 +97,12 @@ sync
echo "Unmount modified disk image and convert to compressed read-only image"
hdiutil detach "${DEVICE}"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch.dmg"
hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg"
echo "Attach icon to .dmg file"
echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch.dmg
SetFile -a C LAMMPS_GUI-macOS-multiarch.dmg
Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
SetFile -a C LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
rm icon.rsrc
echo "Delete temporary disk images"

5
cmake/packaging/build_windows_cross_zip.sh
View File

@ -3,9 +3,10 @@
APP_NAME=lammps-gui
DESTDIR=${PWD}/LAMMPS_GUI
SYSROOT="$1"
VERSION="$2"
echo "Delete old files, if they exist"
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64.zip
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
@ -60,5 +61,5 @@ cat > ${DESTDIR}/bin/qt.conf <<EOF
[Paths]
Plugins = ../qt5plugins
EOF
zip -9rvD LAMMPS-Win10-amd64.zip LAMMPS_GUI
zip -9rvD LAMMPS-Win10-amd64-${VERSION}.zip LAMMPS_GUI

14
cmake/packaging/linux_wrapper.sh
View File

@ -4,15 +4,17 @@
# reset locale to avoid problems with decimal numbers
export LC_ALL=C
BASEDIR=$(dirname "$0")
EXENAME=$(basename "$0")
BASEDIR="$(dirname "$0")"
EXENAME="$(basename "$0")"
PATH="${BASEDIR}/bin:${PATH}"
# append to LD_LIBRARY_PATH to prefer local (newer) libs
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
# set some environment variables for LAMMPS etc.
LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
exec "${BASEDIR}/bin/${EXENAME}" "$@"

1074
cmake/packaging/xdg-open Executable file
View File

File diff suppressed because it is too large Load Diff

5
cmake/presets/all_off.cmake
View File

@ -26,8 +26,9 @@ set(ALL_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -60,6 +61,7 @@ set(ALL_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -80,6 +82,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK

5
cmake/presets/all_on.cmake
View File

@ -28,8 +28,9 @@ set(ALL_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -62,6 +63,7 @@ set(ALL_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -82,6 +84,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK

4
cmake/presets/clang.cmake
View File

@ -1,10 +1,10 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
find_program(CLANG_FORTRAN NAMES flang-new flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
if ((_tmp_fc STREQUAL "flang") OR (_tmp_fc STREQUAL "flang-new"))
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()

29
cmake/presets/kokkos-sycl-intel.cmake Normal file
View File

@ -0,0 +1,29 @@
# preset that enables KOKKOS and selects SYCL compilation with OpenMP
# enabled as well. Also sets some performance related compiler flags.
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_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-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)

0
cmake/presets/kokkos-sycl.cmake → cmake/presets/kokkos-sycl-nvidia.cmake
View File

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

@ -22,8 +22,9 @@ set(WIN_PACKAGES
DPD-REACT
DPD-SMOOTH
DRUDE
ELECTRODE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -32,7 +33,6 @@ set(WIN_PACKAGES
FEP
GPU
GRANULAR
INTEL
INTERLAYER
KSPACE
LEPTON
@ -50,6 +50,7 @@ set(WIN_PACKAGES
ML-POD
ML-RANN
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -66,6 +67,7 @@ set(WIN_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SHOCK
SMTBQ

3
cmake/presets/most.cmake
View File

@ -26,6 +26,7 @@ set(ALL_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -45,6 +46,7 @@ set(ALL_PACKAGES
ML-IAP
ML-POD
ML-SNAP
ML-UF3
MOFFF
MOLECULE
OPENMP
@ -58,6 +60,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SHOCK
SPH

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)

5
cmake/presets/windows.cmake
View File

@ -22,6 +22,7 @@ set(WIN_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -42,6 +43,7 @@ set(WIN_PACKAGES
ML-IAP
ML-POD
ML-SNAP
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -50,14 +52,15 @@ set(WIN_PACKAGES
ORIENT
PERI
PHONON
POEMS
PLUGIN
POEMS
PTM
QEQ
QTB
REACTION
REAXFF
REPLICA
RHEO
RIGID
SHOCK
SMTBQ

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

13
doc/Makefile
View File

@ -83,7 +83,10 @@ $(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
@(\
@ -113,7 +116,7 @@ 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)
fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@$(MAKE) $(MFLAGS) -C graphviz all
@mkdir -p fasthtml
@ -132,7 +135,7 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@rm -rf fasthtml/PDF/.[sg]*
@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
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 +146,7 @@ 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 +169,7 @@ 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

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

20
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "7 February 2024" "2024-02-07"
.TH LAMMPS "1" "19 November 2024" "2024-11-19"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 7 February 2024
\- Molecular Dynamics Simulator. Version 19 November 2024
.SH SYNOPSIS
.B lmp
@ -226,6 +226,20 @@ arguments of the "dump" command. See the
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-r2info <restart file> <keyword> ...\fR or
\fB\-restart2info <restart file> <keyword> ...\fR
Write information about the <restart file> previously written by
.B LAMMPS
to the screen and immediately exit. Following <restart file>
argument, additional keywords for the
.B LAMMPS
"info" command may be added to increase the amount of information
written. By default "system" "group" "fix" "compute" are already
set. See the
.B LAMMPS
manual for details on the "info" command.
.TP
.TP
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
Specify a file for
.B LAMMPS
@ -297,7 +311,7 @@ the chapter on errors in the
manual gives some additional information about error messages, if possible.
.SH COPYRIGHT
© 2003--2022 Sandia Corporation
© 2003--2024 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

4
doc/msi2lmp.1
View File

@ -1,4 +1,4 @@
.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
.TH MSI2LMP "1" "v3.9.11" "2024-09-06"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS
@ -101,7 +101,7 @@ msi2lmp decane -c 0 -f oplsaa
.SH COPYRIGHT
© 2003--2022 Sandia Corporation
© 2003--2024 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

458
doc/src/Bibliography.rst
View File

@ -1,6 +1,12 @@
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98
doc/src/Build_basics.rst
View File

@ -37,8 +37,9 @@ standard. A more detailed discussion of that is below.
.. code-block:: bash
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI, else no
-D BUILD_OMP=value # yes or no, default is yes if a compatible compiler is detected
-D BUILD_MPI=value # yes or no, default is yes if CMake finds MPI
-D BUILD_OMP=value # yes or no, default is yes if a compatible
# compiler is detected
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
@ -54,9 +55,9 @@ standard. A more detailed discussion of that is below.
.. code-block:: bash
make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
make mpi # parallel build, produces lmp_mpi using Makefile.mpi
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Any ``make machine`` command will look up the make settings from a
file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
@ -74,15 +75,15 @@ standard. A more detailed discussion of that is below.
this is ``-fopenmp``\ , which can be added to the ``CC`` and
``LINK`` makefile variables.
For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
For the serial build the following make variables are set (see ``src/MAKE/Makefile.serial``):
.. code-block:: make
CC = g++
LINK = g++
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
CC = g++
LINK = g++
MPI_INC = -I../STUBS
MPI_PATH = -L../STUBS
MPI_LIB = -lmpi_stubs
You also need to build the STUBS library for your platform before
making LAMMPS itself. A ``make serial`` build does this for you
@ -159,7 +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.
@ -231,24 +232,32 @@ LAMMPS.
.. code-block:: bash
# Building with GNU Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
# Building with Intel Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ \
-DCMAKE_Fortran_COMPILER=gfortran ../cmake
# Building with Intel Classic Compilers:
cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc \
-DCMAKE_Fortran_COMPILER=ifort ../cmake
# Building with Intel oneAPI Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx \
-DCMAKE_Fortran_COMPILER=ifx ../cmake
# Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
-DCMAKE_Fortran_COMPILER=flang ../cmake
# Building with PGI/Nvidia Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ \
-DCMAKE_Fortran_COMPILER=pgfortran ../cmake
# Building with the NVHPC Compilers:
cmake -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ \
-DCMAKE_Fortran_COMPILER=nvfortran ../cmake
For compiling with the Clang/LLVM compilers a CMake preset is
provided that can be loaded with
`-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the compiler
toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
``-C ../cmake/presets/clang.cmake``. Similarly,
``-C ../cmake/presets/intel.cmake`` should switch the compiler
toolchain to the legacy Intel compilers, ``-C ../cmake/presets/oneapi.cmake``
will switch to the LLVM based oneAPI Intel compilers,
and `-C ../cmake/presets/pgi.cmake`
will switch the compiler to the PGI compilers.
``-C ../cmake/presets/pgi.cmake`` will switch the compiler to the PGI compilers,
and ``-C ../cmake/presets/nvhpc.cmake`` will switch to the NVHPC compilers.
Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts.
@ -259,7 +268,7 @@ LAMMPS.
When the cmake command completes, it prints a summary to the
screen which compilers it is using and what flags and settings
will be used for the compilation. Note that if the top-level
compiler is mpicxx, it is simply a wrapper on a real compiler.
compiler is ``mpicxx``, it is simply a wrapper on a real compiler.
The underlying compiler info is what CMake will try to
determine and report. You should check to confirm you are
using the compiler and optimization flags you want.
@ -278,19 +287,19 @@ LAMMPS.
.. code-block:: make
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O
CC = mpicxx
CCFLAGS = -g -O3
LINK = mpicxx
LINKFLAGS = -g -O
Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
.. code-block:: make
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O
CC = g++
CCFLAGS = -g -O3
LINK = g++
LINKFLAGS = -g -O
.. note::
@ -316,10 +325,10 @@ LAMMPS.
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
``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
``src/MAKE/OPTIONS`` directory. They correspond to each of the 5
accelerator packages and their hardware variants:
.. code-block:: bash
@ -388,7 +397,8 @@ running LAMMPS from Python via its library interface.
make machine # build LAMMPS executable lmp_machine
make mode=static machine # same as "make machine"
make mode=shared machine # build LAMMPS shared lib liblammps_machine.so instead
make mode=shared machine # build LAMMPS shared lib liblammps_machine.so
# instead
The "static" build will generate a static library called
``liblammps_machine.a`` and an executable named ``lmp_machine``\ ,
@ -450,7 +460,7 @@ installation.
Including or removing debug support
-----------------------------------
By default the compilation settings will include the *-g* flag which
By default the compilation settings will include the ``-g`` flag which
instructs the compiler to include debug information (e.g. which line of
source code a particular instruction correspond to). This can be
extremely useful in case LAMMPS crashes and can help to provide crucial
@ -463,7 +473,7 @@ If this is a concern, you can change the compilation settings or remove
the debug information from the LAMMPS executable:
- **Traditional make**: edit your ``Makefile.<machine>`` to remove the
*-g* flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
``-g`` flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
- **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset
the applicable compiler flags (best done using the text mode or
graphical user interface).
@ -488,9 +498,12 @@ using CMake or Make.
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-D BUILD_LAMMPS_SHELL=value # yes or no (default). Build lammps-shell
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build lammps-gui
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt,
# 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).
@ -505,8 +518,9 @@ using CMake or Make.
make chain # build only chain tool
make micelle2d # build only micelle2d tool
cd lammps/tools/lammps-shell
make # build LAMMPS shell
.. note::
Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
----------

