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Merge branch 'lammps:develop' into mala

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This commit is contained in:
Lenz Fiedler
2023-05-23 10:23:42 +02:00
committed by GitHub
parent be94176c03 ed03d04a70
commit e169327162
7500 changed files with 953099 additions and 310425 deletions
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1
.gitattributes vendored
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@ -3,6 +3,7 @@
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore
CITATION.cff export-ignore
* text=auto
*.jpg -text
*.pdf -text

76
.github/CODEOWNERS vendored
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@ -13,39 +13,45 @@ lib/kim/* @ellio167
lib/mesont/* @iafoss
# whole packages
src/COMPRESS/* @rbberger
src/GPU/* @ndtrung81
src/KOKKOS/* @stanmoore1
src/KIM/* @ellio167
src/LATTE/* @cnegre
src/MESSAGE/* @sjplimp
src/MLIAP/* @athomps
src/SNAP/* @athomps
src/SPIN/* @julient31
src/ADIOS/* @pnorbert
src/AMOEBA/* @sjplimp
src/BPM/* @jtclemm
src/BROWNIAN/* @samueljmcameron
src/CG-DNA/* @ohenrich
src/CG-SDK/* @akohlmey
src/CG-SPICA/* @yskmiyazaki
src/COLVARS/* @giacomofiorin
src/COMPRESS/* @rbberger
src/DIELECTRIC/* @ndtrung81
src/ELECTRODE/* @ludwig-ahrens
src/FEP/* @agiliopadua
src/ML-HDNNP/* @singraber
src/GPU/* @ndtrung81
src/GRANULAR/* @jtclemm @dsbolin
src/INTEL/* @wmbrownintel
src/KIM/* @ellio167
src/KOKKOS/* @stanmoore1
src/LATTE/* @cnegre
src/MANIFOLD/* @Pakketeretet2
src/MDI/* @taylor-a-barnes
src/MDI/* @taylor-a-barnes @sjplimp
src/MEAM/* @martok
src/MESONT/* @iafoss
src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde @rohskopf
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
src/ML-PACE/* @yury-lysogorskiy
src/PLUMED/* @gtribello
src/PHONON/* @lingtikong
src/PTM/* @pmla
src/OPENMP/* @akohlmey
src/PHONON/* @lingtikong
src/PLUGIN/* @akohlmey
src/PLUMED/* @gtribello
src/PTM/* @pmla
src/QMMM/* @akohlmey
src/REAXFF/* @hasanmetin @stanmoore1
src/REACTION/* @jrgissing
src/REAXFF/* @hasanmetin @stanmoore1
src/SCAFACOS/* @rhalver
src/SNAP/* @athomps
src/SPIN/* @julient31
src/TALLY/* @akohlmey
src/UEF/* @danicholson
src/VTK/* @rbberger
@ -57,7 +63,10 @@ src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/MISC/*_tracker.* @jtclemm
src/MC/fix_gcmc.* @athomps
src/MC/fix_sgcmc.* @athomps
# core LAMMPS classes
src/lammps.* @sjplimp
@ -119,41 +128,46 @@ src/dump_movie.* @akohlmey
src/exceptions.h @rbberger
src/fix_nh.* @athomps
src/info.* @akohlmey @rbberger
src/timer.* @akohlmey
src/min* @sjplimp @stanmoore1
src/platform.* @akohlmey
src/timer.* @akohlmey
src/utils.* @akohlmey @rbberger
src/verlet.* @sjplimp @stanmoore1
src/math_eigen_impl.h @jewettaij
# tools
tools/msi2lmp/* @akohlmey
tools/coding_standard/* @akohlmey @rbberger
tools/emacs/* @HaoZeke
tools/singularity/* @akohlmey @rbberger
tools/coding_standard/* @rbberger
tools/valgrind/* @akohlmey
tools/swig/* @akohlmey
tools/lammps-shell/* @akohlmey
tools/msi2lmp/* @akohlmey
tools/offline/* @rbberger
tools/singularity/* @akohlmey @rbberger
tools/swig/* @akohlmey
tools/valgrind/* @akohlmey
tools/vim/* @hammondkd
# tests
unittest/* @akohlmey @rbberger
unittest/* @akohlmey
# cmake
cmake/* @junghans @rbberger
cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
cmake/* @rbberger
cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
cmake/Modules/MPI4WIN.cmake @akohlmey
cmake/Modules/OpenCLLoader.cmake @akohlmey
cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
cmake/presets/*.cmake @akohlmey
# python
python/* @rbberger
# fortran
fortran/* @akohlmey
fortran/* @akohlmey @hammondkd
# docs
doc/utils/*/* @rbberger
doc/Makefile @rbberger
doc/README @rbberger
doc/* @akohlmey
examples/plugin/* @akohlmey
examples/PACKAGES/pace/plugin/* @akohlmey
# for releases
src/version.h @sjplimp

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

6
.github/codecov.yml vendored
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@ -7,7 +7,7 @@ coverage:
threshold: 10%
only_pulls: false
branches:
- "master"
- "develop"
flags:
- "unit"
paths:
@ -16,14 +16,14 @@ coverage:
project:
default:
branches:
- "master"
- "develop"
paths:
- "src"
informational: true
patch:
default:
branches:
- "master"
- "develop"
paths:
- "src"
informational: true

4
.github/workflows/codeql-analysis.yml vendored
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@ -49,7 +49,9 @@ jobs:
shell: bash
working-directory: build
run: |
cmake -C ../cmake/presets/most.cmake ../cmake
cmake -C ../cmake/presets/most.cmake \
-D DOWNLOAD_POTENTIALS=off \
../cmake
cmake --build . --parallel 2
- name: Perform CodeQL Analysis

17
.github/workflows/compile-msvc.yml vendored
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@ -3,7 +3,11 @@ name: "Native Windows Compilation and Unit Tests"
on:
push:
branches: [develop]
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
@ -22,20 +26,25 @@ jobs:
- name: Select Python version
uses: actions/setup-python@v4
with:
python-version: '3.10'
python-version: '3.11'
- name: Building LAMMPS via CMake
shell: bash
run: |
python3 -m pip install numpy
python3 -m pip install pyyaml
nuget install MSMPIsdk
nuget install MSMPIDIST
cmake -C cmake/presets/windows.cmake \
-D 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
cmake --build build --config Release --parallel 2
- name: Run LAMMPS executable
shell: bash
@ -46,4 +55,4 @@ jobs:
- name: Run Unit Tests
working-directory: build
shell: bash
run: ctest -V -C Release
run: ctest -V -C Release -E FixTimestep:python_move_nve

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

8
.github/workflows/unittest-macos.yml vendored
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@ -3,7 +3,11 @@ name: "Unittest for MacOS"
on:
push:
branches: [develop]
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
@ -39,9 +43,11 @@ jobs:
working-directory: build
run: |
ccache -z
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -C ../cmake/presets/clang.cmake \
-C ../cmake/presets/most.cmake \
-D DOWNLOAD_POTENTIALS=off \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D ENABLE_TESTING=on \

2
.gitignore vendored
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@ -55,3 +55,5 @@ out/RelWithDebInfo
out/Release
out/x86
out/x64
src/Makefile.package-e
src/Makefile.package.settings-e

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

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

35
SECURITY.md
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@ -14,14 +14,14 @@ and tested by the LAMMPS developers, so it is easy to import bad
behavior from calling functions in one of those libraries.
Thus is is quite easy to crash LAMMPS through malicious input and do all
kinds of filesystem manipulations. And because of that LAMMPS should
kinds of file system manipulations. And because of that LAMMPS should
**NEVER** be compiled or **run** as superuser, either from a "root" or
"administrator" account directly or indirectly via "sudo" or "su".
Therefore what could be seen as a security vulnerability is usually
either a user mistake or a bug in the code. Bugs can be reported in
the LAMMPS project
[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
either a user mistake or a bug in the code. Bugs can be reported in the
LAMMPS project [issue tracker on
GitHub](https://github.com/lammps/lammps/issues).
To mitigate issues with using homoglyphs or bidirectional reordering in
unicode, which have been demonstrated as a vector to obfuscate and hide
@ -30,10 +30,23 @@ for unicode characters and only all-ASCII source code is accepted.
# Version Updates
LAMMPS follows continuous release development model. We aim to keep all
release versions (stable or patch) fully functional and employ a variety
of automatic testing procedures to detect failures of existing
functionality from adding new features before releases are made. Thus
bugfixes and updates are only integrated into the current development
branch and thus the next (patch) release and users are recommended to
update regularly.
LAMMPS follows a continuous release development model. We aim to keep
the development version (`develop` branch) always fully functional and
employ a variety of automatic testing procedures to detect failures of
existing functionality from adding or modifying features. Most of those
tests are run on pull requests and must be passed *before* merging to
the `develop` branch. The `develop` branch is protected, so all changes
*must* be submitted as a pull request and thus cannot avoid the
automated tests.
Additional tests are run *after* merging. Before releases are made
*all* tests must have cleared. Then a release tag is applied and the
`release` branch is fast-forwarded to that tag. This is referred to to
as a "feature release". Bug fixes and updates are applied first to the
`develop` branch. Later, they appear in the `release` branch when the
next patch release occurs. For stable releases, backported bug fixes
and infrastructure updates are first applied to the `maintenance` branch
and then merged to `stable` and published as "updates". For a new
stable release the `stable` branch is updated to the corresponding state
of the `release` branch and a new stable tag is applied in addition to
the release tag.

26
bench/in.chain
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@ -1,25 +1,25 @@
# FENE beadspring benchmark
units lj
atom_style bond
units lj
atom_style bond
special_bonds fene
read_data data.chain
read_data data.chain
neighbor 0.4 bin
neigh_modify every 1 delay 1
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
timestep 0.012
run 100
run 100

36
bench/in.chain.scaled
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@ -1,32 +1,32 @@
# FENE beadspring benchmark
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
units lj
atom_style bond
atom_modify map hash
units lj
atom_style bond
atom_modify map hash
special_bonds fene
read_data data.chain
read_data data.chain
replicate $x $y $z
replicate $x $y $z
neighbor 0.4 bin
neigh_modify every 1 delay 1
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
timestep 0.012
run 100
run 100

44
bench/in.chute
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@ -1,33 +1,33 @@
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.chute
read_data data.chute
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify every 1 delay 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
run 100

50
bench/in.chute.scaled
View File

@ -1,38 +1,38 @@
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
variable x index 1
variable y index 1
variable x index 1
variable y index 1
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.chute
read_data data.chute
replicate $x $y 1
replicate $x $y 1
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify every 1 delay 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
run 100

40
bench/in.eam
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@ -1,32 +1,32 @@
# bulk Cu lattice
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
units metal
atom_style atomic
lattice fcc 3.615
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 3.615
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style eam
pair_coeff 1 1 Cu_u3.eam
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
fix 1 all nve
timestep 0.005
thermo 50
timestep 0.005
thermo 50
run 100
run 100

40
bench/in.lj
View File

@ -1,30 +1,30 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
fix 1 all nve
run 100
run 100

28
bench/in.rhodo
View File

@ -1,27 +1,27 @@
# Rhodopsin model
units real
neigh_modify delay 5 every 1
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt temp 300.0 300.0 100.0 &
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
thermo_style multi
timestep 2.0
run 100
run 100

38
bench/in.rhodo.scaled
View File

@ -1,34 +1,34 @@
# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
units real
neigh_modify delay 5 every 1
units real
neigh_modify delay 5 every 1
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
replicate $x $y $z
replicate $x $y $z
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt temp 300.0 300.0 100.0 &
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
thermo_style multi
timestep 2.0
run 100
run 100

197
cmake/CMakeLists.txt
View File

@ -3,15 +3,31 @@
# This file is part of LAMMPS
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.10)
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
cmake_policy(SET CMP0074 NEW)
endif()
# set policy to silence warnings about ignoring ${CMAKE_REQUIRED_LIBRARIES} but use it
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about missing executable permissions in
# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
########################################
# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
if(CMAKE_VERSION VERSION_LESS 3.12)
unset(CONFIGURE_DEPENDS)
else()
set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
endif()
########################################
project(lammps CXX)
@ -100,7 +116,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
else()
set(CMAKE_TUNE_DEFAULT "-xHost")
set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
endif()
endif()
endif()
@ -135,13 +151,11 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
# and prints lots of pointless warnings about "unsafe" functions
if(MSVC)
if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
if((CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Intel"))
add_compile_options(/Zc:__cplusplus)
add_compile_options(/wd4244)
add_compile_options(/wd4267)
if(LAMMPS_EXCEPTIONS)
add_compile_options(/EHsc)
endif()
add_compile_options(/EHsc)
endif()
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
@ -154,6 +168,19 @@ endif()
########################################################################
# User input options #
########################################################################
# set path to python interpreter and thus enforcing python version when
# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
else()
set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
endif()
set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
" Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)
@ -175,8 +202,8 @@ else()
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
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})
add_library(lammps ${ALL_SOURCES})
@ -194,6 +221,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -202,7 +230,7 @@ set(STANDARD_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -229,7 +257,7 @@ set(STANDARD_PACKAGES
KIM
KSPACE
LATBOLTZ
LATTE
LEPTON
MACHDYN
MANIFOLD
MANYBODY
@ -245,6 +273,7 @@ set(STANDARD_PACKAGES
ML-QUIP
ML-RANN
ML-SNAP
ML-POD
MOFFF
MOLECULE
MOLFILE
@ -295,6 +324,15 @@ if(PKG_ADIOS)
# script that defines the MPI::MPI_C target
enable_language(C)
find_package(ADIOS2 REQUIRED)
if(BUILD_MPI)
if(NOT ADIOS2_HAVE_MPI)
message(FATAL_ERROR "ADIOS2 must be built with MPI support when LAMMPS has MPI enabled")
endif()
else()
if(ADIOS2_HAVE_MPI)
message(FATAL_ERROR "ADIOS2 must be built without MPI support when LAMMPS has MPI disabled")
endif()
endif()
target_link_libraries(lammps PRIVATE adios2::adios2)
endif()
@ -358,17 +396,19 @@ pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(SCAFACOS MPI)
pkg_depends(AMOEBA KSPACE)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)
pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
find_package(OpenMP QUIET)
if(OpenMP_FOUND)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
find_package(OpenMP COMPONENTS CXX QUIET)
if(OpenMP_CXX_FOUND)
check_omp_h_include()
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
@ -377,8 +417,8 @@ endif()
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
find_package(OpenMP COMPONENTS CXX REQUIRED)
check_omp_h_include()
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
@ -400,21 +440,19 @@ if(BUILD_OMP)
target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
enable_language(C)
find_package(LAPACK)
find_package(BLAS)
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
include(CheckGeneratorSupport)
if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
endif()
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
find_package(BLAS)
endif()
if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
add_library(linalg STATIC ${LINALG_SOURCES})
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
target_link_libraries(lammps PRIVATE linalg)
else()
list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
endif()
@ -482,7 +520,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM MSCG COMPRESS ML-PACE LEPTON)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -499,7 +537,10 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine
separate_arguments(CMAKE_TUNE_FLAGS)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
target_compile_options(lammps PRIVATE ${_FLAG})
target_compile_options(lmp 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 ${_FLAG})
endif()
endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
@ -527,6 +568,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
########################################################
# Fetch missing external files and archives for packages
########################################################
option(DOWNLOAD_POTENTIALS "Automatically download large potential files" ON)
mark_as_advanced(DOWNLOAD_POTENTIALS)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
@ -539,8 +582,8 @@ endforeach()
foreach(PKG ${STANDARD_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -567,8 +610,8 @@ endforeach()
foreach(PKG ${SUFFIX_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
# check for package files in src directory due to old make system
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@ -579,18 +622,11 @@ endforeach()
##############################################
# add lib sources of (simple) enabled packages
############################################
foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
foreach(PKG_LIB POEMS ATC AWPMD H5MD)
if(PKG_${PKG_LIB})
string(TOLOWER "${PKG_LIB}" PKG_LIB)
if(PKG_LIB STREQUAL "mesont")
enable_language(Fortran)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
else()
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
endif()
file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB})
@ -604,7 +640,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
endif()
endforeach()
if(PKG_ELECTRODE)
if(PKG_ELECTRODE OR PKG_ML-POD)
target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
endif()
@ -633,7 +669,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -706,18 +742,17 @@ list(FIND LANGUAGES "Fortran" _index)
if(_index GREATER -1)
target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
if(LAMMPS_EXCEPTIONS)
list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
endif()
set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
set(LAMMPS_FMT_HEADERS core.h format.h)
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
set_target_properties(lammps PROPERTIES PREFIX "lib")
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
@ -726,6 +761,14 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS})
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
endif()
endforeach()
foreach(_HEADER ${LAMMPS_FMT_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER})
add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER})
add_dependencies(lammps fmt_${_HEADER})
if(BUILD_SHARED_LIBS)
install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
endif()
endforeach()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
add_library(LAMMPS::lammps ALIAS lammps)
get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
@ -780,9 +823,13 @@ if(BUILD_SHARED_LIBS)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(BUILD_IS_MULTI_CONFIG)
@ -793,9 +840,8 @@ if(BUILD_SHARED_LIBS)
set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
if(Python_EXECUTABLE)
add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
install-python ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR} -v ${LAMMPS_SOURCE_DIR}/version.h
COMMENT "Installing LAMMPS Python module")
else()
add_custom_target(
@ -808,26 +854,6 @@ else()
${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
endif()
###############################################################################
# Add LAMMPS python module to "install" target. This is taylored for building
# LAMMPS for package managers and with different prefix settings.
# This requires either a shared library or that the PYTHON package is included.
###############################################################################
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
endif()
endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
@ -839,6 +865,23 @@ if(ClangFormat_FOUND)
WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
endif()
# extract Kokkos compilation settings
get_cmake_property(_allvars VARIABLES)
foreach(_var ${_allvars})
if(${_var})
string(REGEX MATCH "Kokkos_ENABLE_(SERIAL|THREADS|OPENMP|CUDA|HIP|SYCL|OPENMPTARGET|HPX)" _match ${_var})
if(_match)
string(REGEX REPLACE "Kokkos_ENABLE_(OPENMP|SERIAL|CUDA|HIP|SYCL)" "\\1" _match ${_var})
list(APPEND KOKKOS_DEVICE ${_match})
endif()
string(REGEX MATCH "Kokkos_ARCH" _match ${_var})
if(_match)
string(REGEX REPLACE "Kokkos_ARCH_(.*)" "\\1" _match ${_var})
list(APPEND KOKKOS_ARCH ${_match})
endif()
endif()
endforeach()
get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
if(BUILD_IS_MULTI_CONFIG)
set(LAMMPS_BUILD_TYPE "Multi-Config")
@ -850,6 +893,7 @@ feature_summary(DESCRIPTION "The following tools and libraries have been found a
message(STATUS "<<< Build configuration >>>
LAMMPS Version: ${PROJECT_VERSION}
Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
CMake Version: ${CMAKE_VERSION}
Build type: ${LAMMPS_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
@ -936,7 +980,10 @@ if(PKG_GPU)
message(STATUS "GPU precision: ${GPU_PREC}")
endif()
if(PKG_KOKKOS)
message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
message(STATUS "Kokkos Devices: ${KOKKOS_DEVICE}")
if(KOKKOS_ARCH)
message(STATUS "Kokkos Architecture: ${KOKKOS_ARCH}")
endif()
endif()
if(PKG_KSPACE)
message(STATUS "<<< FFT settings >>>

6
cmake/CMakeSettings.json
View File

@ -72,7 +72,7 @@
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
@ -105,7 +105,7 @@
"configurationType": "Release",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
"buildCommandArgs": "",
"ctestCommandArgs": "-V",
"inheritEnvironments": [ "clang_cl_x64" ],
@ -305,4 +305,4 @@
]
}
]
}
}

4
cmake/Modules/CodingStandard.cmake
View File

@ -5,6 +5,10 @@ if(CMAKE_VERSION VERSION_LESS 3.12)
set(Python3_VERSION ${PYTHON_VERSION_STRING})
endif()
else()
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.5)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 COMPONENTS Interpreter QUIET)
endif()

16
cmake/Modules/DetectHIPInstallation.cmake Normal file
View File

@ -0,0 +1,16 @@
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
"Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
endif()
if(NOT DEFINED ROCM_PATH)
if(NOT DEFINED ENV{ROCM_PATH})
set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
else()
set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
endif()
endif()
list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})

35
cmake/Modules/Documentation.cmake
View File

@ -4,20 +4,24 @@
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
# Sphinx 3.x requires at least Python 3.5
# Current Sphinx versions require at least Python 3.8
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp 3.5 REQUIRED)
find_package(PythonInterp 3.8 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
else()
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 REQUIRED COMPONENTS Interpreter)
if(Python3_VERSION VERSION_LESS 3.5)
message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
if(Python3_VERSION VERSION_LESS 3.8)
message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
endif()
set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
endif()
find_package(Doxygen 1.8.10 REQUIRED)
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
add_custom_command(
@ -56,16 +60,27 @@ if(BUILD_DOC)
)
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
mark_as_advanced(MATHJAX_URL)
GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)
# download mathjax distribution and unpack to folder "mathjax"
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
file(DOWNLOAD ${MATHJAX_URL}
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 ${MATHJAX_MD5})
if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
endif()
if(NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}")
file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz DL_MD5)
if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}"))
message(WARNING "Download from primary URL ${MATHJAX_URL} failed\nTrying fallback URL ${MATHJAX_FALLBACK}")
file(DOWNLOAD ${MATHJAX_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${MATHJAX_MD5} SHOW_PROGRESS)
endif()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
endif()

18
cmake/Modules/ExternalCMakeProject.cmake
View File

@ -9,8 +9,22 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
get_filename_component(archive ${url} NAME)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
message(STATUS "Downloading ${url}")
file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
if(EXISTS ${CMAKE_BINARY_DIR}/_deps/${archive})
file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${hash}")
message(STATUS "Downloading ${url}")
file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${hash}"))
set(${target}_URL ${url})
GetFallbackURL(${target}_URL fallback)
message(WARNING "Download from primary URL ${url} failed\nTrying fallback URL ${fallback}")
file(DOWNLOAD ${fallback} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
endif()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/_deps/${archive}")
endif()
message(STATUS "Unpacking and configuring ${archive}")
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)

29
cmake/Modules/FindClangFormat.cmake
View File

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

2
cmake/Modules/FindCythonize.cmake
View File

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

19
cmake/Modules/FindZMQ.cmake
View File

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

128
cmake/Modules/LAMMPSInterfacePlugin.cmake
View File

@ -6,6 +6,9 @@ if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
"Please remove CMakeCache.txt and CMakeFiles first.")
endif()
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty"
CACHE STRING "URL for thirdparty package downloads")
# global LAMMPS/plugin build settings
set(LAMMPS_SOURCE_DIR "" CACHE PATH "Location of LAMMPS sources folder")
if(NOT LAMMPS_SOURCE_DIR)
@ -62,7 +65,7 @@ endfunction(validate_option)
# helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable)
file(GLOB _dirs ${path})
file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>")
foreach(_dir ${_dirs})
@ -78,6 +81,25 @@ function(get_newest_file path variable)
set(${variable} ${_bestfile} PARENT_SCOPE)
endfunction()
# get LAMMPS version date
function(get_lammps_version version_header variable)
file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1\\2\\3" date "${line}")
set(${variable} "${date}" PARENT_SCOPE)
endfunction()
# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
function(GetFallbackURL input output)
string(REPLACE "_URL" "" _tmp ${input})
string(TOLOWER ${_tmp} libname)
string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
if ("${newurl}" STREQUAL "${${input}}")
set(${output} "" PARENT_SCOPE)
else()
set(${output} ${newurl} PARENT_SCOPE)
endif()
endfunction(GetFallbackURL)
#################################################################################
# LAMMPS C++ interface. We only need the header related parts except on windows.
add_library(lammps INTERFACE)
@ -89,6 +111,7 @@ endif()
################################################################################
# MPI configuration
if(NOT CMAKE_CROSSCOMPILING)
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
else()
@ -101,45 +124,76 @@ if(BUILD_MPI)
set(MPI_CXX_SKIP_MPICXX TRUE)
# We use a non-standard procedure to cross-compile with MPI on Windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
else()
find_package(MPI REQUIRED)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)