22
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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
@ -42,9 +42,9 @@ that want to modify or extend LAMMPS.
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
@ -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
@ -131,21 +131,21 @@ 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.
user interface. The ``-D`` flag can be used several times in one command.
For your convenience, we provide :ref:`CMake presets <cmake_presets>`
that combine multiple settings to enable optional LAMMPS packages or use
a different compiler tool chain. Those are loaded with the *-C* flag
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
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
command-line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
.. _cmake_multiconfig:
@ -171,7 +171,7 @@ files. E.g. with:
In that case the resulting binaries are not in the build folder directly
but in subdirectories corresponding to the build type (i.e. Release in
the example from above). Similarly, for running unit tests the
configuration is selected with the *-C* flag:
configuration is selected with the ``-C`` flag:
.. code-block:: bash

185
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@ -88,8 +88,8 @@ on recording all commands required to do the compilation.
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------
Address, Leak, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in the code
@ -110,6 +110,7 @@ compilation and linking stages. This is done through setting the
-D ENABLE_SANITIZER=none # no sanitizer active (default)
-D ENABLE_SANITIZER=address # enable address sanitizer / memory leak checker
-D ENABLE_SANITIZER=hwaddress # enable hardware assisted address sanitizer / memory leak checker
-D ENABLE_SANITIZER=leak # enable memory leak checker (only)
-D ENABLE_SANITIZER=undefined # enable undefined behavior sanitizer
-D ENABLE_SANITIZER=thread # enable thread sanitizer
@ -137,12 +138,27 @@ during development:
The status of this automated testing can be viewed on `https://ci.lammps.org
<https://ci.lammps.org>`_.
The scripts and inputs for integration, run, and regression testing
are maintained in a
`separate repository <https://github.com/lammps/lammps-testing>`_
of the LAMMPS project on GitHub. A few tests are also run as GitHub
Actions and their configuration files are in the ``.github/workflows/``
folder of the LAMMPS git tree.
The scripts and inputs for integration, run, and legacy regression
testing are maintained in a `separate repository
<https://github.com/lammps/lammps-testing>`_ of the LAMMPS project on
GitHub. A few tests are also run as GitHub Actions and their
configuration files are in the ``.github/workflows/`` folder of the
LAMMPS git tree.
Regression tests can also be performed locally with the :ref:`regression
tester tool <regression>`. The tool checks if a given LAMMPS binary run
with selected input examples produces thermo output that is consistent
with the provided log files. The script can be run in one pass over all
available input files, but it can also first create multiple lists of
inputs or folders that can then be run with multiple workers
concurrently to speed things up. Another mode allows to do a quick
check of inputs that contain commands that have changes in the current
checkout branch relative to a git branch. This works similar to the two
pass mode, but will select only shorter runs and no more than 100 inputs
that are chosen randomly. This ensures that this test runs
significantly faster compared to the full test run. These test runs can
also be performed with instrumented LAMMPS binaries (see previous
section).
The unit testing facility is integrated into the CMake build process of
the LAMMPS source code distribution itself. It can be enabled by
@ -152,7 +168,12 @@ development headers to compile (if those are not found locally a recent
version of that library will be downloaded and compiled along with
LAMMPS and the test programs) and will download and compile a specific
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
test framework that is used to implement the tests.
test framework that is used to implement the tests. Those unit tests
may be combined with memory access and leak checking with valgrind
(see below for how to enable it). In that case, running so-called
death tests will create a lot of false positives and thus they can be
disabled by configuring compilation with the additional setting
``-D SKIP_DEATH_TESTS=on``.
.. admonition:: Software version and LAMMPS configuration requirements
:class: note
@ -175,24 +196,24 @@ The output of this command will be looking something like this:
$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: RunLammps
1/563 Test #1: RunLammps .......................................... Passed 0.28 sec
1/563 Test #1: RunLammps .................................. Passed 0.28 sec
Start 2: HelpMessage
2/563 Test #2: HelpMessage ........................................ Passed 0.06 sec
2/563 Test #2: HelpMessage ................................ Passed 0.06 sec
Start 3: InvalidFlag
3/563 Test #3: InvalidFlag ........................................ Passed 0.06 sec
3/563 Test #3: InvalidFlag ................................ Passed 0.06 sec
Start 4: Tokenizer
4/563 Test #4: Tokenizer .......................................... Passed 0.05 sec
4/563 Test #4: Tokenizer .................................. Passed 0.05 sec
Start 5: MemPool
5/563 Test #5: MemPool ............................................ Passed 0.05 sec
5/563 Test #5: MemPool .................................... Passed 0.05 sec
Start 6: ArgUtils
6/563 Test #6: ArgUtils ........................................... Passed 0.05 sec
6/563 Test #6: ArgUtils ................................... Passed 0.05 sec
[...]
Start 561: ImproperStyle:zero
561/563 Test #561: ImproperStyle:zero ................................. Passed 0.07 sec
561/563 Test #561: ImproperStyle:zero ......................... Passed 0.07 sec
Start 562: TestMliapPyUnified
562/563 Test #562: TestMliapPyUnified ................................. Passed 0.16 sec
562/563 Test #562: TestMliapPyUnified ......................... Passed 0.16 sec
Start 563: TestPairList
563/563 Test #563: TestPairList ....................................... Passed 0.06 sec
563/563 Test #563: TestPairList ............................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 563
@ -207,24 +228,25 @@ The output of this command will be looking something like this:
The ``ctest`` command has many options, the most important ones are:
.. list-table::
:widths: 20 80
* - Option
- Function
* - -V
* - ``-V``
- verbose output: display output of individual test runs
* - -j <num>
* - ``-j <num>``
- parallel run: run <num> tests in parallel
* - -R <regex>
* - ``-R <regex>``
- run subset of tests matching the regular expression <regex>
* - -E <regex>
* - ``-E <regex>``
- exclude subset of tests matching the regular expression <regex>
* - -L <regex>
* - ``-L <regex>``
- run subset of tests with a label matching the regular expression <regex>
* - -LE <regex>
* - ``-LE <regex>``
- exclude subset of tests with a label matching the regular expression <regex>
* - -N
* - ``-N``
- dry-run: display list of tests without running them
* - -T memcheck
* - ``-T memcheck``
- run tests with valgrind memory checker (if available)
In its full implementation, the unit test framework will consist of multiple
@ -241,9 +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
@ -330,16 +352,17 @@ paths in the individual source files.
The force style test programs have a common set of options:
.. list-table::
:widths: 25 75
* - Option
- Function
* - -g <newfile>
* - ``-g <newfile>``
- regenerate reference data in new YAML file
* - -u
* - ``-u``
- update reference data in the original YAML file
* - -s
* - ``-s``
- print error statistics for each group of comparisons
* - -v
* - ``-v``
- verbose output: also print the executed LAMMPS commands
The ``ctest`` tool has no mechanism to directly pass flags to the individual
@ -353,10 +376,10 @@ set in an environment variable ``TEST_ARGS``. Example:
To add a test for a style that is not yet covered, it is usually best
to copy a YAML file for a similar style to a new file, edit the details
of the style (how to call it, how to set its coefficients) and then
run test command with either the *-g* and the replace the initial
test file with the regenerated one or the *-u* option. The *-u* option
run test command with either the ``-g`` and the replace the initial
test file with the regenerated one or the ``-u`` option. The ``-u`` option
will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested
so using ``-g`` is recommended unless the YAML file is fully tested
and working.
Some of the force style tests are rather slow to run and some are very
@ -397,7 +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
@ -506,27 +529,51 @@ After post-processing with ``gen_coverage_html`` the results are in
a folder ``coverage_html`` and can be viewed with a web browser.
The images below illustrate how the data is presented.
.. list-table::
.. only:: not latex
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
.. list-table::
Top of the overview page
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
Top of the overview page
Styles with good coverage
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
Styles with good coverage
Top of individual source page
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Top of individual source page
Source page with branches
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Source page with branches
.. only:: latex
.. figure:: JPG/coverage-overview-top.png
:width: 60%
Top of the overview page
.. figure:: JPG/coverage-overview-manybody.png
:width: 60%
Styles with good coverage
.. figure:: JPG/coverage-file-top.png
:width: 60%
Top of individual source page
.. figure:: JPG/coverage-file-branches.png
:width: 60%
Source page with branches
Coding style utilities
----------------------
@ -595,14 +642,38 @@ The following target are available for both, GNU make and CMake:
.. _gh-cli:
GitHub command line interface
GitHub command-line interface
-----------------------------
GitHub is developing a `tool for the command line
<https://cli.github.com>`_ that interacts with the GitHub website via a
command called ``gh``. This can be extremely convenient when working
with a Git repository hosted on GitHub (like LAMMPS). It is thus highly
recommended to install it when doing LAMMPS development.
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
when doing LAMMPS development. To use ``gh`` you must be within a git
checkout of a repository and you must obtain an authentication token
to connect your checkout with a GitHub user. This is done with the
command: ``gh auth login`` where you then have to follow the prompts.
Here are some examples:
The capabilities of the ``gh`` command is continually expanding, so
please see the documentation at https://cli.github.com/manual/
.. list-table::
:header-rows: 1
:widths: 34 66
* - Command
- Description
* - ``gh pr list``
- List currently open pull requests
* - ``gh pr checks 404``
- Shows the status of all checks for pull request #404
* - ``gh pr view 404``
- Shows the description and recent comments for pull request #404
* - ``gh co 404``
- Check out the branch from pull request #404; set up for pushing changes
* - ``gh issue list``
- List currently open issues
* - ``gh issue view 430 --comments``
- Shows the description and all comments for issue #430
The capabilities of the ``gh`` command are continually expanding, so
for more details please see the documentation at https://cli.github.com/manual/
or use ``gh --help`` or ``gh <command> --help`` for embedded help.

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@ -37,7 +37,7 @@ executable code from the library is copied into the calling executable.
.. tab:: CMake build
This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the
``LAMMPS_MACHINE`` name, installed with ``make install``, and the
``PKG_CONFIG_PATH`` environment variable has been updated to
include the ``liblammps.pc`` file installed into the configured
destination folder. The commands to compile and link a coupled
@ -45,8 +45,8 @@ executable code from the library is copied into the calling executable.
.. code-block:: bash
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
mpicc -c -O $(pkg-config --cflags liblammps) caller.c
mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
.. tab:: Traditional make
@ -59,10 +59,10 @@ executable code from the library is copied into the calling executable.
mpicc -c -O -I${HOME}/lammps/src caller.c
mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
The *-I* argument is the path to the location of the ``library.h``
The ``-I`` argument is the path to the location of the ``library.h``
header file containing the interface to the LAMMPS C-style library
interface. The *-L* argument is the path to where the
``liblammps_mpi.a`` file is located. The *-llammps_mpi* argument
interface. The ``-L`` argument is the path to where the
``liblammps_mpi.a`` file is located. The ``-llammps_mpi`` argument
is shorthand for telling the compiler to link the file
``liblammps_mpi.a``. If LAMMPS has been built as a shared
library, then the linker will use ``liblammps_mpi.so`` instead.
@ -142,7 +142,7 @@ When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included
in the shared library or registered as a dependent library in the shared
library file. Thus, those libraries need not be specified when linking
the calling executable. Only the *-I* flags are needed. So the example
the calling executable. Only the ``-I`` flags are needed. So the example
case from above of the serial version static LAMMPS library with the
POEMS package installed becomes:
@ -155,8 +155,8 @@ POEMS package installed becomes:
.. code-block:: bash
mpicc -c -O $(pkgconf liblammps --cflags) caller.c
mpicxx -o caller caller.o -$(pkgconf --libs)
mpicc -c -O $(pkg-config --cflags liblammps) caller.c
mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
.. tab:: Traditional make

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@ -25,7 +25,7 @@ additional tools to be available and functioning.
require adding flags like ``-std=c++11`` to enable the C++11 mode.
* 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
* 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.