84
cmake/Modules/LAMMPSUtils.cmake
View File

@ -24,9 +24,24 @@ function(validate_option name values)
endif()
endfunction(validate_option)
# helper function to check for usable omp.h header
function(check_omp_h_include)
find_package(OpenMP COMPONENTS CXX QUIET)
if(OpenMP_CXX_FOUND)
set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
check_include_file_cxx(omp.h _have_omp_h)
else()
set(_have_omp_h FALSE)
endif()
set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE)
endfunction()
# helper function for getting the most recently modified file or folder from a glob pattern
function(get_newest_file path variable)
file(GLOB _dirs ${path})
file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
set(_besttime 2000-01-01T00:00:00)
set(_bestfile "<unknown>")
foreach(_dir ${_dirs})
@ -65,8 +80,8 @@ endfunction()
function(check_for_autogen_files source_dir)
message(STATUS "Running check for auto-generated files from make-based build system")
file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
foreach(_SRC ${SRC_AUTOGEN_FILES})
@ -84,8 +99,15 @@ function(check_for_autogen_files source_dir)
endfunction()
macro(pkg_depends PKG1 PKG2)
if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
if(DEFINED BUILD_${PKG2})
if(PKG_${PKG1} AND NOT BUILD_${PKG2})
message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be built with -D BUILD_${PKG2}=ON")
endif()
elseif(DEFINED PKG_${PKG2})
if(PKG_${PKG1} AND NOT PKG_${PKG2})
message(WARNING "The ${PKG1} package depends on the ${PKG2} package. Enabling it.")
set(PKG_${PKG2} ON CACHE BOOL "" FORCE)
endif()
endif()
endmacro()
@ -103,32 +125,48 @@ endfunction(GenerateBinaryHeader)
# fetch missing potential files
function(FetchPotentials pkgfolder potfolder)
if(EXISTS "${pkgfolder}/potentials.txt")
file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
foreach(line ${linelist})
string(FIND ${line} " " blank)
math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum)
if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
endif()
if(NOT sum STREQUAL oldsum)
message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
endif()
endforeach()
if(DOWNLOAD_POTENTIALS)
if(EXISTS "${pkgfolder}/potentials.txt")
file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
foreach(line ${linelist})
string(FIND ${line} " " blank)
math(EXPR plusone "${blank}+1")
string(SUBSTRING ${line} 0 ${blank} pot)
string(SUBSTRING ${line} ${plusone} -1 sum)
if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
endif()
if(NOT sum STREQUAL oldsum)
message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
string(RANDOM LENGTH 10 TMP_EXT)
file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
endif()
endforeach()
endif()
endif()
endfunction(FetchPotentials)
# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
file(STRINGS /etc/os-release distro REGEX "^NAME=")
string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
string(REGEX REPLACE "NAME=\"?([^ ]+).*\"?" "\\1" distro "${distro}")
file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
set(CMAKE_LINUX_DISTRO ${distro})
set(CMAKE_DISTRO_VERSION ${disversion})
endif()
# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
function(GetFallbackURL input output)
string(REPLACE "_URL" "" _tmp ${input})
string(TOLOWER ${_tmp} libname)
string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
if ("${newurl}" STREQUAL "${${input}}")
set(${output} "" PARENT_SCOPE)
else()
set(${output} ${newurl} PARENT_SCOPE)
endif()
endfunction(GetFallbackURL)

107
cmake/Modules/MPI4WIN.cmake
View File

@ -1,39 +1,74 @@
# Download and configure custom MPICH files for Windows
message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
# Download and configure MinGW compatible MPICH development files for Windows
option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
if(USE_MSMPI)
message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
else()
message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
include(ExternalProject)
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN64_DEVEL_URL}
URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
else()
ExternalProject_Add(mpi4win_build
URL ${MPICH2_WIN32_DEVEL_URL}
URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)
# set variables for status reporting at the end of CMake run
set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

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

@ -1,20 +1,15 @@
set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
option(COLVARS_DEBUG "Debugging messages for Colvars (quite verbose)" OFF)
option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)
# Build Lepton by default
option(COLVARS_LEPTON "Build and link the Lepton library" ON)
option(COLVARS_LEPTON "Use the Lepton library for custom expressions" ON)
if(COLVARS_LEPTON)
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
add_library(lepton STATIC ${LEPTON_SOURCES})
# Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
if(NOT LEPTON_SOURCE_DIR)
include(Packages/LEPTON)
endif()
endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
@ -30,14 +25,11 @@ target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
target_link_libraries(lammps PRIVATE colvars)
if(COLVARS_DEBUG)
# Need to export the macro publicly to also affect the proxy
# Need to export the define publicly to be valid in interface code
target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)
endif()
if(COLVARS_LEPTON)
target_link_libraries(lammps PRIVATE lepton)
target_compile_definitions(colvars PRIVATE -DLEPTON)
# Disable the line below when linking Lepton as a DLL with MSVC
target_compile_definitions(colvars PRIVATE -DLEPTON_USE_STATIC_LIBRARIES)
target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
target_link_libraries(colvars PUBLIC lepton)
endif()

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

@ -1,4 +1,9 @@
find_package(ZLIB REQUIRED)
find_package(ZLIB)
if(NOT ZLIB_FOUND)
message(WARNING "No Zlib development support found. Disabling COMPRESS package...")
set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
return()
endif()
target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
find_package(PkgConfig QUIET)

154
cmake/Modules/Packages/GPU.cmake
View File

@ -26,7 +26,20 @@ elseif(GPU_PREC STREQUAL "SINGLE")
set(GPU_PREC_SETTING "SINGLE_SINGLE")
endif()
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
option(GPU_DEBUG "Enable debugging code of the GPU package" OFF)
mark_as_advanced(GPU_DEBUG)
if(PKG_AMOEBA AND FFT_SINGLE)
message(FATAL_ERROR "GPU acceleration of AMOEBA is not (yet) compatible with single precision FFT")
endif()
if (PKG_AMOEBA)
list(APPEND GPU_SOURCES
${GPU_SOURCES_DIR}/amoeba_convolution_gpu.h
${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
endif()
file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
@ -47,15 +60,15 @@ if(GPU_API STREQUAL "CUDA")
option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
if(CUDA_MPS_SUPPORT)
if(CUDPP_OPT)
message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DCUDA_MPS_SUPPORT=ON")
endif()
set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
endif()
set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
# ensure that no *cubin.h files exist from a compile in the lib/gpu folder
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
if(GPU_LIB_OLD_CUBIN_HEADERS)
message(FATAL_ERROR "########################################################################\n"
"Found file(s) generated by the make-based build system in lib/gpu\n"
@ -65,15 +78,15 @@ if(GPU_API STREQUAL "CUDA")
"########################################################################")
endif()
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
@ -82,11 +95,14 @@ if(GPU_API STREQUAL "CUDA")
# apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
# only the Kepler achitecture and beyond is supported
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
if(CUDA_VERSION VERSION_LESS 8.0)
message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
set(GPU_CUDA_GENCODE "-arch=all")
elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
set(GPU_CUDA_GENCODE "-arch=all")
else()
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
@ -120,14 +136,14 @@ if(GPU_API STREQUAL "CUDA")
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
# Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
# # Lovelace (GPU Arch 9.x) is supported by CUDA 12.0? and later
#if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
# string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_9x,code=[sm_9x,compute_9x]")
#endif()
endif()
cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@ -150,14 +166,17 @@ if(GPU_API STREQUAL "CUDA")
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} ${GPU_CUDA_MPS_FLAGS})
if(GPU_DEBUG)
target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
else()
target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
endif()
if(CUDPP_OPT)
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
endif()
target_link_libraries(lammps PRIVATE gpu)
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
@ -182,7 +201,7 @@ elseif(GPU_API STREQUAL "OPENCL")
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@ -191,6 +210,7 @@ elseif(GPU_API STREQUAL "OPENCL")
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu
)
foreach(GPU_KERNEL ${GPU_LIB_CU})
@ -207,6 +227,7 @@ elseif(GPU_API STREQUAL "OPENCL")
GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
GenerateOpenCLHeader(hippo ${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu)
list(APPEND GPU_LIB_SOURCES
${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
@ -216,36 +237,26 @@ elseif(GPU_API STREQUAL "OPENCL")
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h
)
add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
target_link_libraries(lammps PRIVATE gpu)
target_compile_definitions(gpu PRIVATE -DUSE_OPENCL -D_${GPU_PREC_SETTING})
if(GPU_DEBUG)
target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
else()
target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
endif()
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
add_dependencies(ocl_get_devices OpenCL::OpenCL)
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
endif()
endif()
if(NOT DEFINED ROCM_PATH)
if(NOT DEFINED ENV{ROCM_PATH})
set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
else()
set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
endif()
endif()
list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
include(DetectHIPInstallation)
find_package(hip REQUIRED)
option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
@ -259,8 +270,10 @@ elseif(GPU_API STREQUAL "HIP")
set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
if(HIP_PLATFORM STREQUAL "amd")
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "spirv")
set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "nvcc")
find_package(CUDA REQUIRED)
set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
@ -273,6 +286,7 @@ elseif(GPU_API STREQUAL "HIP")
else()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
# comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
# Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
@ -302,14 +316,22 @@ elseif(GPU_API STREQUAL "HIP")
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
# Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
# Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
endif()
endif()
endif()
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
set(GPU_LIB_CU_HIP "")
@ -321,7 +343,7 @@ elseif(GPU_API STREQUAL "HIP")
set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
if(HIP_PLATFORM STREQUAL "amd")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
if(HIP_COMPILER STREQUAL "clang")
@ -340,7 +362,14 @@ elseif(GPU_API STREQUAL "HIP")
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
DEPENDS ${CU_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
elseif(HIP_PLATFORM STREQUAL "spirv")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Gerating ${CU_NAME}.cubin")
endif()
add_custom_command(OUTPUT ${CUBIN_H_FILE}
COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILE=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake
@ -354,8 +383,12 @@ elseif(GPU_API STREQUAL "HIP")
add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_HIP)
target_compile_definitions(gpu PRIVATE -DUSE_HIP -D_${GPU_PREC_SETTING})
if(GPU_DEBUG)
target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
else()
target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
endif()
target_link_libraries(gpu PRIVATE hip::host)
if(HIP_USE_DEVICE_SORT)
@ -364,7 +397,8 @@ elseif(GPU_API STREQUAL "HIP")
set_property(TARGET gpu PROPERTY CXX_STANDARD 14)
endif()
# add hipCUB
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
find_package(hipcub REQUIRED)
target_link_libraries(gpu PRIVATE hip::hipcub)
target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
if(HIP_PLATFORM STREQUAL "nvcc")
@ -380,15 +414,17 @@ elseif(GPU_API STREQUAL "HIP")
if(DOWNLOAD_CUB)
message(STATUS "CUB download requested")
set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
# TODO: test update to current version 1.17.2
set(CUB_URL "https://github.com/nvidia/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
mark_as_advanced(CUB_URL)
mark_as_advanced(CUB_MD5)
GetFallbackURL(CUB_URL CUB_FALLBACK)
include(ExternalProject)
ExternalProject_Add(CUB
URL ${CUB_URL}
URL ${CUB_URL} ${CUB_FALLBACK}
URL_MD5 ${CUB_MD5}
PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
CONFIGURE_COMMAND ""
@ -411,35 +447,25 @@ elseif(GPU_API STREQUAL "HIP")
add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
target_link_libraries(hip_get_devices hip::host)
target_link_libraries(hip_get_devices PRIVATE hip::host)
if(HIP_PLATFORM STREQUAL "nvcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
elseif(HIP_PLATFORM STREQUAL "hcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
elseif(HIP_PLATFORM STREQUAL "amd")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
endif()
target_link_libraries(lammps PRIVATE gpu)
endif()
if(BUILD_OMP)
find_package(OpenMP COMPONENTS CXX REQUIRED)
target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX)
endif()
target_link_libraries(lammps PRIVATE gpu)
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
# detect styles which have a GPU version
RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)

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

@ -112,9 +112,5 @@ if(PKG_KSPACE)
RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
if(PKG_ELECTRODE)
list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/electrode_accel_intel.cpp)
endif()
target_sources(lammps PRIVATE ${INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

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

@ -19,7 +19,7 @@ if(CURL_FOUND)
target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
endif()
endif()
set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
option(KIM_EXTRA_UNITTESTS "Enable extra unit tests for the KIM package." OFF)
mark_as_advanced(KIM_EXTRA_UNITTESTS)
find_package(PkgConfig QUIET)
set(DOWNLOAD_KIM_DEFAULT ON)

54
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -3,6 +3,7 @@
if(CMAKE_CXX_STANDARD LESS 14)
message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
@ -15,8 +16,9 @@ if(Kokkos_ENABLE_OPENMP)
if(NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
else()
if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
# NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
endif()
endif()
endif()
@ -47,12 +49,14 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "b5c44ea961031795f434002cd7b31c20" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "f140e02b826223b1045207d9bc10d404" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
ExternalProject_Add(kokkos_build
URL ${KOKKOS_URL}
URL ${KOKKOS_URL} ${KOKKOS_FALLBACK}
URL_MD5 ${KOKKOS_MD5}
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a
@ -68,13 +72,11 @@ if(DOWNLOAD_KOKKOS)
set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.6.00 REQUIRED CONFIG)
find_package(Kokkos 3.7.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
target_link_libraries(lmp PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@ -88,14 +90,12 @@ else()
endif()
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
${LAMMPS_LIB_KOKKOS_BIN_DIR})
target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE kokkos)
target_link_libraries(lmp PRIVATE kokkos)
if(BUILD_SHARED_LIBS_WAS_ON)
set(BUILD_SHARED_LIBS ON)
endif()
@ -121,9 +121,14 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
# fix wall/gran has been refactored in an incompatible way. Use old version of base class for now
if(PKG_GRANULAR)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fix_wall_gran_old.cpp)
endif()
if(PKG_KSPACE)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
if(Kokkos_ENABLE_CUDA)
if(NOT (FFT STREQUAL "KISS"))
@ -132,12 +137,37 @@ if(PKG_KSPACE)
endif()
elseif(Kokkos_ENABLE_HIP)
if(NOT (FFT STREQUAL "KISS"))
include(DetectHIPInstallation)
find_package(hipfft REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
target_link_libraries(lammps PRIVATE hipfft)
target_link_libraries(lammps PRIVATE hip::hipfft)
endif()
endif()
endif()
if(PKG_ML-IAP)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_model_python_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_unified_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp)
# Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included
if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
COMMAND ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
WORKING_DIRECTORY ${MLIAP_BINARY_DIR}
MAIN_DEPENDENCY ${MLIAP_CYTHON_FILE}
COMMENT "Generating C++ sources with cythonize...")
list(APPEND KOKKOS_PKG_SOURCES ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
endforeach()
endif()
endif()
if(PKG_PHONON)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)

52
cmake/Modules/Packages/LATTE.cmake
View File

@ -1,52 +0,0 @@
enable_language(Fortran)
# using lammps in a super-build setting
if(TARGET LATTE::latte)
target_link_libraries(lammps PRIVATE LATTE::latte)
return()
endif()
find_package(LATTE 1.2.2 CONFIG)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
else()
set(DOWNLOAD_LATTE_DEFAULT ON)
endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
message(STATUS "LATTE download requested - we will build our own")
set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
mark_as_advanced(LATTE_URL)
mark_as_advanced(LATTE_MD5)
# CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
endif()
include(ExternalProject)
ExternalProject_Add(latte_build
URL ${LATTE_URL}
URL_MD5 ${LATTE_MD5}
SOURCE_SUBDIR cmake
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/liblatte.a
)
ExternalProject_get_property(latte_build INSTALL_DIR)
add_library(LAMMPS::LATTE UNKNOWN IMPORTED)
set_target_properties(LAMMPS::LATTE PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/liblatte.a"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
add_dependencies(LAMMPS::LATTE latte_build)
else()
find_package(LATTE 1.2.2 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE LATTE::latte)
endif()

35
cmake/Modules/Packages/LEPTON.cmake Normal file
View File

@ -0,0 +1,35 @@
# avoid including this file twice
if(LEPTON_SOURCE_DIR)
return()
endif()
set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64"))
option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" ON)
else()
option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" OFF)
endif()
if(LEPTON_ENABLE_JIT)
file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
endif()
add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})
set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
target_compile_definitions(lepton PUBLIC LEPTON_BUILDING_STATIC_LIBRARY=1)
target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR}/include)
if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
find_library(LIB_RT rt QUIET)
target_link_libraries(lepton PUBLIC ${LIB_RT})
endif()
if(LEPTON_ENABLE_JIT)
target_compile_definitions(lepton PUBLIC "LEPTON_USE_JIT=1;ASMJIT_BUILD_X86=1;ASMJIT_STATIC=1;ASMJIT_BUILD_RELEASE=1")
target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR})
endif()
target_link_libraries(lammps PRIVATE lepton)

9
cmake/Modules/Packages/MC.cmake Normal file
View File

@ -0,0 +1,9 @@
# fix sgcmc may only be installed if also the EAM pair style from MANYBODY is installed
if(NOT PKG_MANYBODY)
get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.h)
set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
endif()

50
cmake/Modules/Packages/MDI.cmake
View File

@ -8,10 +8,11 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
GetFallbackURL(MDI_URL MDI_FALLBACK)
enable_language(C)
# only ON/OFF are allowed for "mpi" flag when building MDI library
@ -26,8 +27,21 @@ if(DOWNLOAD_MDI)
# detect if we have python development support and thus can enable python plugins
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_VERSION VERSION_LESS 3.12)
if(NOT PYTHON_VERSION_STRING)
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
# search for interpreter first, so we have a consistent library
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
endif()
# search for the library matching the selected interpreter
set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
find_package(PythonLibs QUIET) # Deprecated since version 3.12
if(PYTHONLIBS_FOUND)
if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
endif()
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
else()
@ -36,16 +50,25 @@ if(DOWNLOAD_MDI)
set(MDI_USE_PYTHON_PLUGINS ON)
endif()
endif()
# python plugins are not supported and thus must be always off on Windows
if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
unset(Python_Development_FOUND)
set(MDI_USE_PYTHON_PLUGINS OFF)
if(CMAKE_CROSSCOMPILING)
set(CMAKE_INSTALL_LIBDIR lib)
endif()
endif()
# download/ build MDI library
# always build static library with -fpic
# support cross-compilation and ninja-build
include(ExternalProject)
ExternalProject_Add(mdi_build
URL ${MDI_URL}
URL ${MDI_URL} ${MDI_FALLBACK}
URL_MD5 ${MDI_MD5}
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
CMAKE_ARGS
-DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@ -54,25 +77,26 @@ if(DOWNLOAD_MDI)
-Dlanguage=C
-Dlibtype=STATIC
-Dmpi=${MDI_USE_MPI}
-Dplugins=ON
-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
)
# where is the compiled library?
ExternalProject_get_property(mdi_build BINARY_DIR)
set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
ExternalProject_get_property(mdi_build PREFIX)
# workaround for older CMake versions
file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
file(MAKE_DIRECTORY ${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi)
file(MAKE_DIRECTORY ${PREFIX}/include/mdi)
# create imported target for the MDI library
add_library(LAMMPS::MDI UNKNOWN IMPORTED)
add_dependencies(LAMMPS::MDI mdi_build)
set_target_properties(LAMMPS::MDI PROPERTIES
IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
)
IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
)
set(MDI_DEP_LIBS "")
# if compiling with python plugins we need

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

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

13
cmake/Modules/Packages/ML-HDNNP.cmake
View File

@ -6,10 +6,11 @@ else()
endif()
option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT})
if(DOWNLOAD_N2P2)
set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball")
set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.2.0.tar.gz" CACHE STRING "URL for n2p2 tarball")
set(N2P2_MD5 "a2d9ab7f676b3a74a324fc1eda0a911d" CACHE STRING "MD5 checksum of N2P2 tarball")
mark_as_advanced(N2P2_URL)
mark_as_advanced(N2P2_MD5)
GetFallbackURL(N2P2_URL N2P2_FALLBACK)
# adjust settings from detected compiler to compiler platform in n2p2 library
# set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
@ -44,7 +45,9 @@ if(DOWNLOAD_N2P2)
else()
# get path to MPI include directory
get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
foreach (_INCL ${N2P2_MPI_INCLUDE})
set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -I${_INCL}")
endforeach()
endif()
# prefer GNU make, if available. N2P2 lib seems to need it.
@ -70,12 +73,12 @@ if(DOWNLOAD_N2P2)
# download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
include(ExternalProject)
ExternalProject_Add(n2p2_build
URL ${N2P2_URL}
URL ${N2P2_URL} ${N2P2_FALLBACK}
URL_MD5 ${N2P2_MD5}
UPDATE_COMMAND ""
CONFIGURE_COMMAND ""
PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
BUILD_COMMAND ${N2P2_MAKE} -C <SOURCE_DIR>/src -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
BUILD_ALWAYS YES
INSTALL_COMMAND ""
BUILD_IN_SOURCE 1

31
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -2,7 +2,13 @@
set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
if(PKG_PYTHON)
find_package(Cythonize QUIET)
if(Cythonize_FOUND)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
find_package(Python COMPONENTS NumPy QUIET)
else()
# assume we have NumPy
set(Python_NumPy_FOUND ON)
endif()
if(Cythonize_FOUND AND Python_NumPy_FOUND)
set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
endif()
endif()
@ -11,6 +17,9 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
if(MLIAP_ENABLE_PYTHON)
find_package(Cythonize REQUIRED)
if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
find_package(Python COMPONENTS NumPy REQUIRED)
endif()
if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif()
@ -25,16 +34,18 @@ if(MLIAP_ENABLE_PYTHON)
endif()
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
COMMAND ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
WORKING_DIRECTORY ${MLIAP_BINARY_DIR}
MAIN_DEPENDENCY ${MLIAP_CYTHON_SRC}
COMMENT "Generating C++ sources with cythonize...")
foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
add_custom_command(OUTPUT ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
COMMAND ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
WORKING_DIRECTORY ${MLIAP_BINARY_DIR}
MAIN_DEPENDENCY ${MLIAP_CYTHON_FILE}
COMMENT "Generating C++ sources with cythonize...")
target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
endforeach()
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
endif()

36
cmake/Modules/Packages/ML-PACE.cmake
View File

@ -1,11 +1,25 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
# download library sources to build folder
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
endif()
if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
message(STATUS "Downloading ${PACELIB_URL}")
file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
endif()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
# uncompress downloaded sources
execute_process(
@ -15,23 +29,9 @@ execute_process(
)
get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
# enforce building libyaml-cpp as static library and turn off optional features
set(YAML_BUILD_SHARED_LIBS OFF)
set(YAML_CPP_BUILD_CONTRIB OFF)
set(YAML_CPP_BUILD_TOOLS OFF)
add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
target_link_libraries(pace PRIVATE yaml-cpp-pace)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
endif()

5
cmake/Modules/Packages/ML-QUIP.cmake
View File

@ -16,6 +16,7 @@ if(DOWNLOAD_QUIP)
set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
@ -58,12 +59,12 @@ if(DOWNLOAD_QUIP)
BUILD_COMMAND env QUIP_ARCH=lammps make libquip
INSTALL_COMMAND ""
BUILD_IN_SOURCE YES
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}
)
ExternalProject_get_property(quip_build SOURCE_DIR)
add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
set_target_properties(LAMMPS::QUIP PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
add_dependencies(LAMMPS::QUIP quip_build)

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

@ -7,8 +7,8 @@ else()
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
mark_as_advanced(MSCG_URL)
mark_as_advanced(MSCG_MD5)

236
cmake/Modules/Packages/PLUMED.cmake
View File

@ -1,105 +1,169 @@
set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
set(PLUMED_MODE_VALUES static shared runtime)
set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
# Plumed2 support for PLUMED package
set(PLUMED_LINK_LIBS)
if(PLUMED_MODE STREQUAL "STATIC")
find_package(LAPACK REQUIRED)
find_package(BLAS REQUIRED)
find_package(GSL REQUIRED)
list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
find_package(ZLIB QUIET)
if(ZLIB_FOUND)
list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
endif()
find_package(FFTW3 QUIET)
if(FFTW3_FOUND)
list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
endif()
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
set(PLUMED_CONFIG_CPP "-I ${MPI_CXX_INCLUDE_PATH}")
set(PLUMED_CONFIG_LIB "${MPI_CXX_LIBRARIES}")
set(PLUMED_CONFIG_DEP "mpi4win_build")
else()
set(PLUMED_CONFIG_MPI "--disable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
set(PLUMED_CONFIG_CPP "")
set(PLUMED_CONFIG_LIB "")
set(PLUMED_CONFIG_DEP "")
endif()
if(BUILD_OMP)
set(PLUMED_CONFIG_OMP "--enable-openmp")
else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
find_package(PkgConfig QUIET)
set(DOWNLOAD_PLUMED_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(PLUMED QUIET plumed)
if(PLUMED_FOUND)
set(DOWNLOAD_PLUMED_DEFAULT OFF)
endif()
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
set(CROSS_CONFIGURE mingw64-configure)
elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
set(CROSS_CONFIGURE mingw32-configure)
else()
set(PLUMED_CONFIG_MPI "--disable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
message(FATAL_ERROR "Unsupported target system: ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}")
endif()
if(BUILD_OMP)
set(PLUMED_CONFIG_OMP "--enable-openmp")
else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
message(STATUS "PLUMED download requested - we will build our own")
if(PLUMED_MODE STREQUAL "STATIC")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
elseif(PLUMED_MODE STREQUAL "SHARED")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
message(STATUS "Downloading and cross-compiling Plumed2 for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR} with ${CROSS_CONFIGURE}")
include(ExternalProject)
ExternalProject_Add(plumed_build
URL ${PLUMED_URL}
URL ${PLUMED_URL} ${PLUMED_FALLBACK}
URL_MD5 ${PLUMED_MD5}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
--disable-python --enable-cxx=11
--enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
${PLUMED_CONFIG_OMP}
${PLUMED_CONFIG_MPI}
CXX=${PLUMED_CONFIG_CXX}
CC=${PLUMED_CONFIG_CC}
CPPFLAGS=${PLUMED_CONFIG_CPP}
LIBS=${PLUMED_CONFIG_LIB}
INSTALL_COMMAND ""
BUILD_BYPRODUCTS "<SOURCE_DIR>/src/lib/install/libplumed.a" "<SOURCE_DIR>/src/lib/install/plumed.exe"
DEPENDS "${PLUMED_MPI_CONFIG_DEP}"
)
ExternalProject_Get_Property(plumed_build SOURCE_DIR)
set(PLUMED_BUILD_DIR ${SOURCE_DIR})
set(PLUMED_INSTALL_DIR ${PLUMED_BUILD_DIR}/src/lib/install)
file(MAKE_DIRECTORY ${PLUMED_BUILD_DIR}/src/include)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
set_target_properties(LAMMPS::PLUMED PROPERTIES
IMPORTED_LOCATION "${PLUMED_INSTALL_DIR}/libplumed.a"
INTERFACE_LINK_LIBRARIES "-Wl,--image-base -Wl,0x10000000 -lfftw3 -lz -fstack-protector -lssp -fopenmp"
INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_BUILD_DIR}/src/include")
add_custom_target(plumed_copy ALL ${CMAKE_COMMAND} -E rm -rf ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed_patches
COMMAND ${CMAKE_COMMAND} -E copy ${PLUMED_INSTALL_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed.exe
COMMAND ${CMAKE_COMMAND} -E copy_directory ${PLUMED_BUILD_DIR}/patches ${CMAKE_BINARY_DIR}/patches
BYPRODUCTS ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/patches
DEPENDS plumed_build
COMMENT "Copying Plumed files"
)
else()
set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
set(PLUMED_MODE_VALUES static shared runtime)
set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
set(PLUMED_LINK_LIBS)
if(PLUMED_MODE STREQUAL "STATIC")
find_package(LAPACK REQUIRED)
find_package(BLAS REQUIRED)
find_package(GSL REQUIRED)
list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
find_package(ZLIB QUIET)
if(ZLIB_FOUND)
list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
endif()
find_package(FFTW3 QUIET)
if(FFTW3_FOUND)
list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
endif()
endif()
find_package(PkgConfig QUIET)
set(DOWNLOAD_PLUMED_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(PLUMED QUIET plumed)
if(PLUMED_FOUND)
set(DOWNLOAD_PLUMED_DEFAULT OFF)
endif()
endif()
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
message(STATUS "PLUMED download requested - we will build our own")
if(PLUMED_MODE STREQUAL "STATIC")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
endif()
include(ExternalProject)
ExternalProject_Add(plumed_build
URL ${PLUMED_URL} ${PLUMED_FALLBACK}
URL_MD5 ${PLUMED_MD5}
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
--enable-cxx=11
--disable-python
${PLUMED_CONFIG_MPI}
${PLUMED_CONFIG_OMP}
CXX=${PLUMED_CONFIG_CXX}
CC=${PLUMED_CONFIG_CC}
BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/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}")
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