59
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@ -62,6 +62,7 @@ packages:
* :ref:`POEMS <poems>`
* :ref:`PYTHON <python>`
* :ref:`QMMM <qmmm>`
* :ref:`RHEO <rheo>`
* :ref:`SCAFACOS <scafacos>`
* :ref:`VORONOI <voronoi>`
* :ref:`VTK <vtk>`
@ -99,10 +100,10 @@ versus make.
.. code-block:: bash
cd lammps/src
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed
Examples:
@ -171,18 +172,41 @@ make a copy of one of them and modify it to suit your needs.
.. code-block:: bash
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake # change settings to use the GNU compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake # change settings to use the PGI compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
# enable just a few core packages
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake
# enable most packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake
# enable packages which download sources or potential files
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake
# disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake
# change settings to use the Clang compilers by default
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake
# change settings to use the GNU compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake
# change settings to use the Intel compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake
# change settings to use the PGI compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake
# enable all packages
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake
# disable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake
# compile with MinGW cross-compilers
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake
# compile serial multi-arch binaries on macOS
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake
Presets that have names starting with "windows" are specifically for
compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@ -208,7 +232,8 @@ Example
# GPU package and configure it for using CUDA. You can run.
mkdir build
cd build
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
-D PKG_GPU=on -D GPU_API=cuda ../cmake
# to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on .

218
doc/src/Build_settings.rst
View File

@ -1,3 +1,7 @@
.. raw:: latex
\clearpage
Optional build settings
=======================
@ -8,7 +12,8 @@ explains how to do this for building both with CMake and make.
* `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 JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `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`_
* `Memory allocation alignment`_
* `Workaround for long long integers`_
* `Exception handling when using LAMMPS as a library`_ to capture errors
@ -19,7 +24,7 @@ explains how to do this for building both with CMake and make.
.. _cxx11:
C++11 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
@ -31,12 +36,16 @@ flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
CCFLAGS = -g -O3 -std=c++11
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>`.
----------
.. _fft:
FFT library
---------------------
-----------
When the KSPACE package is included in a LAMMPS build, the
:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
@ -58,8 +67,10 @@ libraries and better pipelining for packing and communication.
.. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
-D FFT=value # FFTW3 or MKL or NVPL or KISS,
# default is FFTW3 if found, else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or NVPL or KISS or CUFFT
# or HIPFFT or MKL_GPU, default is KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
@ -67,11 +78,11 @@ libraries and better pipelining for packing and communication.
.. note::
When the Kokkos variant of a package is compiled and selected at run time,
the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
the FFT library selected by the ``FFT_KOKKOS`` variable applies. Otherwise,
the FFT library selected by the FFT variable applies.
The same FFT settings apply to both. FFT_KOKKOS must be compatible with the
The same FFT settings apply to both. ``FFT_KOKKOS`` must be compatible with the
Kokkos back end - for example, when using the CUDA back end of Kokkos,
you must use either CUFFT or KISS.
you must use either ``CUFFT`` or ``KISS``.
Usually these settings are all that is needed. If FFTW3 is
selected, then CMake will try to detect, if threaded FFTW
@ -89,8 +100,11 @@ libraries and better pipelining for packing and communication.
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
# heFFTe back end
-D Heffte_ROOT=path # path to an existing heFFTe installation
-D nvpl_fft_INCLUDE_DIR=path # path to NVPL FFT include files
-D nvpl_fft_LIBRARY_DIR=path # path to NVPL FFT libraries
.. note::
@ -108,30 +122,58 @@ libraries and better pipelining for packing and communication.
.. code-block:: make
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_KOKKOS_CUFFT # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT_PACK_ARRAY if not specified
FFT_INC = -DFFT_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), NVPL, or MKL
FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), NVPL, MKL, CUFFT,
# HIPFFT, or MKL_GPU
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT_PACK_ARRAY if not specified
.. code-block:: make
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lhipfft # hipFFT either precision
FFT_LIB = -lcufft # cuFFT either precision
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler, serial interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compiler, serial interface
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core # MKL with GNU compiler, threaded interface
FFT_LIB = -lmkl_rt # MKL with automatic runtime selection of interface libs
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
# hipFFT either precision
FFT_LIB = -lhipfft
# cuFFT either precision
FFT_LIB = -lcufft
# MKL_GPU either precision
FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -lmkl_core -ltbb
# FFTW3 double precision
FFT_LIB = -lfftw3
# FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3_omp
# FFTW3 single precision
FFT_LIB = -lfftw3 -lfftw3f
# serial MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
# serial MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
# threaded MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
# threaded MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core
# MKL with automatic runtime selection of interface libs
FFT_LIB = -lmkl_rt
# threaded NVPL FFT
FFT_LIB = -lnvpl_fftw
As with CMake, you do not need to set paths in ``FFT_INC`` or
``FFT_PATH``, if the compiler can find the FFT header and library
@ -147,11 +189,11 @@ libraries and better pipelining for packing and communication.
FFT_PATH =
FFT_LIB = $(heffte_link) $(heffte_libs)
The heFFTe install path will contain `HeffteMakefile.in`.
which will define the `heffte_` include variables needed to link to heFFTe from
The heFFTe install path will contain ``HeffteMakefile.in``.
which will define the ``heffte_`` include variables needed to link to heFFTe from
an external project using traditional make.
The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
The ``-DFFT_HEFFTE`` is required to switch to using heFFTe, while the optional ``-DFFT_HEFFTE_FFTW``
selects the desired heFFTe back end, e.g., ``-DFFT_HEFFTE_FFTW`` or ``-DFFT_HEFFTE_MKL``,
omitting the variable will default to the `stock` back end.
The heFFTe `stock` back end is intended to be used for testing and debugging,
but is not performance optimized for large scale production runs.
@ -179,17 +221,22 @@ it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type ``./configure --help`` to see
the ``--prefix`` option of configure. Type ``./configure --help`` to see
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
above).
The NVIDIA Performance Libraries (NVPL) FFT library is optimized for NVIDIA
Grace Armv9.0 architecture. You can download it from https://docs.nvidia.com/nvpl/
The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
AMD's HIP installations, respectively. These FFT libraries require the
Kokkos acceleration package to be enabled and the Kokkos back end to be
GPU-resident (i.e., HIP or CUDA).
GPU-resident (i.e., HIP or CUDA). Similarly, GPU offload of FFTs on
Intel GPUs with oneMKL currently requires the Kokkos acceleration
package to be enabled with the SYCL back end.
Performing 3d FFTs in parallel can be time-consuming due to data access
and required communication. This cost can be reduced by performing
@ -215,7 +262,7 @@ produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
modes (ARRAY, POINTER, MEMCPY) as set by the ``FFT_PACK`` syntax above.
Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
@ -232,6 +279,10 @@ and those variables will be passed into the heFFTe build.
----------
.. raw:: latex
\clearpage
.. _size:
Size of LAMMPS integer types and size limits
@ -272,7 +323,7 @@ LAMMPS system size restrictions
.. list-table::
:header-rows: 1
:widths: auto
:widths: 18 27 28 27
:align: center
* -
@ -341,8 +392,8 @@ in whichever ``lib/gpu/Makefile`` is used must be the same as above.
.. _graphics:
Output of JPG, PNG, and movie files
--------------------------------------------------
Output of JPEG, PNG, and movie files
------------------------------------
The :doc:`dump image <dump_image>` command has options to output JPEG or
PNG image files. Likewise, the :doc:`dump movie <dump_image>` command
@ -355,12 +406,13 @@ requires the following settings:
.. code-block:: bash
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG development files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB development files,
# else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
Usually these settings are all that is needed. If CMake cannot
find the graphics header, library, executable files, you can set
@ -382,8 +434,10 @@ requires the following settings:
LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h headers
# if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so)
# files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names
As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
@ -414,8 +468,8 @@ Read or write compressed files
If this option is enabled, large files can be read or written with
compression by ``gzip`` or similar tools by several LAMMPS commands,
including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
:doc:`dump <dump>`. Supported compression tools are currently
``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
:doc:`dump <dump>`. Supported compression tools and algorithms are currently
``gzip``, ``bzip2``, ``zstd``, ``xz``, ``lz4``, and ``lzma`` (via xz).
.. tabs::
@ -423,8 +477,8 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
.. code-block:: bash
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find the gzip program, else no
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find the gzip program
.. tab:: Traditional make
@ -446,18 +500,64 @@ during a run.
available using a compression library instead, which is what the
:ref:`COMPRESS package <PKG-COMPRESS>` enables.
--------------------------------------------------
.. _libcurl:
Support for downloading files
-----------------------------
.. versionadded:: 29Aug2024
The :doc:`geturl command <geturl>` command uses the `the libcurl library
<https://curl.se/libcurl/>`_ to download files. This requires that
LAMMPS is compiled accordingly which needs the following settings:
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D WITH_CURL=value # yes or no
# default = yes if CMake finds CURL development files, else no
Usually these settings are all that is needed. If CMake cannot
find the graphics header, library, executable files, you can set
these variables:
.. code-block:: bash
-D CURL_INCLUDE_DIR=path # path to folder which contains curl.h header file
-D CURL_LIBRARY=path # path to libcurls.a (.so) file
.. tab:: Traditional make
.. code-block:: make
LMP_INC = -DLAMMPS_CURL <other LMP_INC settings>
CURL_INC = -I/usr/local/include # path to curl folder with curl.h
CURL_PATH = -L/usr/lib # paths to libcurl.a(.so) if make cannot find it
CURL_LIB = -lcurl # library names
As with CMake, you do not need to set ``CURL_INC`` or ``CURL_PATH``,
if make can find the libcurl header and library files in their
default system locations. You must specify ``CURL_LIB`` with a
paths or linker flags to link to libcurl.
----------
.. _align:
Memory allocation alignment
---------------------------------------
---------------------------
This setting enables the use of the "posix_memalign()" call instead of
"malloc()" when LAMMPS allocates large chunks of memory. Vector
This setting enables the use of the ``posix_memalign()`` call instead of
``malloc()`` when LAMMPS allocates large chunks of memory. Vector
instructions on CPUs may become more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries. On most
current operating systems, the "malloc()" implementation returns
current operating systems, the ``malloc()`` implementation returns
pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being aligned
on 64-byte boundaries.
@ -471,9 +571,9 @@ on 64-byte boundaries.
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
"posix_memalign()" and revert to using the "malloc()" C-library
``posix_memalign()`` and revert to using the ``malloc()`` C-library
function instead. When compiling LAMMPS for Windows systems,
"malloc()" will always be used and this setting is ignored.
``malloc()`` will always be used and this setting is ignored.
.. tab:: Traditional make
@ -482,7 +582,7 @@ on 64-byte boundaries.
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
allocated with the "malloc()" function call
allocated with the ``malloc()`` function call
instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
Windows different function calls with different semantics for
allocating aligned memory, that are not compatible with how LAMMPS

6
doc/src/Build_windows.rst
View File

@ -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
doc/src/Classes_lammps.rst
View File

@ -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

39
doc/src/Commands_all.rst
View File

@ -1,26 +1,30 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 5
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. raw:: latex
\clearpage
General commands
================
An alphabetic list of general LAMMPS commands. Note that style
commands with many variants, can be more easily accessed via the small
table above.
An alphabetic list of general LAMMPS commands.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
@ -54,6 +58,7 @@ table above.
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
* :doc:`geturl <geturl>`
* :doc:`group <group>`
* :doc:`if <if>`
* :doc:`improper_coeff <improper_coeff>`
@ -121,7 +126,7 @@ commands have accelerated versions. This is indicated by an
additional letter in parenthesis: k = KOKKOS.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`dynamical_matrix (k) <dynamical_matrix>`
* :doc:`group2ndx <group2ndx>`

59
doc/src/Commands_bond.rst
View File

@ -1,21 +1,7 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:
Bond_style potentials
=====================
Bond styles
===========
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -23,11 +9,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
* :doc:`hybrid <bond_hybrid>`
* :doc:`hybrid (k) <bond_hybrid>`
*
*
*
*
*
@ -54,13 +42,14 @@ OPT.
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`rheo/shell <bond_rheo_shell>`
* :doc:`special <bond_special>`
* :doc:`table (o) <bond_table>`
.. _angle:
Angle_style potentials
======================
Angle styles
============
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -68,11 +57,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid <angle_hybrid>`
* :doc:`hybrid (k) <angle_hybrid>`
*
*
*
*
*
@ -89,6 +80,7 @@ OPT.
* :doc:`cosine/shift (o) <angle_cosine_shift>`
* :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
* :doc:`cosine/squared (o) <angle_cosine_squared>`
* :doc:`cosine/squared/restricted (o) <angle_cosine_squared_restricted>`
* :doc:`cross <angle_cross>`
* :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>`
@ -99,13 +91,13 @@ OPT.
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`spica (o) <angle_spica>`
* :doc:`spica (ko) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
Dihedral_style potentials
=========================
Dihedral styles
===============
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -113,11 +105,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <dihedral_none>`
* :doc:`zero <dihedral_zero>`
* :doc:`hybrid <dihedral_hybrid>`
* :doc:`hybrid (k) <dihedral_hybrid>`
*
*
*
*
*
@ -127,6 +121,7 @@ OPT.
* :doc:`charmmfsw (k) <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`
* :doc:`fourier (io) <dihedral_fourier>`
* :doc:`harmonic (iko) <dihedral_harmonic>`
* :doc:`helix (o) <dihedral_helix>`
@ -141,8 +136,8 @@ OPT.
.. _improper:
Improper_style potentials
=========================
Improper styles
===============
All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -150,11 +145,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <improper_none>`
* :doc:`zero <improper_zero>`
* :doc:`hybrid <improper_hybrid>`
* :doc:`hybrid (k) <improper_hybrid>`
*
*
*
*
*

40
doc/src/Commands_category.rst
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@ -1,3 +1,7 @@
.. raw:: latex
\clearpage
Commands by category
====================
@ -6,8 +10,8 @@ This page lists most of the LAMMPS commands, grouped by category. The
alphabetically. Style options for entries like fix, compute, pair etc.
have their own pages where they are listed alphabetically.
Initialization:
------------------------------
Initialization
--------------
.. table_from_list::
:columns: 5
@ -18,8 +22,8 @@ Initialization:
* :doc:`suffix <suffix>`
* :doc:`units <units>`
Setup simulation box:
------------------------------
Setup simulation box
--------------------
.. table_from_list::
:columns: 4
@ -31,8 +35,8 @@ Setup simulation box:
* :doc:`lattice <lattice>`
* :doc:`region <region>`
Setup atoms:
------------------------------
Setup atoms
-----------
.. table_from_list::
:columns: 4
@ -55,8 +59,8 @@ Setup atoms:
* :doc:`set <set>`
* :doc:`velocity <velocity>`
Force fields:
------------------------------
Force fields
------------
.. table_from_list::
:columns: 4
@ -79,8 +83,8 @@ Force fields:
* :doc:`pair_write <pair_write>`
* :doc:`special_bonds <special_bonds>`
Settings:
------------------------------
Settings
--------
.. table_from_list::
:columns: 4
@ -98,8 +102,8 @@ Settings:
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
Operations within timestepping (fixes) and diagnostics (computes):
------------------------------------------------------------------------------------------
Operations within timestepping (fixes) and diagnostics (computes)
-----------------------------------------------------------------
.. table_from_list::
:columns: 4
@ -111,8 +115,8 @@ Operations within timestepping (fixes) and diagnostics (computes):
* :doc:`uncompute <uncompute>`
* :doc:`unfix <unfix>`
Output:
------------------------------
Output
------
.. table_from_list::
:columns: 4
@ -131,8 +135,8 @@ Output:
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`
Actions:
------------------------------
Actions
-------
.. table_from_list::
:columns: 6
@ -146,8 +150,8 @@ Actions:
* :doc:`tad <tad>`
* :doc:`temper <temper>`
Input script control:
------------------------------
Input script control
--------------------
.. table_from_list::
:columns: 7

25
doc/src/Commands_compute.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================
Compute styles
==============
An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
Some styles have accelerated versions. This is indicated by
@ -21,7 +7,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k =
KOKKOS, o = OPENMP, t = OPT.
.. table_from_list::
:columns: 5
:columns: 4
* :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>`
@ -108,6 +94,10 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`pe/mol/tally <compute_tally>`
* :doc:`pe/tally <compute_tally>`
* :doc:`plasticity/atom <compute_plasticity_atom>`
* :doc:`pod/atom <compute_pod_atom>`
* :doc:`podd/atom <compute_pod_atom>`
* :doc:`pod/local <compute_pod_atom>`
* :doc:`pod/global <compute_pod_atom>`
* :doc:`pressure <compute_pressure>`
* :doc:`pressure/alchemy <compute_pressure_alchemy>`
* :doc:`pressure/uef <compute_pressure_uef>`
@ -122,6 +112,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`reduce <compute_reduce>`
* :doc:`reduce/chunk <compute_reduce_chunk>`
* :doc:`reduce/region <compute_reduce>`
* :doc:`rheo/property/atom <compute_rheo_property_atom>`
* :doc:`rigid/local <compute_rigid_local>`
* :doc:`saed <compute_saed>`
* :doc:`slcsa/atom <compute_slcsa_atom>`

20
doc/src/Commands_dump.rst
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@ -1,24 +1,10 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
Dump styles
===========
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`

38
doc/src/Commands_fix.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============
Fix styles
==========
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -21,13 +7,14 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 5
:columns: 4
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`add/heat <fix_add_heat>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`alchemy <fix_alchemy>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
@ -56,7 +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>`
@ -147,7 +134,7 @@ 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>`
@ -174,6 +161,8 @@ OPT.
* :doc:`phonon <fix_phonon>`
* :doc:`pimd/langevin <fix_pimd>`
* :doc:`pimd/nvt <fix_pimd>`
* :doc:`pimdb/langevin <fix_pimdb>`
* :doc:`pimdb/nvt <fix_pimdb>`
* :doc:`planeforce <fix_planeforce>`
* :doc:`plumed <fix_plumed>`
* :doc:`poems <fix_poems>`
@ -191,6 +180,7 @@ 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>`
@ -199,11 +189,17 @@ 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>`
* :doc:`rheo/pressure <fix_rheo_pressure>`
* :doc:`rheo/thermal <fix_rheo_thermal>`
* :doc:`rheo/viscosity <fix_rheo_viscosity>`
* :doc:`rhok <fix_rhok>`
* :doc:`rigid (o) <fix_rigid>`
* :doc:`rigid/meso <fix_rigid_meso>`
@ -275,7 +271,7 @@ 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>`

18
doc/src/Commands_input.rst
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@ -10,14 +10,14 @@ for any commands that may be processed later. Commands may set an
internal variable, read in a file, or run a simulation. These actions
can be grouped into three categories:
a) commands that change a global setting (examples: timestep, newton,
echo, log, thermo, restart),
a) commands that change a global setting (examples: :doc:`timestep <timestep>`, :doc:`newton <newton>`,
:doc:`echo <echo>`, :doc:`log <log>`, :doc:`thermo <thermo>`, :doc:`restart <restart>`),
b) commands that add, modify, remove, or replace "styles" that are
executed during a "run" (examples: pair_style, fix, compute, dump,
thermo_style, pair_modify), and
executed during a "run" (examples: :doc:`pair_style <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, :doc:`dump <dump>`,
:doc:`thermo_style <thermo_style>`, :doc:`pair_modify <pair_modify>`), and
c) commands that execute a "run" or perform some other computation or
operation (examples: print, run, minimize, temper, write_dump, rerun,
read_data, read_restart)
operation (examples: :doc:`print <print>`, :doc:`run <run>`, :doc:`minimize <minimize>`, :doc:`temper <temper>`, :doc:`write_dump <write_dump>`, :doc:`rerun <rerun>`,
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`)
Commands in category a) have default settings, which means you only
need to use the command if you wish to change the defaults.
@ -61,7 +61,7 @@ between commands in the c) category. The following rules apply:
<read_data>` command initializes the system by setting up the
simulation box and assigning atoms to processors. If default values
are not desired, the :doc:`processors <processors>` and
:doc:`boundary <boundary>` commands need to be used before read_data
:doc:`boundary <boundary>` commands need to be used before ``read_data``
to tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
@ -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
to have LAMMPS skip the execution of any "run", "minimize", or similar
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.