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

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

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

@ -18,6 +18,8 @@ if(DOWNLOAD_SCAFACOS)
set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
mark_as_advanced(SCAFACOS_URL)
mark_as_advanced(SCAFACOS_MD5)
GetFallbackURL(SCAFACOS_URL SCAFACOS_FALLBACK)
# version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
@ -30,7 +32,7 @@ if(DOWNLOAD_SCAFACOS)
include(ExternalProject)
ExternalProject_Add(scafacos_build
URL ${SCAFACOS_URL}
URL ${SCAFACOS_URL} ${SCAFACOS_FALLBACK}
URL_MD5 ${SCAFACOS_MD5}
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc

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

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

127
cmake/Modules/StyleHeaderUtils.cmake
View File

@ -1,5 +1,5 @@
function(FindStyleHeaders path style_class file_pattern headers)
file(GLOB files "${path}/${file_pattern}*.h")
file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
get_property(hlist GLOBAL PROPERTY ${headers})
foreach(file_name ${files})
@ -95,73 +95,76 @@ function(RegisterIntegrateStyle path)
endfunction(RegisterIntegrateStyle)
function(RegisterStyles search_path)
FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body
FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force
FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input
FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update
FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor
FindStyleHeaders(${search_path} NSTENCIL_CLASS nstencil_ NSTENCIL ) # nstencil ) # neighbor
FindStyleHeaders(${search_path} NTOPO_CLASS ntopo_ NTOPO ) # ntopo ) # neighbor
FindStyleHeaders(${search_path} PAIR_CLASS pair_ PAIR ) # pair ) # force
FindStyleHeaders(${search_path} READER_CLASS reader_ READER ) # reader ) # read_dump
FindStyleHeaders(${search_path} REGION_CLASS region_ REGION ) # region ) # domain
FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force
FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid
FindStyleHeaders(${search_path} BODY_CLASS body_ BODY ) # body ) # atom_vec_body
FindStyleHeaders(${search_path} BOND_CLASS bond_ BOND ) # bond ) # force
FindStyleHeaders(${search_path} COMMAND_CLASS "[^.]" COMMAND ) # command ) # input
FindStyleHeaders(${search_path} COMPUTE_CLASS compute_ COMPUTE ) # compute ) # modify
FindStyleHeaders(${search_path} DIHEDRAL_CLASS dihedral_ DIHEDRAL ) # dihedral ) # force
FindStyleHeaders(${search_path} DUMP_CLASS dump_ DUMP ) # dump ) # output write_dump
FindStyleHeaders(${search_path} FIX_CLASS fix_ FIX ) # fix ) # modify
FindStyleHeaders(${search_path} GRAN_SUB_MOD_CLASS gran_sub_mod_ GRAN_SUB_MOD ) # gran_sub_mod ) # granular_model
FindStyleHeaders(${search_path} IMPROPER_CLASS improper_ IMPROPER ) # improper ) # force
FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]" INTEGRATE ) # integrate ) # update
FindStyleHeaders(${search_path} KSPACE_CLASS "[^.]" KSPACE ) # kspace ) # force
FindStyleHeaders(${search_path} MINIMIZE_CLASS min_ MINIMIZE ) # minimize ) # update
FindStyleHeaders(${search_path} NBIN_CLASS nbin_ NBIN ) # nbin ) # neighbor
FindStyleHeaders(${search_path} NPAIR_CLASS npair_ NPAIR ) # npair ) # neighbor
FindStyleHeaders(${search_path} NSTENCIL_CLASS nstencil_ NSTENCIL ) # nstencil ) # neighbor
FindStyleHeaders(${search_path} NTOPO_CLASS ntopo_ NTOPO ) # ntopo ) # neighbor
FindStyleHeaders(${search_path} PAIR_CLASS pair_ PAIR ) # pair ) # force
FindStyleHeaders(${search_path} READER_CLASS reader_ READER ) # reader ) # read_dump
FindStyleHeaders(${search_path} REGION_CLASS region_ REGION ) # region ) # domain
endfunction(RegisterStyles)
function(RegisterStylesExt search_path extension sources)
FindStyleHeadersExt(${search_path} ANGLE_CLASS ${extension} ANGLE ${sources})
FindStyleHeadersExt(${search_path} ATOM_CLASS ${extension} ATOM_VEC ${sources})
FindStyleHeadersExt(${search_path} BODY_CLASS ${extension} BODY ${sources})
FindStyleHeadersExt(${search_path} BOND_CLASS ${extension} BOND ${sources})
FindStyleHeadersExt(${search_path} COMMAND_CLASS ${extension} COMMAND ${sources})
FindStyleHeadersExt(${search_path} COMPUTE_CLASS ${extension} COMPUTE ${sources})
FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS ${extension} DIHEDRAL ${sources})
FindStyleHeadersExt(${search_path} DUMP_CLASS ${extension} DUMP ${sources})
FindStyleHeadersExt(${search_path} FIX_CLASS ${extension} FIX ${sources})
FindStyleHeadersExt(${search_path} IMPROPER_CLASS ${extension} IMPROPER ${sources})
FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension} INTEGRATE ${sources})
FindStyleHeadersExt(${search_path} KSPACE_CLASS ${extension} KSPACE ${sources})
FindStyleHeadersExt(${search_path} MINIMIZE_CLASS ${extension} MINIMIZE ${sources})
FindStyleHeadersExt(${search_path} NBIN_CLASS ${extension} NBIN ${sources})
FindStyleHeadersExt(${search_path} NPAIR_CLASS ${extension} NPAIR ${sources})
FindStyleHeadersExt(${search_path} NSTENCIL_CLASS ${extension} NSTENCIL ${sources})
FindStyleHeadersExt(${search_path} NTOPO_CLASS ${extension} NTOPO ${sources})
FindStyleHeadersExt(${search_path} PAIR_CLASS ${extension} PAIR ${sources})
FindStyleHeadersExt(${search_path} READER_CLASS ${extension} READER ${sources})
FindStyleHeadersExt(${search_path} REGION_CLASS ${extension} REGION ${sources})
FindStyleHeadersExt(${search_path} ANGLE_CLASS ${extension} ANGLE ${sources})
FindStyleHeadersExt(${search_path} ATOM_CLASS ${extension} ATOM_VEC ${sources})
FindStyleHeadersExt(${search_path} BODY_CLASS ${extension} BODY ${sources})
FindStyleHeadersExt(${search_path} BOND_CLASS ${extension} BOND ${sources})
FindStyleHeadersExt(${search_path} COMMAND_CLASS ${extension} COMMAND ${sources})
FindStyleHeadersExt(${search_path} COMPUTE_CLASS ${extension} COMPUTE ${sources})
FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS ${extension} DIHEDRAL ${sources})
FindStyleHeadersExt(${search_path} DUMP_CLASS ${extension} DUMP ${sources})
FindStyleHeadersExt(${search_path} FIX_CLASS ${extension} FIX ${sources})
FindStyleHeadersExt(${search_path} GRAN_SUB_MOD_CLASS ${extension} GRAN_SUB_MOD ${sources})
FindStyleHeadersExt(${search_path} IMPROPER_CLASS ${extension} IMPROPER ${sources})
FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension} INTEGRATE ${sources})
FindStyleHeadersExt(${search_path} KSPACE_CLASS ${extension} KSPACE ${sources})
FindStyleHeadersExt(${search_path} MINIMIZE_CLASS ${extension} MINIMIZE ${sources})
FindStyleHeadersExt(${search_path} NBIN_CLASS ${extension} NBIN ${sources})
FindStyleHeadersExt(${search_path} NPAIR_CLASS ${extension} NPAIR ${sources})
FindStyleHeadersExt(${search_path} NSTENCIL_CLASS ${extension} NSTENCIL ${sources})
FindStyleHeadersExt(${search_path} NTOPO_CLASS ${extension} NTOPO ${sources})
FindStyleHeadersExt(${search_path} PAIR_CLASS ${extension} PAIR ${sources})
FindStyleHeadersExt(${search_path} READER_CLASS ${extension} READER ${sources})
FindStyleHeadersExt(${search_path} REGION_CLASS ${extension} REGION ${sources})
endfunction(RegisterStylesExt)
function(GenerateStyleHeaders output_path)
message(STATUS "Generating style headers...")
GenerateStyleHeader(${output_path} ANGLE angle ) # force
GenerateStyleHeader(${output_path} ATOM_VEC atom ) # atom atom_vec_hybrid
GenerateStyleHeader(${output_path} BODY body ) # atom_vec_body
GenerateStyleHeader(${output_path} BOND bond ) # force
GenerateStyleHeader(${output_path} COMMAND command ) # input
GenerateStyleHeader(${output_path} COMPUTE compute ) # modify
GenerateStyleHeader(${output_path} DIHEDRAL dihedral ) # force
GenerateStyleHeader(${output_path} DUMP dump ) # output write_dump
GenerateStyleHeader(${output_path} FIX fix ) # modify
GenerateStyleHeader(${output_path} IMPROPER improper ) # force
GenerateStyleHeader(${output_path} INTEGRATE integrate ) # update
GenerateStyleHeader(${output_path} KSPACE kspace ) # force
GenerateStyleHeader(${output_path} MINIMIZE minimize ) # update
GenerateStyleHeader(${output_path} NBIN nbin ) # neighbor
GenerateStyleHeader(${output_path} NPAIR npair ) # neighbor
GenerateStyleHeader(${output_path} NSTENCIL nstencil ) # neighbor
GenerateStyleHeader(${output_path} NTOPO ntopo ) # neighbor
GenerateStyleHeader(${output_path} PAIR pair ) # force
GenerateStyleHeader(${output_path} READER reader ) # read_dump
GenerateStyleHeader(${output_path} REGION region ) # domain
GenerateStyleHeader(${output_path} ANGLE angle ) # force
GenerateStyleHeader(${output_path} ATOM_VEC atom ) # atom atom_vec_hybrid
GenerateStyleHeader(${output_path} BODY body ) # atom_vec_body
GenerateStyleHeader(${output_path} BOND bond ) # force
GenerateStyleHeader(${output_path} COMMAND command ) # input
GenerateStyleHeader(${output_path} COMPUTE compute ) # modify
GenerateStyleHeader(${output_path} DIHEDRAL dihedral ) # force
GenerateStyleHeader(${output_path} DUMP dump ) # output write_dump
GenerateStyleHeader(${output_path} FIX fix ) # modify
GenerateStyleHeader(${output_path} GRAN_SUB_MOD gran_sub_mod ) # granular_model
GenerateStyleHeader(${output_path} IMPROPER improper ) # force
GenerateStyleHeader(${output_path} INTEGRATE integrate ) # update
GenerateStyleHeader(${output_path} KSPACE kspace ) # force
GenerateStyleHeader(${output_path} MINIMIZE minimize ) # update
GenerateStyleHeader(${output_path} NBIN nbin ) # neighbor
GenerateStyleHeader(${output_path} NPAIR npair ) # neighbor
GenerateStyleHeader(${output_path} NSTENCIL nstencil ) # neighbor
GenerateStyleHeader(${output_path} NTOPO ntopo ) # neighbor
GenerateStyleHeader(${output_path} PAIR pair ) # force
GenerateStyleHeader(${output_path} READER reader ) # read_dump
GenerateStyleHeader(${output_path} REGION region ) # domain
endfunction(GenerateStyleHeaders)
function(DetectBuildSystemConflict lammps_src_dir)
@ -184,7 +187,7 @@ endfunction(DetectBuildSystemConflict)
function(FindPackagesHeaders path style_class file_pattern headers)
file(GLOB files "${path}/${file_pattern}*.h")
file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
get_property(plist GLOBAL PROPERTY ${headers})
foreach(file_name ${files})

20
cmake/Modules/Testing.cmake
View File

@ -6,7 +6,7 @@ if(ENABLE_TESTING)
find_program(VALGRIND_BINARY NAMES valgrind)
# generate custom suppression file
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
file(READ ${SUPP} SUPPRESSIONS)
file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
@ -18,29 +18,33 @@ if(ENABLE_TESTING)
# we need to build and link a LOT of tester executables, so it is worth checking if
# a faster linker is available. requires GNU or Clang compiler, newer CMake.
# also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
# also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND
((CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04) OR (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
include(CheckCXXCompilerFlag)
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
check_cxx_compiler_flag(-fuse-ld=mold HAVE_MOLD_LINKER_FLAG)
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
find_program(HAVE_MOLD_LINKER_BIN ld.mold)
find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
find_program(HAVE_GOLD_LINKER_BIN ld.gold)
find_program(HAVE_BFD_LINKER_BIN ld.bfd)
if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
if(HAVE_MOLD_LINKER_FLAG AND HAVE_MOLD_LINKER_BIN)
set(CMAKE_CUSTOM_LINKER_DEFAULT mold)
elseif(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
endif()
set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
set(CMAKE_CUSTOM_LINKER_VALUES mold lld gold bfd default)
set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (mold, lld, gold, bfd, default)")
validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
mark_as_advanced(CMAKE_CUSTOM_LINKER)
if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")

10
cmake/Modules/Tools.cmake
View File

@ -26,13 +26,15 @@ if(BUILD_TOOLS)
enable_language(C)
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES})
if(STANDARD_MATH_LIB)
target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
endif()
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
endif()
if(BUILD_LAMMPS_SHELL)
@ -50,12 +52,16 @@ if(BUILD_LAMMPS_SHELL)
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()
target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
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/)

6
cmake/presets/all_off.cmake
View File

@ -3,6 +3,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -11,7 +12,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -42,7 +43,7 @@ set(ALL_PACKAGES
KOKKOS
KSPACE
LATBOLTZ
LATTE
LEPTON
MACHDYN
MANIFOLD
MANYBODY
@ -55,6 +56,7 @@ set(ALL_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP

6
cmake/presets/all_on.cmake
View File

@ -5,6 +5,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -13,7 +14,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -44,7 +45,7 @@ set(ALL_PACKAGES
KOKKOS
KSPACE
LATBOLTZ
LATTE
LEPTON
MACHDYN
MANIFOLD
MANYBODY
@ -57,6 +58,7 @@ set(ALL_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP

20
cmake/presets/clang.cmake
View File

@ -3,6 +3,13 @@
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()
set(FC_STD_VERSION "-std=f2003")
endif()
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
@ -21,10 +28,3 @@ set(MPI_CXX "clang++" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "clang" CACHE STRING "" FORCE)
set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

3
cmake/presets/download.cmake
View File

@ -1,14 +1,13 @@
# Preset that turns on packages with automatic downloads of sources or potentials.
# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
set(ALL_PACKAGES KIM MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
foreach(PKG ${ALL_PACKAGES})
set(PKG_${PKG} ON CACHE BOOL "" FORCE)
endforeach()
set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)

8
cmake/presets/gcc.cmake
View File

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

8
cmake/presets/intel.cmake
View File

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

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

@ -1,4 +1,5 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
ATC
AWPMD
@ -7,7 +8,7 @@ set(WIN_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -34,7 +35,7 @@ set(WIN_PACKAGES
INTEL
INTERLAYER
KSPACE
LATTE
LEPTON
MACHDYN
MANIFOLD
MANYBODY
@ -46,6 +47,7 @@ set(WIN_PACKAGES
MISC
ML-HDNNP
ML-IAP
ML-POD
ML-RANN
ML-SNAP
MOFFF

6
cmake/presets/most.cmake
View File

@ -3,13 +3,14 @@
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES
AMOEBA
ASPHERE
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -34,12 +35,15 @@ set(ALL_PACKAGES
GRANULAR
INTERLAYER
KSPACE
LEPTON
MACHDYN
MANYBODY
MC
MEAM
MESONT
MISC
ML-IAP
ML-POD
ML-SNAP
MOFFF
MOLECULE

3
cmake/presets/nolib.cmake
View File

@ -12,10 +12,9 @@ set(PACKAGES_WITH_LIB
KIM
KOKKOS
LATBOLTZ
LATTE
LEPTON
MACHDYN
MDI
MESONT
ML-HDNNP
ML-PACE
ML-QUIP

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

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

6
cmake/presets/oneapi.cmake
View File

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

9
cmake/presets/pedantic.cmake
View File

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

7
cmake/presets/pgi.cmake
View File

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

8
cmake/presets/windows.cmake
View File

@ -1,11 +1,13 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
AWPMD
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -19,6 +21,7 @@ set(WIN_PACKAGES
DPD-SMOOTH
DRUDE
EFF
ELECTRODE
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -28,12 +31,15 @@ set(WIN_PACKAGES
GRANULAR
INTERLAYER
KSPACE
LEPTON
MANIFOLD
MANYBODY
MC
MEAM
MESONT
MISC
ML-IAP
ML-POD
ML-SNAP
MOFFF
MOLECULE

72
doc/Makefile
View File

@ -38,16 +38,14 @@ endif
# override settings for PIP commands
# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
# temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
# grab list of sources from doxygen config file.
# we only want to use explicitly listed files.
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
# ------------------------------------------
@ -88,15 +86,19 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@$(MAKE) $(MFLAGS) -C graphviz all
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
ln -sf Manual.html html/index.html;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
echo "############################################" ;\
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
rst_anchor_check src/*.rst ;\
python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
$(PYTHON) $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
)
@ -113,8 +115,10 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@$(MAKE) $(MFLAGS) -C graphviz all
@mkdir -p fasthtml
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
deactivate ;\
)
@rm -rf fasthtml/_sources
@ -128,8 +132,8 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
spelling: xmlgen $(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 ; env PYTHONWARNINGS= \
cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
. $(VENV)/bin/activate ; \
cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build -b spelling -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
deactivate ;\
@ -143,7 +147,9 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@rm -f LAMMPS.epub
@cp src/JPG/*.* epub/JPG
@(\
. $(VENV)/bin/activate ;\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
deactivate ;\
@ -162,14 +168,18 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
@$(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
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
echo "############################################" ;\
echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
rst_anchor_check src/*.rst ;\
python utils/check-packages.py -s ../src -d src ;\
$(PYTHON) utils/check-packages.py -s ../src -d src ;\
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
python utils/check-styles.py -s ../src -d src ;\
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
)
@ -192,28 +202,39 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
anchor_check : $(ANCHORCHECK)
@(\
. $(VENV)/bin/activate ;\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
rst_anchor_check src/*.rst ;\
deactivate ;\
)
style_check : $(VENV)
@(\
. $(VENV)/bin/activate ;\
python utils/check-styles.py -s ../src -d src ;\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
deactivate ;\
)
package_check : $(VENV)
@(\
. $(VENV)/bin/activate ;\
python utils/check-packages.py -s ../src -d src ;\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
$(PYTHON) utils/check-packages.py -s ../src -d src ;\
deactivate ;\
)
char_check :
@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
role_check :
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
link_check : $(VENV) html
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
linkchecker -F html --check-extern html/Manual.html ;\
deactivate ;\
)
xmlgen : doxygen/xml/index.xml
doxygen/Doxyfile: doxygen/Doxyfile.in
@ -241,8 +262,7 @@ $(MATHJAX):
$(ANCHORCHECK): $(VENV)
@( \
. $(VENV)/bin/activate; \
(cd utils/converters;\
python setup.py develop);\
. $(VENV)/bin/activate; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
pip $(PIP_OPTIONS) install -e utils/converters;\
deactivate;\
)

5
doc/README
View File

@ -40,8 +40,9 @@ environment and local folders.
Installing prerequisites for the documentation build
To run the HTML documention build toolchain, python 3.x, doxygen, git,
and virtualenv have to be installed. Also internet access is initially
required to download external files and tools.
and the venv python module have to be installed if not already available.
Also internet access is initially required to download external files
and tools.
Building the PDF format manual requires in addition a compatible LaTeX
installation with support for PDFLaTeX and several add-on LaTeX packages

113
doc/documentation_conventions.md
View File

@ -4,45 +4,44 @@ This purpose of this document is to provide a point of reference
for LAMMPS developers and contributors as to what conventions
should be used to structure and format files in the LAMMPS manual.
Last change: 2020-04-23
Last change: 2022-12-30
## File format and tools
In fall 2019, the LAMMPS documentation file format has changed from
a home grown minimal markup designed to generate HTML format files
from a mostly plain text format to using the reStructuredText file
format. 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 integration into the manual. Since the transition to
reStructured text as source format, many of the artifacts or the
translation have been removed though and parts of the documentation
refactored and expanded to take advantage of the capabilities
reStructuredText and associated tools. The conversion from the
source to the final formats (HTML, PDF, and optionally e-book
reader formats ePUB and MOBI) is mostly automated and controlled
by a Makefile in the `doc` folder. This makefile assumes that the
processing is done on a Unix-like machine and Python 3.5 or later
and a matching virtualenv module are available. Additional Python
packages (like the Sphinx tool and several extensions) are
transparently installed into a virtual environment over the
internet using the `pip` package manager. Further requirements
and details are discussed in the manual.
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
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
integration into the manual. Since that transition to reStructured
text, many of the artifacts of the translation have been removed though,
and parts of the documentation refactored and expanded to take advantage
of the capabilities reStructuredText and associated tools. The
conversion from the source to the final formats (HTML, PDF, and
optionally e-book reader formats ePUB and MOBI) is mostly automated and
controlled by a Makefile in the `doc` folder. This makefile assumes that
the processing is done on a Unix-like machine and Python 3.5 or later
and a matching venv module are available. Additional Python
packages (like the Sphinx tool and several extensions) are transparently
installed into a virtual environment over the internet using the `pip`
package manager. Further requirements and details are discussed in the
manual.
## Work in progress
The refactoring and improving of the documentation is an ongoing
process, so statements in this document may not always be fully
up-to-date. If in doubt, contact the LAMMPS developers.
up-to-date. When in doubt, contact the LAMMPS developers.
## General structure
The layout and formatting of added files should follow the example
of the existing files. Since those are directly derived from their
former .txt format versions and the manual has been maintained in
The layout and formatting of added files should follow the example of
the existing files. Since many of those were initially derived from
their former .txt format versions and the manual has been maintained in
that format for many years, there is a large degree of consistency
already, so comparison with similar files should give you a good
idea what kind of information and sections are needed.
already, so comparison with similar files should give you a good idea
what kind of information and sections are needed.
## Formatting conventions
@ -52,21 +51,27 @@ 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.
Filenames, folders, paths, (shell) commands, definitions, makefile
File names, folders, paths, (shell) commands, definitions, makefile
settings and similar should be formatted as "literals" with
double backward quotes bracketing the item: \`\`path/to/some/file\`\`
Keywords and options are formatted in italics: \*option\*
Mathematical expressions, equations, symbols are typeset using
either a `.. math:`` block or the `:math:` role.
either a `.. math:` block or the `:math:` role.
Groups of shell commands or LAMMPS input script or C/C++ source
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`, or `python`. When no syntax style
is indicated, no syntax highlighting is performed.
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`,
`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
commands with a shell prompt and use `bash` highlighting, except when
the block also shows the output from that command. In the latter case,
please use a dollar sign as the shell prompt and `console` for syntax
highlighting.
As an alternative, e.g. to typeset the syntax of file formats
a `.. parsed-literal::` block can be used, which allows some
@ -89,22 +94,30 @@ by ` :class: note`.
## Required steps when adding a custom style to LAMMPS
When adding a new style (e.g. pair style or a compute or a fix)
or a new command, it is **required** to include the corresponding
documentation. Those are often new files that need to be added.
In order to be included in the documentation, those new files
need to be reference in a `.. toctree::` block. Most of those
use patterns with wildcards, so the addition will be automatic.
However, those additions also need to be added to some lists of
styles or commands. The `make style\_check` command will perform
a test and report any missing entries and list the affected files.
Any references defined with `.. \_refname:` have to be unique
across all documentation files and this can be checked for with
`make anchor\_check`. Finally, a spell-check should be done,
which is triggered via `make spelling`. Any offenses need to
be corrected and false positives should be added to the file
`utils/sphinx-config/false\_positives.txt`.
When adding a new style (e.g. pair style or a compute or a fix) or a new
command, it is **required** to include the **corresponding documentation**
in [reStructuredText format](https://docutils.sourceforge.io/rst.html).
Those are often new files that need to be added. In order to be
included in the documentation, those new files need to be referenced in a
`.. toctree::` block. Most of those use patterns with wild cards, so the
addition will be automatic. However, those additions also need to be
added to some lists of styles or commands. The `make style\_check`
command when executed in the `doc` folder will perform a test and report
any missing entries and list the affected files. Any references defined
with `.. \_refname:` have to be unique across all documentation files
and this can be checked for with `make anchor\_check`. Finally, a
spell-check should be done, which is triggered via `make spelling`. Any
offenses need to be corrected and false positives should be added to the
file `utils/sphinx-config/false\_positives.txt`.
## Required additional steps when adding a new package to LAMMPS
TODO
When adding a new package, the package must be added to the list of
packages in the `Packages_list.rst` file. If additional build instructions
need to be followed, a corresponding section should be added to the
`Build_extras.rst` file and linked from the list at the top of the
file as well as the equivalent list in the `Build_packages.rst` file.
A detailed description of the package and pointers to configuration,
included commands and examples, external pages, author information and
more should be added to the `Packages_details.rst` file.