20
doc/src/Commands_kspace.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
KSpace solvers
==============
KSpace styles
=============
All LAMMPS :doc:`kspace_style <kspace_style>` solvers. Some styles have
accelerated versions. This is indicated by additional letters in
@ -21,7 +7,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`ewald (o) <kspace_style>`
* :doc:`ewald/disp <kspace_style>`

44
doc/src/Commands_pair.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
Pair styles
===========
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -21,20 +7,20 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 3
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>`
* :doc:`hybrid (ko) <pair_hybrid>`
* :doc:`hybrid/molecular (o) <pair_hybrid>`
* :doc:`hybrid/overlay (ko) <pair_hybrid>`
* :doc:`hybrid/scaled (o) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
* :doc:`tracker <pair_tracker>`
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -58,7 +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>`
@ -73,6 +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>`
@ -94,9 +81,10 @@ OPT.
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (gko) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -190,7 +178,7 @@ OPT.
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/long (gko) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
@ -245,7 +233,8 @@ OPT.
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pod <pair_pod>`
* :doc:`pedone (o) <pair_pedone>`
* :doc:`pod (k) <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
@ -258,6 +247,8 @@ OPT.
* :doc:`rebo (io) <pair_airebo>`
* :doc:`rebomos (o) <pair_rebomos>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`rheo <pair_rheo>`
* :doc:`rheo/solid <pair_rheo_solid>`
* :doc:`saip/metal (t) <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smatb <pair_smatb>`
@ -268,7 +259,7 @@ OPT.
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`soft (gko) <pair_soft>`
* :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj (g) <pair_sph_lj>`
@ -302,6 +293,7 @@ OPT.
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`uf3 (k) <pair_uf3>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`

12
doc/src/Commands_parse.rst
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@ -42,8 +42,8 @@ LAMMPS:
If the $ is followed by text in curly brackets '{}', then the
variable name is the text inside the curly brackets. If no curly
brackets follow the $, then the variable name is the single character
immediately following the $. Thus ${myTemp} and $x refer to variables
named "myTemp" and "x", while "$xx" will be interpreted as a variable
immediately following the $. Thus ``${myTemp}`` and ``$x`` refer to variables
named "myTemp" and "x", while ``$xx`` will be interpreted as a variable
named "x" followed by an "x" character.
How the variable is converted to a text string depends on what style
@ -79,10 +79,10 @@ LAMMPS:
Additionally, the entire "immediate" variable expression may be
followed by a colon, followed by a C-style format string,
e.g. ":%f" or ":%.10g". The format string must be appropriate for
e.g. ``:%f`` or ``:%.10g``. The format string must be appropriate for
a double-precision floating-point value. The format string is used
to output the result of the variable expression evaluation. If a
format string is not specified, a high-precision "%.20g" is used as
format string is not specified, a high-precision ``%.20g`` is used as
the default format.
This can be useful for formatting print output to a desired precision:
@ -101,8 +101,8 @@ LAMMPS:
variable b2 equal 4
print "B2 = ${b$a}"
Nor can you specify an expression like "$($x-1.0)" for an immediate
variable, but you could use $(v_x-1.0), since the latter is valid
Nor can you specify an expression like ``$($x-1.0)`` for an immediate
variable, but you could use ``$(v_x-1.0)``, since the latter is valid
syntax for an :doc:`equal-style variable <variable>`.
See the :doc:`variable <variable>` command for more details of how

35
doc/src/Commands_removed.rst
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@ -8,6 +8,18 @@ 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
------------------------------------------
@ -148,12 +160,19 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
and the :ref:`GPU package <PKG-GPU>` are maintained
and allow running LAMMPS with GPU acceleration.
restart2data tool
-----------------
i-PI tool
---------
.. versionchanged:: 27Jun2024
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPI via pip are provided.
LAMMPS shell
------------
.. versionchanged:: 29Aug2024
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
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>`

8
doc/src/Commands_structure.rst
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@ -8,10 +8,10 @@ page.
A LAMMPS input script typically has 4 parts:
1. :ref:`Initialization <init>`
2. :ref:`System definition <system>`
3. :ref:`Simulation settings <settings>`
4. :ref:`Run a simulation <run>`
#. :ref:`Initialization <init>`
#. :ref:`System definition <system>`
#. :ref:`Simulation settings <settings>`
#. :ref:`Run a simulation <run>`
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4

12
doc/src/Developer_atom.rst
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@ -2,7 +2,7 @@ Accessing per-atom data
-----------------------
This page discusses how per-atom data is managed in LAMMPS, how it can
be accessed, what communication patters apply, and some of the utility
be accessed, what communication patterns apply, and some of the utility
functions that exist for a variety of purposes.
@ -14,11 +14,11 @@ As described on the :doc:`parallel partitioning algorithms
simulation domain, either in a *brick* or *tiled* manner. Each MPI
process *owns* exactly one subdomain and the atoms within it. To compute
forces for tuples of atoms that are spread across sub-domain boundaries,
also a "halo" of *ghost* atoms are maintained within a the communication
also a "halo" of *ghost* atoms are maintained within the communication
cutoff distance of its subdomain.
The total number of atoms is stored in `Atom::natoms` (within any
typical class this can be referred to at `atom->natoms`. The number of
typical class this can be referred to at `atom->natoms`). The number of
*owned* (or "local" atoms) are stored in `Atom::nlocal`; the number of
*ghost* atoms is stored in `Atom::nghost`. The sum of `Atom::nlocal`
over all MPI processes should be `Atom::natoms`. This is by default
@ -27,8 +27,8 @@ LAMMPS stops with a "lost atoms" error. For convenience also the
property `Atom::nmax` is available, this is the maximum of
`Atom::nlocal + Atom::nghost` across all MPI processes.
Per-atom properties are either managed by the atom style, or individual
classes. or as custom arrays by the individual classes. If only access
Per-atom properties are either managed by the atom style, individual
classes, or as custom arrays by the individual classes. If only access
to *owned* atoms is needed, they are usually allocated to be of size
`Atom::nlocal`, otherwise of size `Atom::nmax`. Please note that not all
per-atom properties are available or updated on *ghost* atoms. For
@ -61,7 +61,7 @@ can be found via the `Atom::sametag` array. It points to the next atom
index with the same tag or -1 if there are no more atoms with the same
tag. The list will be exhaustive when starting with an index of an
*owned* atom, since the atom IDs are unique, so there can only be one
such atom. Example code to count atoms with same atom ID in subdomain:
such atom. Example code to count atoms with same atom ID in a subdomain:
.. code-block:: c++

9
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@ -69,7 +69,7 @@ The basic LAMMPS class hierarchy which is created by the LAMMPS class
constructor is shown in :ref:`class-topology`. When input commands
are processed, additional class instances are created, or deleted, or
replaced. Likewise, specific member functions of specific classes are
called to trigger actions such creating atoms, computing forces,
called to trigger actions such as creating atoms, computing forces,
computing properties, time-propagating the system, or writing output.
Compositing and Inheritance
@ -110,9 +110,10 @@ As mentioned above, there can be multiple instances of classes derived
from the ``Fix`` or ``Compute`` base classes. They represent a
different facet of LAMMPS' flexibility, as they provide methods which
can be called at different points within a timestep, as explained in
`Developer_flow`. This allows the input script to tailor how a specific
simulation is run, what diagnostic computations are performed, and how
the output of those computations is further processed or output.
the :doc:`How a timestep works <Developer_flow>` doc page. This allows
the input script to tailor how a specific simulation is run, what
diagnostic computations are performed, and how the output of those
computations is further processed or output.
Additional code sharing is possible by creating derived classes from the
derived classes (e.g., to implement an accelerated version of a pair

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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@ -128,7 +128,7 @@ reflect particles off box boundaries in the :doc:`FixWallReflect class
The ``decide()`` method in the Neighbor class determines whether
neighbor lists need to be rebuilt on the current timestep (conditions
can be changed using the :doc:`neigh_modify every/delay/check
<neigh_modify>` command. If not, coordinates of ghost atoms are
<neigh_modify>` command). If not, coordinates of ghost atoms are
acquired by each processor via the ``forward_comm()`` method of the Comm
class. If neighbor lists need to be built, several operations within
the inner if clause of the pseudocode are first invoked. The

2
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@ -433,7 +433,7 @@ from owned to ghost cells, or ghost to owned cells, respectively, as
described above. The *caller* argument should be one of these values
-- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
depending on the style of the caller class. The *ptr* argument is the
"this" pointer to the caller class. These 2 arguments are used to
"this" pointer to the caller class. These two arguments are used to
call back to pack()/unpack() functions in the caller class, as
explained below.

33
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@ -20,7 +20,7 @@ Available topics are:
Reading and parsing of text and text files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
It is frequently required for a class in LAMMPS to read in additional
Classes in LAMMPS frequently need to read in additional
data from a file, e.g. potential parameters from a potential file for
manybody potentials. LAMMPS provides several custom classes and
convenience functions to simplify the process. They offer the
@ -128,9 +128,8 @@ that determines the kind of neighbor list requested. The default value
used here asks for a perpetual "half" neighbor list.
Non-default values of the second argument need to be used to adjust a
neighbor list request to the specific needs of a style an additional
request flag is needed. The :doc:`tersoff <pair_tersoff>` pair style,
for example, needs a "full" neighbor list:
neighbor list request to the specific needs of a style. The :doc:`tersoff
<pair_tersoff>` pair style, for example, needs a "full" neighbor list:
.. code-block:: c++
@ -141,8 +140,8 @@ for example, needs a "full" neighbor list:
}
When a pair style supports r-RESPA time integration with different cutoff regions,
the request flag may depend on the corresponding r-RESPA settings. Here an example
from pair style lj/cut:
the request flag may depend on the corresponding r-RESPA settings. Here is an
example from pair style lj/cut:
.. code-block:: c++
@ -160,7 +159,7 @@ from pair style lj/cut:
}
Granular pair styles need neighbor lists based on particle sizes and not cutoff
and also may require to have the list of previous neighbors available ("history").
and also may need to store data across timesteps ("history").
For example with:
.. code-block:: c++
@ -169,7 +168,7 @@ For example with:
else neighbor->add_request(this, NeighConst::REQ_SIZE);
In case a class would need to make multiple neighbor list requests with different
settings each request can set an id which is then used in the corresponding
settings, each request can set an id which is then used in the corresponding
``init_list()`` function to assign it to the suitable pointer variable. This is
done for example by the :doc:`pair style meam <pair_meam>`:
@ -279,8 +278,8 @@ And here is how the code operates:
* The :doc:`thermo_style custom <thermo_style>` command defines
*ecouple* and *econserve* keywords.
* These keywords sum the energy contributions from all the
*ecouple_flag* = 1 fixes by invoking the energy_couple() method in
the Modify class, which calls the compute_scalar() method of each
*ecouple_flag* = 1 fixes by invoking the *energy_couple()* method in
the Modify class, which calls the *compute_scalar()* method of each
fix in the list.
------------------
@ -320,19 +319,19 @@ The fix must also do the following:
The ev_init() and ev_tally() methods also account for global and
peratom virial contributions. Thus you do not need to invoke the
v_init() and v_tally() methods, if the fix also calculates peratom
v_init() and v_tally() methods if the fix also calculates peratom
energies.
The fix must also specify whether (by default) to include or exclude
these contributions to the global/peratom energy/virial of the system.
For the fix to include the contributions, set either of both of these
For the fix to include the contributions, set either or both of these
variables in the constructor:
* *thermo_energy* = 1, for global and peratom energy
* *thermo_virial* = 1, for global and peratom virial
Note that these variables are zeroed in fix.cpp. Thus if you don't
set the variables, the contributions will be excluded (by default)
set the variables, the contributions will be excluded (by default).
However, the user has ultimate control over whether to include or
exclude the contributions of the fix via the :doc:`fix modify
@ -406,9 +405,11 @@ processor owns, within the global grid:
.. parsed-literal::
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells
nFOO_in = 3d decomposition brick
nFOO_fft = FFT decomposition brick
nFOO_out = 3d decomposition brick + ghost cells
where ``FOO`` corresponds to ``xlo, xhi, ylo, yhi, zlo,`` or ``zhi``.
The ``in`` and ``fft`` indices are from 0 to N-1 inclusive in each
dimension, where N is the grid size.

4
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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.