162
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@ -1,12 +1,12 @@
# Outline of the GitHub Development Workflow
This purpose of this document is to provide a point of reference for the
The purpose of this document is to provide a point of reference for the
core LAMMPS developers and other LAMMPS contributors to understand the
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 accordingly. Last change 2021-09-02.
is likely to change as our experiences and needs change, and we try to
adapt it accordingly. Last change 2023-02-10.
## Table of Contents
@ -22,47 +22,50 @@ adapt accordingly. Last change 2021-09-02.
## GitHub Merge Management
In the interest of consistency, ONLY ONE of the core LAMMPS developers
should doing the merging itself. This is currently
should do the merging. This is currently
[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer). If this
assignment needs to be changed, it shall be done right after a stable
release. If the currently assigned developer cannot merge outstanding
pull requests in a timely manner, or in other extenuating circumstances,
other core LAMMPS developers with merge rights can merge pull requests,
when necessary.
other core LAMMPS developers with merge permission may merge pull
requests.
## Pull Requests
ALL changes to the LAMMPS code and documentation, however trivial, MUST
be submitted as a pull request to GitHub. All changes to the "develop"
branch must be made exclusively through merging pull requests. The
"release" and "stable" branches, respectively are only to be updated
upon patch or stable releases with fast-forward merges based on the
associated tags. Pull requests may also be submitted to (long-running)
feature branches created by LAMMPS developers inside the LAMMPS project,
if needed. Those are not subject to the merge and review restrictions
discussed in this document, though, but get managed as needed on a
case-by-case basis.
*ALL* changes to the LAMMPS code and documentation, however trivial,
MUST be submitted as a pull request to GitHub. All changes to the
"develop" branch must be made exclusively through merging pull requests.
The "release" and "stable" branches, respectively, are only to be
updated upon feature or stable releases based on the associated
tags. Updates to the stable release in between stable releases
(for example, back-ported bug fixes) are first merged into the "maintenance"
branch and then into the "stable" branch as update releases.
Pull requests may also be submitted to (long-running) feature branches
created by LAMMPS developers inside the LAMMPS project, if needed. Those
are not subject to the merge and review restrictions discussed in this
document, though, but get managed as needed on a case-by-case basis.
### Pull Request Assignments
Pull requests can be "chaperoned" by one of the LAMMPS core developers.
This is indicated by who the pull request is assigned to. LAMMPS core
developers can self-assign or they can decide to assign a pull request
This is indicated by whom the pull request is assigned to. LAMMPS core
developers can self-assign, or they can decide to assign a pull request
to a different LAMMPS developer. Being assigned to a pull request means,
that this pull request may need some work and the assignee is tasked to
determine whether this might be needed or not, and may either implement
the required changes or ask the submitter of the pull request to implement
them. Even though, all LAMMPS developers may have write access to pull
requests (if enabled by the submitter, which is the default), only the
submitter or the assignee of a pull request may do so. During this
period the `work_in_progress` label may be applied to the pull
request. The assignee gets to decide what happens to the pull request
next, e.g. whether it should be assigned to a different developer for
additional checks and changes, or is recommended to be merged. Removing
the `work_in_progress` label and assigning the pull request to the
developer tasked with merging signals that a pull request is ready to be
merged. In addition, a `ready_for_merge` label may also be assigned
to signal urgency to merge this pull request quickly.
determine whether this might be needed or not. The assignee may either
choose to implement required changes or ask the submitter of the pull
request to implement them. Even though, all LAMMPS developers may have
write access to pull requests (if enabled by the submitter, which is the
default), only the submitter or the assignee of a pull request should do
so. During this period, the `work_in_progress` label may be applied to
the pull request. The assignee gets to decide what happens to the pull
request next, e.g. whether it should be assigned to a different
developer for additional checks and changes, or is recommended to be
merged. Removing the `work_in_progress` label and assigning the pull
request to the developer tasked with merging signals that a pull request
is ready to be merged. In addition, a `ready_for_merge` label may also
be assigned to signal urgency to merge this pull request quickly.
### Pull Request Reviews
@ -70,32 +73,33 @@ 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
* They can be automatically assigned, because a developers matches
a file pattern in the `.github/CODEOWNERS` file, which associates
developers with the code they contributed and maintain.
* 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
maintain.
Reviewers are requested to state their appraisal of the proposed changes
and either approve or request changes. People may unassign themselves
from review, if they feel not competent about the changes proposed. At
least two approvals from LAMMPS developers with write access are required
before merging in addition to the automated compilation 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 feature, that reviews from code owners are "hard"
reviews (i.e. they must all be approved before merging is allowed), is
currently disabled and it is in the discretion of the merge maintainer to
assess when a sufficient degree of approval, especially from external
contributors, has been reached in these cases. Reviews may be
(automatically) dismissed, when the reviewed code has been changed,
and then approval is required a second time.
least two approvals from LAMMPS developers with write access are
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
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.
### Pull Request Discussions
All discussions about a pull request should be kept as much as possible
on the pull request discussion page on GitHub, so that other developers
can later review the entire discussion after the fact and understand the
rationale behind choices made. Exceptions to this policy are technical
discussions, that are centered on tools or policies themselves
rationale behind choices that were made. Exceptions to this policy are
technical discussions, that are centered on tools or policies themselves
(git, GitHub, c++) rather than on the content of the pull request.
## GitHub Issues
@ -109,39 +113,47 @@ marker in the subject. This is automatically done when using the
corresponding template for submitting an issue. Issues may be assigned
to one or more developers, if they are working on this feature or
working to resolve an issue. Issues that have nobody working
on them at the moment or in the near future, have the label
on them at the moment, or in the near future, have the label
`volunteer needed` attached.
When an issue, say `#125` is resolved by a specific pull request,
the comment for the pull request shall contain the text `closes #125`
or `fixes #125`, so that the issue is automatically deleted when
the pull request is merged. The template for pull requests includes
a header where connections between pull requests and issues can be listed
and thus were this comment should be placed.
When an issue, say `#125` is resolved by a specific pull request, the
comment for the pull request shall contain the text `closes #125` or
`fixes #125`, so that the issue is automatically deleted when the pull
request is merged. The template for pull requests includes a header
where connections between pull requests and issues can be listed, and
thus where this comment should be placed.
## Milestones and Release Planning
## Release Planning
LAMMPS uses a continuous release development model with incremental
changes, i.e. significant effort is made - including automated pre-merge
testing - that the code in the branch "develop" does not get easily
changes, i.e. significant effort is made -- including automated pre-merge
testing -- that the code in the branch "develop" does not get easily
broken. These tests are run after every update to a pull request. More
extensive and time consuming tests (including regression testing) are
performed after code is merged to the "develop" branch. There are patch
releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
developers feel, that a sufficient amount of changes have happened, and
the post-merge testing has been successful. These patch releases are
extensive and time-consuming tests (including regression testing) are
performed after code is merged to the "develop" branch. There are feature
releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
developers feel, that a sufficient number of changes have been included
and all post-merge testing has been successful. These feature releases are
marked with a `patch_<version date>` tag and the "release" branch
follows only these versions (and thus is always supposed to be of
production quality, unlike "develop", which may be temporary broken, in
the case of larger change sets or unexpected incompatibilities or side
effects.
follows only these versions with fast-forward merges. While "develop" may
be temporarily broken through issues only detected by the post-merge tests,
The "release" branch is always supposed to be of production quality.
About 1-2 times each year, there are going to be "stable" releases of
LAMMPS. These have seen additional, manual testing and review of
results from testing with instrumented code and static code analysis.
Also, the last 1-3 patch releases before a stable release are "release
candidate" versions which only contain bugfixes and documentation
updates. For release planning and the information of code contributors,
issues and pull requests being actively worked on are assigned a
"milestone", which corresponds to the next stable release or the stable
release after that, with a tentative release date.
About once each year, there is a "stable" release of LAMMPS. These have
seen additional, manual testing and review of results from testing with
instrumented code and static code analysis. Also, the last few feature
releases before a stable release are "release candidate" versions which
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.
## Project Management
For release planning and the information of code contributors, issues
and pull requests are being managed with GitHub Project Boards. There
are currently three boards: LAMMPS Feature Requests, LAMMPS Bug Reports,
and LAMMPS Pull Requests. Each board is organized in columns where
submissions are categorized. Within each column the entries are
(manually) sorted according their priority.

6
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "2 June 2022" "2022-6-2"
.TH LAMMPS "1" "28 March 2023" "2023-03-28"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 2 June 2022
\- Molecular Dynamics Simulator. Version 28 March 2023
.SH SYNOPSIS
.B lmp
@ -161,7 +161,7 @@ list references for specific cite-able features used during a
run.
.TP
\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
Invoke the \fBpackage\R command with <style> and optional arguments.
Invoke the \fBpackage\fR command with <style> and optional arguments.
The syntax is the same as if the command appeared in an input script.
For example "-pk gpu 2" is the same as "package gpu 2" in the input
script. The possible styles and options are discussed in the

7
doc/msi2lmp.1
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@ -1,11 +1,11 @@
.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS
.SH SYNOPSIS
.B msi2lmp
<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
[-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
.SH DESCRIPTION
.PP
@ -22,6 +22,9 @@ needed between .frc and .car/.mdf files are the atom types.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-help\fR,
Print detailed help message to the screen and stop.
.TP
\fB\<ROOTNAME>\fR
This has to be the first argument and is a
.B mandatory

2
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@ -63,7 +63,7 @@ In the src directory, there is one top-level Makefile and several
low-level machine-specific files named Makefile.xxx where xxx = the
machine name. If a low-level Makefile exists for your platform, you do
not need to edit the top-level Makefile. However you should check the
system-specific section of the low-level Makefile to insure the
system-specific section of the low-level Makefile to ensure the
various paths are correct for your environment. If a low-level
Makefile does not exist for your platform, you will need to add a
suitable target to the top-level Makefile. You will also need to

2
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@ -1206,7 +1206,7 @@ this command is not typically needed if the &quot;nonbond style&quot; and &quot;
an exception to this is if a short cutoff is used initially,
but a longer cutoff will be used for a subsequent run (in the same
input script), in this case the &quot;maximum cutoff&quot; command should be
used to insure enough memory is allocated for the later run
used to ensure enough memory is allocated for the later run
note that a restart file contains nonbond cutoffs (so it is not necessary
to use a &quot;nonbond style&quot; command before &quot;read restart&quot;), but LAMMPS
still needs to know what the maximum cutoff will be before the