5
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@ -4,8 +4,7 @@ Communication
Following the selected partitioning scheme, all per-atom data is
distributed across the MPI processes, which allows LAMMPS to handle very
large systems provided it uses a correspondingly large number of MPI
processes. Since The per-atom data (atom IDs, positions, velocities,
types, etc.) To be able to compute the short-range interactions, MPI
processes. To be able to compute the short-range interactions, MPI
processes need not only access to the data of atoms they "own" but also
information about atoms from neighboring subdomains, in LAMMPS referred
to as "ghost" atoms. These are copies of atoms storing required
@ -37,7 +36,7 @@ be larger than half the simulation domain.
Efficient communication patterns are needed to update the "ghost" atom
data, since that needs to be done at every MD time step or minimization
step. The diagrams of the `ghost-atom-comm` figure illustrate how ghost
step. The diagrams of the :ref:`ghost-atom-comm` figure illustrate how ghost
atom communication is performed in two stages for a 2d simulation (three
in 3d) for both a regular and irregular partitioning of the simulation
box. For the regular case (left) atoms are exchanged first in the

4
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@ -93,7 +93,7 @@ processors, since each tile in the initial tiling overlaps with a
handful of tiles in the final tiling.
The transformations could also be done using collective communication
across all $P$ processors with a single call to ``MPI_Alltoall()``, but
across all :math:`P` processors with a single call to ``MPI_Alltoall()``, but
this is typically much slower. However, for the specialized brick and
pencil tiling illustrated in :ref:`fft-parallel` figure, collective
communication across the entire MPI communicator is not required. In
@ -138,7 +138,7 @@ grid/particle operations that LAMMPS supports:
:math:`O(P^{\frac{1}{2}})`.
- For efficiency in performing 1d FFTs, the grid transpose
operations illustrated in Figure \ref{fig:fft} also involve
operations illustrated in Figure :ref:`fft-parallel` also involve
reordering the 3d data so that a different dimension is contiguous
in memory. This reordering can be done during the packing or
unpacking of buffers for MPI communication.

2
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@ -149,7 +149,7 @@ supports:
- Dependent on the "pair" setting of the :doc:`newton <newton>` command,
the "half" neighbor lists may contain **all** pairs of atoms where
atom *j* is a ghost atom (i.e. when the newton pair setting is *off*)
atom *j* is a ghost atom (i.e. when the newton pair setting is *off*).
For the newton pair *on* setting the atom *j* is only added to the
list if its *z* coordinate is larger, or if equal the *y* coordinate
is larger, and that is equal, too, the *x* coordinate is larger. For

6
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@ -1,13 +1,13 @@
OpenMP Parallelism
^^^^^^^^^^^^^^^^^^
The styles in the INTEL, KOKKOS, and OPENMP package offer to use OpenMP
The styles in the INTEL, KOKKOS, and OPENMP packages offer to use OpenMP
thread parallelism to predominantly distribute loops over local data
and thus follow an orthogonal parallelization strategy to the
decomposition into spatial domains used by the :doc:`MPI partitioning
<Developer_par_part>`. For clarity, this section discusses only the
implementation in the OPENMP package, as it is the simplest. The INTEL
and KOKKOS package offer additional options and are more complex since
and KOKKOS packages offer additional options and are more complex since
they support more features and different hardware like co-processors
or GPUs.
@ -16,7 +16,7 @@ keep the changes to the source code small, so that it would be easier to
maintain the code and keep it in sync with the non-threaded standard
implementation. This is achieved by a) making the OPENMP version a
derived class from the regular version (e.g. ``PairLJCutOMP`` from
``PairLJCut``) and overriding only methods that are multi-threaded or
``PairLJCut``) and only overriding methods that are multi-threaded or
need to be modified to support multi-threading (similar to what was done
in the OPT package), b) keeping the structure in the modified code very
similar so that side-by-side comparisons are still useful, and c)

8
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@ -53,7 +53,7 @@ Members of ``lammpsplugin_t``
.. list-table::
:header-rows: 1
:widths: auto
:widths: 15 85
* - Member
- Description
@ -135,7 +135,7 @@ unique inside the entire LAMMPS executable.
Fix style example
^^^^^^^^^^^^^^^^^
If the factory function would be for a fix or compute, which take three
If the factory function is for a fix or compute, which take three
arguments (a pointer to the LAMMPS class, the number of arguments and the
list of argument strings), then the pointer type is ``lammpsplugin_factory2``
and it must be assigned to the *creator.v2* member of the plugin struct.
@ -271,7 +271,7 @@ Plugins need to be compiled with the same compilers and libraries
as the LAMMPS executable and library. Otherwise the plugin will likely
not load due to mismatches in the function signatures (LAMMPS is C++ so
scope, type, and number of arguments are encoded into the symbol names
and thus differences in them will lead to failed plugin load commands.
and thus differences in them will lead to failed plugin load commands).
Compilation of the plugin can be managed via both, CMake or traditional
GNU makefiles. Some examples that can be used as a template are in the
``examples/plugins`` folder. The CMake script code has some small
@ -283,7 +283,7 @@ in the ``examples/kim/plugin`` folder. No changes to the sources of the
KIM package themselves are needed; only the plugin interface and loader
code needs to be added. This example only supports building with CMake,
but is probably a more typical example. To compile you need to run CMake
with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
with ``-DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>``. Other
configuration setting are identical to those for compiling LAMMPS.
A second example for a plugin from a package is in the

35
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@ -44,7 +44,7 @@ available:
.. list-table::
:header-rows: 1
:widths: auto
:widths: 32 18 50
:align: left
* - File name:
@ -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 in either way used
for utility functions and for LAMMPS commands, but use the functions
``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 tries to match the grouping of the
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).
@ -272,7 +272,7 @@ 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
to also implement test wrappers in C++ that will call fortran functions
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.
@ -293,7 +293,7 @@ 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 of atoms with different properties is tested in different ways
deleting 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
@ -411,7 +411,7 @@ With this scheme a large fraction of the code of any tested pair style
will be executed and consistent results are required for different
settings and between different accelerated pair style variants and the
base class, as well as for computing individual pairs through the
``Pair::single()`` where supported.
``Pair::single()`` method where supported.
The ``test_pair_style`` tester is used with 4 categories of test inputs:
@ -443,7 +443,7 @@ 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, for as long as
given system. It does not matter if some forces are large, as long as
they do not diverge.
The template input files define a large number of index variables at the top
@ -476,7 +476,7 @@ 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
@ -535,7 +535,7 @@ 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 text invalid. If you are adding an
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
@ -543,7 +543,7 @@ Tests for the GPU package are time consuming and thus are only run
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 with using KOKKOS with GPU acceleration is currently not supported.
tests when 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"
@ -589,11 +589,10 @@ While the epsilon (relative precision) for a single, `IEEE 754 compliant
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
errors. In some cases specific properties of the tested style. 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()` functions,
and also due to the effect of compiler optimization or differences
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()`
functions, and also due to the effect of compiler optimization or differences
between compilers or platforms, epsilon may need to be further relaxed,
sometimes epsilon can be relaxed to 1.0e-12. If interpolation or lookup
tables are used, epsilon may need to be set to 1.0e-10 or even higher.
@ -610,7 +609,7 @@ and run the test with verbose output. For example,
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,

41
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@ -52,10 +52,9 @@ Rename of pack/unpack_comm() to pack/unpack_forward_comm()
.. versionchanged:: 8Aug2014
In this change set the functions to pack data into communication buffers
and to unpack data from communication buffers for :doc:`forward
communications <Developer_comm_ops>` were renamed from ``pack_comm()``
and ``unpack_comm()`` to ``pack_forward_comm()`` and
In this change set, the functions to pack/unpack data into communication buffers
for :doc:`forward communications <Developer_comm_ops>` were renamed from
``pack_comm()`` and ``unpack_comm()`` to ``pack_forward_comm()`` and
``unpack_forward_comm()``, respectively. Also the meaning of the return
value of these functions was changed: rather than returning the number
of items per atom stored in the buffer, now the total number of items
@ -109,7 +108,7 @@ Use ev_init() to initialize variables derived from eflag and vflag
There are several variables that need to be initialized based on
the values of the "eflag" and "vflag" variables and since sometimes
there are new bits added and new variables need to be set to 1 or 0.
To make this consistent, across all styles, there is now an inline
To make this consistent across all styles, there is now an inline
function ``ev_init(eflag, vflag)`` that makes those settings
consistently and calls either ``ev_setup()`` or ``ev_unset()``.
Example from a pair style:
@ -211,14 +210,14 @@ The :cpp:func:`utils::open_potential()
calls to ``force->open_potential()`` and should be used to replace
``fopen()`` for opening potential files for reading. The custom
function does three additional steps compared to ``fopen()``: 1) it will
try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an
try to parse the ``UNITS:`` and ``DATE:`` metadata and will stop with an
error on a units mismatch and will print the date info, if present, in
the log file; 2) for pair styles that support it, it will set up
possible automatic unit conversions based on the embedded unit
information and LAMMPS' current units setting; 3) it will not only try
to open a potential file at the given path, but will also search in the
folders listed in the ``LAMMPS_POTENTIALS`` environment variable. This
allows to keep potential files in a common location instead of having to
allows potential files to reside in a common location instead of having to
copy them around for simulations.
Old:
@ -246,36 +245,38 @@ to use scoped enumerators instead.
.. list-table::
:header-rows: 1
:widths: auto
:widths: 23 10 23 10 23 10
* - Symbolic Constant
- Value
- Symbolic Constant
- Value
- Symbolic Constant
- Value
* - Atom::GROW
- 0
- Atom::ATOMIC
- 0
- Atom::MAP_NONE
- 0
* - Atom::RESTART
- 1
- Atom::MOLECULAR
- 1
- Atom::MAP_ARRAY
- 1
* - Atom::BORDER
- 2
- Atom::TEMPLATE
- 2
- Atom::MAP_HASH
- 2
* - Atom::ATOMIC
* - AtomVec::PER_ATOM
- 0
- Atom::MAP_YES
- 3
* - Atom::MOLECULAR
- 1
- AtomVec::PER_ATOM
- 0
* - Atom::TEMPLATE
- 2
- AtomVec::PER_TYPE
- 1
- Atom::MAP_YES
- 3
Old:
@ -306,7 +307,7 @@ Simplify customized error messages
Aided by features of the bundled {fmt} library, error messages now
can have a variable number of arguments and the string will be interpreted
as a {fmt} style format string so that custom error messages can be
as a {fmt} style format string so that error messages can be
easily customized without having to use temporary buffers and ``sprintf()``.
Example:
@ -332,7 +333,7 @@ Use of "override" instead of "virtual"
.. versionchanged:: 17Feb2022
Since LAMMPS requires C++11 we switched to use the "override" keyword
Since LAMMPS requires C++11, we switched to use the "override" keyword
instead of "virtual" to indicate polymorphism in derived classes. This
allows the C++ compiler to better detect inconsistencies when an
override is intended or not. Please note that "override" has to be
@ -370,7 +371,7 @@ Simplified function names for forward and reverse communication
.. versionchanged:: 24Mar2022
Rather then using the function name to distinguish between the different
Rather than using the function name to distinguish between the different
forward and reverse communication functions for styles, LAMMPS now uses
the type of the "this" pointer argument.

9
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@ -211,6 +211,9 @@ Argument processing
.. doxygenfunction:: bounds
:project: progguide
.. doxygenfunction:: bounds_typelabel
:project: progguide
.. doxygenfunction:: expand_args
:project: progguide
@ -619,7 +622,7 @@ classes:
of a dense, symmetric, real matrix.
#. The "PEigenDense" class only calculates the principal eigenvalue
(ie. the largest or smallest eigenvalue), and its corresponding
(i.e. the largest or smallest eigenvalue), and its corresponding
eigenvector. However it is much more efficient than "Jacobi" when
applied to large matrices (larger than 13x13). PEigenDense also can
understand complex-valued Hermitian matrices.
@ -635,10 +638,10 @@ Tohoku University (under MIT license)
----------
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort)
:project: progguide
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3])
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort)
:project: progguide
---------------------------

1
doc/src/Developer_write.rst
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@ -12,3 +12,4 @@ details are provided for writing code for LAMMPS.
Developer_write_pair
Developer_write_fix
Developer_write_command

348
doc/src/Developer_write_command.rst Normal file
View File

@ -0,0 +1,348 @@
Writing a new command style
^^^^^^^^^^^^^^^^^^^^^^^^^^^
Command styles allow to do system manipulations or interfaces to the
operating system.
In the text below, we will discuss the implementation of one example. As
shown on the page for :doc:`writing or extending command styles
<Modify_command>`, in order to implement a new command style, a new class
must be written that is either directly or indirectly derived from the
``Command`` class. There is just one method that must be implemented:
``Command::command()``. In addition, a custom constructor is needed to get
access to the members of the ``LAMMPS`` class like the ``Error`` class to
print out error messages. The ``Command::command()`` method processes the
arguments passed to the command in the input and executes it. Any other
methods would be for the convenience of implementation of the new command.
In general, new command styles should be added to the :ref:`EXTRA-COMMAND
package <PKG-EXTRA-COMMAND>`. If you feel that your contribution should be
added to a different package, please consult with the :doc:`LAMMPS
developers <Intro_authors>` first. The contributed code needs to support
the :doc:`traditional GNU make build process <Build_make>` **and** the
:doc:`CMake build process <Build_cmake>`.
----
Case 1: Implementing the geturl command
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In this section, we will describe the procedure of adding a simple command
style to LAMMPS: the :doc:`geturl command <geturl>` that allows to download
files directly without having to rely on an external program like "wget" or
"curl". The complete implementation can be found in the files
``src/EXTRA-COMMAND/geturl.cpp`` and ``src/EXTRA-COMMAND/geturl.h`` of the
LAMMPS source code.
Interfacing the *libcurl* library
"""""""""""""""""""""""""""""""""
Rather than implementing the various protocols for downloading files, we
rely on an external library: `libcurl library <https:://curl.se/libcurl/>`_.
This requires that the library and its headers are installed. For the
traditional GNU make build system, this simply requires edits to the machine
makefile to add compilation flags like for other libraries. For the CMake
based build system, we need to add some lines to the file
``cmake/Modules/Packages/EXTRA-COMMAND.cmake``:
.. code-block:: cmake
find_package(CURL QUIET COMPONENTS HTTP HTTPS)
option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
if(WITH_CURL)
find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
target_link_libraries(lammps PRIVATE CURL::libcurl)
endif()
The first ``find_package()`` command uses a built-in CMake module to find
an existing *libcurl* installation with development headers and support for
using the HTTP and HTTPS protocols. The "QUIET" flag ensures that there is
no screen output and no error if the search fails. The status of the search
is recorded in the "${CURL_FOUND}" variable. That variable sets the default
of the WITH_CURL option, which toggles whether support for *libcurl* is included
or not.
The second ``find_package()`` uses the "REQUIRED" flag to produce an error
if the WITH_CURL option was set to ``True``, but no suitable *libcurl*
implementation with development support was found. This construct is used
so that the CMake script code inside the ``if(WITH_CURL)`` and ``endif()``
block can be expanded later to download and compile *libcurl* as part of the
LAMMPS build process, if it is not found locally. The
``target_compile_definitions()`` function added the define ``-DLAMMPS_CURL``
to the compilation flags when compiling objects for the LAMMPS library.
This allows to always compile the :doc:`geturl command <geturl>`, but use
pre-processing to compile in the interface to *libcurl* only when it is
present and usable and otherwise stop with an error message about the
unavailability of *libcurl* to execute the functionality of the command.
Header file
"""""""""""
The first segment of any LAMMPS source should be the copyright and
license statement. Note the marker in the first line to indicate to
editors like emacs that this file is a C++ source, even though the .h
extension suggests a C source (this is a convention inherited from the
very beginning of the C++ version of LAMMPS).
.. code-block:: c++
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
Every command style must be registered in LAMMPS by including the following
lines of code in the second part of the header after the copyright
message and before the include guards for the class definition:
.. code-block:: c++
#ifdef COMMAND_CLASS
// clang-format off
CommandStyle(geturl,GetURL);
// clang-format on
#else
This block between ``#ifdef COMMAND_CLASS`` and ``#else`` will be
included by the ``Input`` class in ``input.cpp`` to build a map of
"factory functions" that will create an instance of a Command class
and call its ``command()`` method. The map connects the name of the
command ``geturl`` with the name of the class ``GetURL``. During
compilation, LAMMPS constructs a file ``style_command.h`` that contains
``#include`` statements for all "installed" command styles. Before
including ``style_command.h`` into ``input.cpp``, the ``COMMAND_CLASS``
define is set and the ``CommandStyle(name,class)`` macro defined. The
code of the macro adds the installed command styles to the "factory map"
which enables the ``Input`` to execute the command.
The list of header files to include in ``style_command.h`` is automatically
updated by the build system if there are new files, so the presence of the
new header file in the ``src/EXTRA-COMMAND`` folder and the enabling of the
EXTRA-COMMAND package will trigger LAMMPS to include the new command style
when it is (re-)compiled. The "// clang-format" format comments are needed
so that running :ref:`clang-format <clang-format>` on the file will not
insert unwanted blanks which would break the ``CommandStyle`` macro.
The third part of the header file is the actual class definition of the
``GetURL`` class. This has the custom constructor and the ``command()``
method implemented by this command style. For the constructor there is
nothing to do but to pass the ``lmp`` pointer to the base class. Since the
``command()`` method is labeled "virtual" in the base class, it must be
given the "override" property.
.. code-block:: c++
#ifndef LMP_GETURL_H
#define LMP_GETURL_H
#include "command.h"
namespace LAMMPS_NS {
class GetURL : public Command {
public:
GetURL(class LAMMPS *lmp) : Command(lmp) {};
void command(int, char **) override;
};
} // namespace LAMMPS_NS
#endif
#endif
The "override" property helps to detect unexpected mismatches because
compilation will stop with an error in case the signature of a function
is changed in the base class without also changing it in all derived
classes.
Implementation file
"""""""""""""""""""
We move on to the implementation of the ``GetURL`` class in the
``geturl.cpp`` file. This file also starts with a LAMMPS copyright and
license header. Below that notice is typically the space where comments may
be added with additional information about this specific file, the
author(s), affiliation(s), and email address(es). This way the contributing
author(s) can be easily contacted, when there are questions about the
implementation later. Since the file(s) may be around for a long time, it
is beneficial to use some kind of "permanent" email address, if possible.
.. code-block:: c++
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
------------------------------------------------------------------------- */
#include "geturl.h"
#include "comm.h"
#include "error.h"
#if defined(LAMMPS_CURL)
#include <curl/curl.h>
#endif
using namespace LAMMPS_NS;
The second section of the implementation file has various include
statements. The include file for the class header has to come first, then a
couple of LAMMPS classes (sorted alphabetically) followed by the header for
the *libcurl* interface. This is wrapped into an ``#ifdef`` block so that
LAMMPS will compile this file without error when the *libcurl* header is not
available and thus the define not set. The final statement of this segment
imports the ``LAMMPS_NS::`` namespace globally for this file. This way, all
LAMMPS specific functions and classes do not have to be prefixed with
``LAMMPS_NS::``.
The command() function (required)
"""""""""""""""""""""""""""""""""
Since the required custom constructor is trivial and implemented in the
header, there is only one function that must be implemented for a command
style and that is the ``command()`` function.
.. code-block:: c++
void GetURL::command(int narg, char **arg)
{
#if !defined(LAMMPS_CURL)
error->all(FLERR, "LAMMPS has not been compiled with libcurl support");
#else
if (narg < 1) utils::missing_cmd_args(FLERR, "geturl", error);
int verify = 1;
int overwrite = 1;
int verbose = 0;
This first part also has the ``#ifdef`` block depending on the LAMMPS_CURL
define. This way the command will simply print an error, if *libcurl* is
not available but will not fail to compile. Furthermore, it sets the
defaults for the following optional arguments.
.. code-block:: c++
// process arguments
std::string url = arg[0];
// sanity check
if ((url.find(':') == std::string::npos) || (url.find('/') == std::string::npos))
error->all(FLERR, "URL '{}' is not a supported URL", url);
std::string output = url.substr(url.find_last_of('/') + 1);
if (output.empty()) error->all(FLERR, "URL '{}' must end in a file string", url);
This block stores the positional, i.e. non-optional argument of the URL to
be downloaded and adds a couple of sanity checks on the string to make sure it is
a valid URL. Also it derives the default name of the output file from the URL.
.. code-block:: c++
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg], "output") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl output", error);
output = arg[iarg + 1];
++iarg;
} else if (strcmp(arg[iarg], "overwrite") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl overwrite", error);
overwrite = utils::logical(FLERR, arg[iarg + 1], false, lmp);
++iarg;
} else if (strcmp(arg[iarg], "verify") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl verify", error);
verify = utils::logical(FLERR, arg[iarg + 1], false, lmp);
++iarg;
} else if (strcmp(arg[iarg], "verbose") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl verbose", error);
verbose = utils::logical(FLERR, arg[iarg + 1], false, lmp);
++iarg;
} else {
error->all(FLERR, "Unknown geturl keyword: {}", arg[iarg]);
}
++iarg;
}
This block parses the optional arguments following the URL and stops with an
error if there are arguments missing or an unknown argument is encountered.
.. code-block:: c++
// only download files from rank 0
if (comm->me != 0) return;
if (!overwrite && platform::file_is_readable(output)) return;
// open output file for writing
FILE *out = fopen(output.c_str(), "wb");
if (!out)
error->all(FLERR, "Cannot open output file {} for writing: {}", output, utils::getsyserror());
Here all MPI ranks other than 0 will return, so that the URL download will
only happen from a single MPI rank. For that rank the output file is opened
for writing using the C library function ``fopen()``.
.. code-block:: c++
// initialize curl and perform download
CURL *curl;
curl_global_init(CURL_GLOBAL_DEFAULT);
curl = curl_easy_init();
if (curl) {
(void) curl_easy_setopt(curl, CURLOPT_URL, url.c_str());
(void) curl_easy_setopt(curl, CURLOPT_WRITEDATA, (void *) out);
(void) curl_easy_setopt(curl, CURLOPT_FILETIME, 1L);
(void) curl_easy_setopt(curl, CURLOPT_FAILONERROR, 1L);
if (verbose && screen) {
(void) curl_easy_setopt(curl, CURLOPT_VERBOSE, 1L);
(void) curl_easy_setopt(curl, CURLOPT_STDERR, (void *) screen);
}
if (!verify) {
(void) curl_easy_setopt(curl, CURLOPT_SSL_VERIFYPEER, 0L);
(void) curl_easy_setopt(curl, CURLOPT_SSL_VERIFYHOST, 0L);
}
auto res = curl_easy_perform(curl);
if (res != CURLE_OK) {
long response = 0L;
curl_easy_getinfo(curl, CURLINFO_RESPONSE_CODE, &response);
error->one(FLERR, "Download of {} failed with: {} {}", output, curl_easy_strerror(res),
response);
}
curl_easy_cleanup(curl);
This block now implements the actual URL download with the selected options
via the "easy" interface of *libcurl*. For the details of what these
function calls do, please have a look at the `*libcurl documentation
<https://curl.se/libcurl/c/allfuncs.html>`_.
.. code-block:: c++
}
curl_global_cleanup();
fclose(out);
#endif
}
Finally, the previously opened file is closed and the command is complete.

19
doc/src/Developer_write_fix.rst
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@ -74,8 +74,7 @@ The next method we need to implement is ``setmask()``:
Here the we specify which methods of the fix should be called during
:doc:`execution of a timestep <Developer_flow>`. The constant
``END_OF_STEP`` corresponds to the ``end_of_step()`` method. The most
important available methods that are called during a timestep.
``END_OF_STEP`` corresponds to the ``end_of_step()`` method.
.. code-block:: c++
@ -127,7 +126,7 @@ there is no need to inherit from it directly.
The code above computes average velocity for all particles in the
simulation. Yet you have one unused parameter in fix call from the
script: ``group_name``. This parameter specifies the group of atoms
used in the fix. So we should compute average for all particles in the
used in the fix. So we should compute the average for all particles in the
simulation only if ``group_name == "all"``, but it can be any group.
The group membership information of an atom is contained in the *mask*
property of an atom and the bit corresponding to a given group is
@ -142,7 +141,7 @@ stored in the groupbit variable which is defined in Fix base class:
}
Class Atom encapsulates atoms positions, velocities, forces, etc. Users
can access them using particle index. Note, that particle indexes are
can access them using the particle index. Note, that particle indexes are
usually changed every few timesteps because of neighbor list rebuilds
and spatial sorting (to improve cache efficiency).
@ -154,8 +153,8 @@ this situation there are several methods which should be implemented:
- ``double memory_usage()``: return how much memory the fix uses (optional)
- ``void grow_arrays(int)``: do reallocation of the per-particle arrays in your fix
- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
information to j-th. Used when atom sorting is performed. if delflag is set
and atom j owns a body, move the body information to atom i.
information to j-th particle position. Used when atom sorting is performed.
if delflag is set and atom j owns a body, move the body information to atom i.
- ``void set_arrays(int i)``: sets i-th particle related information to zero
Note, that if your class implements these methods, it must add calls of
@ -230,11 +229,11 @@ is just a bunch of template functions for allocating 1D and 2D
arrays. So you need to add include ``memory.h`` to have access to them.
Finally, if you need to write/read some global information used in
your fix to the restart file, you might do it by setting flag
``restart_global = 1`` in the constructor and implementing methods void
``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
your fix to the restart file, you might do it by setting the flag
``restart_global = 1`` in the constructor and implementing methods
``void write_restart(FILE *fp)`` and ``void restart(char *buf)``.
If, in addition, you want to write the per-atom property to restart
files additional settings and functions are needed:
files then these additional settings and functions are needed:
- a fix flag indicating this needs to be set ``restart_peratom = 1;``
- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called

69
doc/src/Developer_write_pair.rst
View File

@ -50,6 +50,30 @@ We are looking at the following cases:
- `Case 3: a potential requiring communication`_
- `Case 4: potentials without a compute() function`_
Package and build system considerations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In general, new pair styles should be added to the :ref:`EXTRA-PAIR
package <PKG-EXTRA-PAIR>` unless they are an accelerated pair style and
then they should be added to the corresponding accelerator package
(:ref:`GPU <PKG-GPU>`, :ref:`INTEL <PKG-INTEL>`, :ref:`KOKKOS
<PKG-KOKKOS>`, :ref:`OPENMP <PKG-OPENMP>`, :ref:`OPT <PKG-OPT>`). If
you feel that your contribution should be added to a different package,
please consult with the LAMMPS developers first.
The contributed code needs to support the :doc:`traditional GNU make
build process <Build_make>` **and** the :doc:`CMake build process
<Build_cmake>`. For the GNU make process and if the package has an
``Install.sh`` file, most likely that file needs to be updated to
correctly copy the sources when installing the package and properly
delete them when uninstalling. This is particularly important when
added a new pair style that is a derived class from an existing pair
style in a package, so that its installation depends on the the
installation status of the package of the derived class. For the CMake
process, it is sometimes necessary to make changes to the package
specific CMake scripting in ``cmake/Modules/Packages``.
----
Case 1: a pairwise additive model
@ -136,7 +160,7 @@ message and before the include guards for the class definition:
#endif
This block of between ``#ifdef PAIR_CLASS`` and ``#else`` will be
This block between ``#ifdef PAIR_CLASS`` and ``#else`` will be
included by the ``Force`` class in ``force.cpp`` to build a map of
"factory functions" that will create an instance of these classes and
return a pointer to it. The map connects the name of the pair style,
@ -286,7 +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
@ -347,9 +371,9 @@ but moving this to a separate function allows users to change global
settings like the default cutoff without having to reissue all
pair_coeff commands or re-read the ``Pair Coeffs`` sections from the
data file. In the ``settings()`` function, also the arrays for storing
parameters, to define cutoffs, track with pairs of parameters have been
explicitly set are allocated and, if needed, initialized. In this case,
the memory allocation and initialization is moved to a function
parameters, to define cutoffs, track which pairs of parameters have been
explicitly set and allocated and, if needed, initialized. In this case,
the memory allocation and initialization are moved to a function
``allocate()``.
.. code-block:: c++
@ -564,17 +588,20 @@ loop atoms are also initialized.
jnum = numneigh[i];
The inner loop (index *j*) processes the neighbor lists. The neighbor
list code encodes in the upper 2 bits whether a pair is a regular pair
of neighbor (= 0) or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3)
:doc:`"special" neighbor <special_bonds>`. The ``sbmask()`` inline
function extracts those bits and converts them into a number. This
number is used to look up the corresponding scaling factor for the
non-bonded interaction from the ``force->special_lj`` array and stores
it in the `factor_lj` variable. Due to the additional bits, the value
of *j* would be out of range when accessing data from per-atom arrays,
so we apply the NEIGHMASK constant with a bit-wise and operation to mask
them out. This step *must* be done, even if a pair style does not use
special bond scaling of forces and energies to avoid segmentation faults.
list code encodes extra information using the upper 3 bits. The 2
highest bits encode whether a pair is a regular pair of neighbor (= 0)
or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3) :doc:`"special" neighbor
<special_bonds>`. The next highest bit encodes whether the pair stores
data in a ``fix neigh/history`` instance (an undocumented internal fix
style). The ``sbmask()`` inline function extracts those bits and
converts them into a number. This number is used to look up the
corresponding scaling factor for the non-bonded interaction from the
``force->special_lj`` array and stores it in the `factor_lj` variable.
Due to the additional bits, the value of *j* would be out of range when
accessing data from per-atom arrays, so we apply the NEIGHMASK constant
with a bit-wise and operation to mask them out. This step *must* be
done, even if a pair style does not use special bond scaling of forces
and energies to avoid segmentation faults.
With the corrected *j* index, it is now possible to compute the distance
of the pair. For efficiency reasons, the square root is only taken
@ -864,10 +891,10 @@ 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
parameters will be read from the data file, if present, and
:doc:`pair_coeff commands <pair_coeff>` may not be needed.
The member variable ``writedata`` should be set to 1 in the constructor,
@ -1095,7 +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
@ -1329,8 +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++

3
doc/src/Errors_common.rst
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@ -39,7 +39,8 @@ figure out your physics or numerical mistakes, like choosing too big a
timestep, specifying erroneous force field coefficients, or putting 2
atoms on top of each other! If you run into errors that LAMMPS
does not catch that you think it should flag, please send an email to
the `developers <https://www.lammps.org/authors.html>`_.
the `developers <https://www.lammps.org/authors.html>`_ or create an new
topic on the dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
If you get an error message about an invalid command in your input
script, you can determine what command is causing the problem by

4
doc/src/Errors_debug.rst
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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

72
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@ -13,15 +13,67 @@ discussions of such cases.
Unknown identifier in data file
-------------------------------
This error happens when LAMMPS encounters a line of text in an unexpected format
while reading a data file. This is most commonly cause by inconsistent header and
section data. The header section informs LAMMPS how many entries or lines are expected in the
various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
or stop reading before the section has ended.
This error happens when LAMMPS encounters a line of text with an
unexpected keyword while :doc:`reading a data file <read_data>`. This
would be either header keywords or section header keywords. This is
most commonly due to a mistyped keyword or due to a keyword that is
inconsistent with the :doc:`atom style <atom_style>` used.
Such a mismatch can happen unexpectedly when the first line of the data
is *not* a comment as required by the format. That would result in
LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
is treated as a comment.
The header section informs LAMMPS how many entries or lines are expected
in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
the data file. If there is a mismatch, LAMMPS will either keep reading
beyond the end of a section or stop reading before the section has
ended. In that case the next line will not contain a recognized keyword.
Such a mismatch can also happen when the first line of the data
is *not* a comment as required by the format, but a line with a valid
header keyword. That would result in LAMMPS expecting, for instance,
0 atoms because the "atoms" header line is the first line and thus
treated as a comment.
Another possibility to trigger this error is to have a keyword in the
data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
but the :doc:`read_data <read_data>` command is missing the (optional)
arguments that identify the fix and the header keyword and section
keyword or those arguments are inconsistent with the keywords in the
data file.
.. _err0002:
Incorrect format in ... section of data file
--------------------------------------------
This error happens when LAMMPS reads the contents of a section of a
:doc:`data file <read_data>` and the number of parameters in the line
differs from what is expected. This most commonly happens, when the
atom style is different from what is expected for a specific data file
since changing the atom style usually changes the format of the line.
This error can also happen 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.
.. _err0003:
Illegal variable command: expected X arguments but found Y
----------------------------------------------------------
This error indicates that there are the wrong number of arguments for a
specific variable command, but a common reason for that is a variable
expression that has whitespace but is not enclosed in single or double
quotes.
To explain, the LAMMPS input parser reads and processes lines. The
resulting line is broken down into "words". Those are usually
individual commands, labels, names, values separated by whitespace (a
space or tab character). For "words" that may contain whitespace, they
have to be enclosed in single (') or double (") quotes. The parser will
then remove the outermost pair of quotes and then pass that string as
"word" to the variable command.
Thus missing quotes or accidental extra whitespace will lead to the
error shown in the header because the unquoted whitespace will result
in the text being broken into more "words", i.e. the variable expression
being split.

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