26
doc/src/Bibliography.rst
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@ -314,7 +314,7 @@ Bibliography
Espanol, Revenga, Physical Review E, 67, 026705 (2003).
**(Espanol1997)**
Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI: 10.1209/epl/i1997-00515-8
Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI:10.1209/epl/i1997-00515-8
**(Evans and Morriss)**
Evans and Morriss, Phys Rev A, 30, 1528 (1984).
@ -368,7 +368,7 @@ Bibliography
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(GLE4MD)**
`http://gle4md.org/ <http://gle4md.org/>`_
`https://gle4md.org/ <https://gle4md.org/>`_
**(Gao)**
Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
@ -401,13 +401,13 @@ Bibliography
Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
**(Groot)**
Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI: 10.1063/1.474784
Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI:10.1063/1.474784
**(Guenole)**
Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).
**(Gullet)**
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
**(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
@ -461,7 +461,7 @@ Bibliography
Hunt, Mol Simul, 42, 347 (2016).
**(IPI)**
`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
`https://ipi-code.org/ <https://ipi-code.org/>`
**(IPI-CPC)**
Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
@ -605,16 +605,16 @@ Bibliography
I.\ Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
**(Li2013_POF)**
Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI: 10.1063/1.4812366.
Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI:10.1063/1.4812366.
**(Li2014_JCP)**
Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003.
Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI:10.1016/j.jcp.2014.02.003.
**(Li2015_CC)**
Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI: 10.1039/C5CC01684C.
Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI:10.1039/C5CC01684C.
**(Li2015_JCP)**
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI: 10.1063/1.4923254.
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI:10.1063/1.4923254.
**(Lisal)**
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
@ -733,8 +733,8 @@ Bibliography
**(Mishin)**
Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).
**(Mitchell and Finchham)**
Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell and Fincham)**
Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell2011)**
Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).
@ -875,7 +875,7 @@ Bibliography
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
**(Park)**
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
@ -1373,7 +1373,7 @@ Bibliography
Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
**(Ziegler)**
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
**(Zimmerman2004)**
Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

6
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@ -6,9 +6,9 @@ either traditional makefiles for use with GNU make (which may require
manual editing), or using a build environment generated by CMake (Unix
Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
As an alternative you can download a package with pre-built executables
or automated build trees as described on the :doc:`Install <Install>`
page.
As an alternative, you can download a package with pre-built executables
or automated build trees, as described in the :doc:`Install <Install>`
section of the manual.
.. toctree::
:maxdepth: 1

90
doc/src/Build_basics.rst
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@ -44,7 +44,7 @@ standard. A more detailed discussion of that is below.
The executable created by CMake (after running make) is named
``lmp`` unless the ``LAMMPS_MACHINE`` option is set. When setting
``LAMMPS_MACHINE=name`` the executable will be called
``LAMMPS_MACHINE=name``, the executable will be called
``lmp_name``. Using ``BUILD_MPI=no`` will enforce building a
serial executable using the MPI STUBS library.
@ -60,7 +60,7 @@ standard. A more detailed discussion of that is below.
Any ``make machine`` command will look up the make settings from a
file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
subdirectories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
folder ``Obj_machine`` with all objects and generated files and an
executable called ``lmp_machine``\ . The standard parallel build
with ``make mpi`` assumes a standard MPI installation with MPI
@ -107,9 +107,9 @@ MPI and OpenMP support in LAMMPS
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If you are installing MPI yourself to build a parallel LAMMPS
executable, we recommend either MPICH or OpenMPI which are regularly
executable, we recommend either MPICH or OpenMPI, which are regularly
used and tested with LAMMPS by the LAMMPS developers. MPICH can be
downloaded from the `MPICH home page <https://www.mpich.org>`_ and
downloaded from the `MPICH home page <https://www.mpich.org>`_, and
OpenMPI can be downloaded correspondingly from the `OpenMPI home page
<https://www.open-mpi.org>`_. Other MPI packages should also work. No
specific vendor provided and standard compliant MPI library is currently
@ -128,14 +128,14 @@ and adds vectorization support when compiled with compatible compilers,
in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
package can be compiled to include OpenMP threading.
In addition, there are a few commands in LAMMPS that have native OpenMP
support included as well. These are commands in the ``MPIIO``,
``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. In addition
some packages support OpenMP threading indirectly through the libraries
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
See the :doc:`Packages details <Packages_details>` page for more
info on these packages and the pages for their respective commands
for OpenMP threading info.
In addition, there are a few commands in LAMMPS that have native
OpenMP support included as well. These are commands in the ``MPIIO``,
``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.
Furthermore, some packages support OpenMP threading indirectly through
the libraries they interface to: e.g. ``KSPACE``, and ``COLVARS``.
See the :doc:`Packages details <Packages_details>` page for more info
on these packages, and the pages for their respective commands for
OpenMP threading info.
For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
and turn on their native OpenMP support and turn on their native OpenMP
@ -144,9 +144,9 @@ variable before you launch LAMMPS.
For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS``
variables in Makefile.machine need to include the compiler flag that
enables OpenMP. For GNU compilers it is ``-fopenmp``\ . For (recent) Intel
compilers it is ``-qopenmp``\ . If you are using a different compiler,
please refer to its documentation.
enables OpenMP. For the GNU compilers or Clang, it is ``-fopenmp``\ .
For (recent) Intel compilers, it is ``-qopenmp``\ . If you are using a
different compiler, please refer to its documentation.
.. _default-none-issues:
@ -174,15 +174,16 @@ Choice of compiler and compile/link options
The choice of compiler and compiler flags can be important for maximum
performance. Vendor provided compilers for a specific hardware can
produce faster code than open-source compilers like the GNU compilers.
On the most common x86 hardware most popular C++ compilers are quite
similar in performance of C/C++ code at high optimization levels. When
using the ``INTEL`` package, there is a distinct advantage in using
the `Intel C++ compiler <intel_>`_ due to much improved vectorization
through SSE and AVX instructions on compatible hardware as the source
code includes changes and Intel compiler specific directives to enable
high degrees of vectorization. This may change over time as equivalent
vectorization directives are included into OpenMP standard revisions and
other compilers adopt them.
On the most common x86 hardware, the most popular C++ compilers are
quite similar in their ability to optimize regular C/C++ source code at
high optimization levels. When using the ``INTEL`` package, there is a
distinct advantage in using the `Intel C++ compiler <intel_>`_ due to
much improved vectorization through SSE and AVX instructions on
compatible hardware. The source code in that package conditionally
includes compiler specific directives to enable these high degrees of
vectorization. This may change over time as equivalent vectorization
directives are included into the OpenMP standard and other compilers
adopt them.
.. _intel: https://software.intel.com/en-us/intel-compilers
@ -196,7 +197,7 @@ LAMMPS.
.. tab:: CMake build
By default CMake will use the compiler it finds according to
internal preferences and it will add optimization flags
internal preferences, and it will add optimization flags
appropriate to that compiler and any :doc:`accelerator packages
<Speed_packages>` you have included in the build. CMake will
check if the detected or selected compiler is compatible with the
@ -250,9 +251,9 @@ LAMMPS.
and `-C ../cmake/presets/pgi.cmake`
will switch the compiler to the PGI compilers.
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By
default this variable is empty.
Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts.
This variable is empty by default.
.. note::
@ -276,7 +277,7 @@ LAMMPS.
Parallel build (see ``src/MAKE/Makefile.mpi``):
.. code-block:: bash
.. code-block:: make
CC = mpicxx
CCFLAGS = -g -O3
@ -296,7 +297,7 @@ LAMMPS.
If compilation stops with a message like the following:
.. code-block::
.. code-block:: output
g++ -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I../STUBS -c ../main.cpp
In file included from ../pointers.h:24:0,
@ -368,10 +369,10 @@ running LAMMPS from Python via its library interface.
# no default value
The compilation will always produce a LAMMPS library and an
executable linked to it. By default this will be a static library
named ``liblammps.a`` and an executable named ``lmp`` Setting
``BUILD_SHARED_LIBS=yes`` will instead produce a shared library
called ``liblammps.so`` (or ``liblammps.dylib`` or
executable linked to it. By default, this will be a static
library named ``liblammps.a`` and an executable named ``lmp``
Setting ``BUILD_SHARED_LIBS=yes`` will instead produce a shared
library called ``liblammps.so`` (or ``liblammps.dylib`` or
``liblammps.dll`` depending on the platform) If
``LAMMPS_MACHINE=name`` is set in addition, the name of the
generated libraries will be changed to either ``liblammps_name.a``
@ -429,7 +430,7 @@ You may need to use ``sudo make install`` in place of the last line if
you do not have write privileges for ``/usr/local/lib`` or use the
``--prefix`` configuration option to select an installation folder,
where you do have write access. The end result should be the file
``/usr/local/lib/libmpich.so``. On many Linux installations the folder
``/usr/local/lib/libmpich.so``. On many Linux installations, the folder
``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
not require superuser or sudo access. In that case the configuration
step becomes:
@ -438,9 +439,10 @@ step becomes:
./configure --enable-shared --prefix=${HOME}/.local
Avoiding to use "sudo" for custom software installation (i.e. from source
and not through a package manager tool provided by the OS) is generally
recommended to ensure the integrity of the system software installation.
Avoiding the use of "sudo" for custom software installation (i.e. from
source and not through a package manager tool provided by the OS) is
generally recommended to ensure the integrity of the system software
installation.
----------
@ -514,11 +516,11 @@ using CMake or Make.
Install LAMMPS after a build
------------------------------------------
After building LAMMPS, you may wish to copy the LAMMPS executable of
library, along with other LAMMPS files (library header, doc files) to
a globally visible place on your system, for others to access. Note
that you may need super-user privileges (e.g. sudo) if the directory
you want to copy files to is protected.
After building LAMMPS, you may wish to copy the LAMMPS executable or
library, along with other LAMMPS files (library header, doc files), to a
globally visible place on your system, for others to access. Note that
you may need super-user privileges (e.g. sudo) if the directory you want
to copy files to is protected.
.. tabs::
@ -536,7 +538,7 @@ you want to copy files to is protected.
environment variable, if you are installing LAMMPS into a non-system
location and/or are linking to libraries in a non-system location that
depend on such runtime path settings.
As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
As an alternative, you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
to ``on`` and then the runtime paths for any linked shared libraries
and the library installation folder for the LAMMPS library will be
embedded and thus the requirement to set environment variables is avoided.

81
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@ -9,10 +9,10 @@ page.
The following text assumes some familiarity with CMake and focuses on
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, change the generated
output files for different build tools and development environments is
on a :doc:`separate page <Howto_cmake>`.
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
environments is on a :doc:`separate page <Howto_cmake>`.
.. note::
@ -22,12 +22,12 @@ on a :doc:`separate page <Howto_cmake>`.
.. warning::
You must not mix the :doc:`traditional make based <Build_make>`
LAMMPS build procedure with using CMake. Thus no packages may be
LAMMPS build procedure with using CMake. No packages may be
installed or a build been previously attempted in the LAMMPS source
directory by using ``make <machine>``. CMake will detect if this is
the case and generate an error. To remove conflicting files from the
``src`` you can use the command ``make no-all purge`` which will
un-install all packages and delete all auto-generated files.
uninstall all packages and delete all auto-generated files.
Advantages of using CMake
@ -44,9 +44,9 @@ software or for people 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 text mode or graphical
user interface. No knowledge of file formats or and complex command
line syntax required.
- CMake supports customization of settings with a command line, text
mode, or graphical user interface. No 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
@ -55,23 +55,23 @@ software or for people that want to modify or extend LAMMPS.
source tree.
- Simplified packaging of LAMMPS for Linux distributions, environment
modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
- Integration of automated regression testing (the LAMMPS side for that
is still under development).
- Integration of automated unit and regression testing (the LAMMPS side
of this is still under active development).
.. _cmake_build:
Getting started
^^^^^^^^^^^^^^^
Building LAMMPS with CMake is a two-step process. First you use CMake
to generate a build environment in a new directory. For that purpose
you can use either the command-line utility ``cmake`` (or ``cmake3``),
the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
utility ``cmake-gui``, or use them interchangeably. The second step is
then the compilation and linking of all objects, libraries, and
executables. Here is a minimal example using the command line version of
CMake to build LAMMPS with no add-on packages enabled and no
customization:
Building LAMMPS with CMake is a two-step process. In the first step,
you use CMake to generate a build environment in a new directory. For
that purpose you can use either the command-line utility ``cmake`` (or
``cmake3``), the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the
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
with no add-on packages enabled and no customization:
.. code-block:: bash
@ -96,17 +96,17 @@ Compilation can take a long time, since LAMMPS is a large project with
many features. If your machine has multiple CPU cores (most do these
days), you can speed this up by compiling sources in parallel with
``make -j N`` (with N being the maximum number of concurrently executed
tasks). Also installation of the `ccache <https://ccache.dev/>`_ (=
Compiler Cache) software may speed up repeated compilation even more,
e.g. during code development.
tasks). Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
Cache) software may speed up repeated compilation even more, e.g. during
code development, especially when repeatedly switching between branches.
After the initial build, whenever you edit LAMMPS source files, enable
or disable packages, change compiler flags or build options, you must
re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
``make``). If the compilation fails for some reason, try running
``cmake .`` and then compile again. The included dependency tracking
should make certain that only the necessary subset of files are
re-compiled. You can also delete compiled objects, libraries and
should make certain that only the necessary subset of files is
re-compiled. You can also delete compiled objects, libraries, and
executables with ``cmake --build . --target clean`` (or ``make clean``).
After compilation, you may optionally install the LAMMPS executable into
@ -132,12 +132,12 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
``CMakeCache.txt``, which is generated at the end of the CMake
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 VARIABLE1_NAME=value``) or
change them in the text mode of graphical user interface. The *-D* flag
can be used several times in one command.
To modify settings, enable or disable features, you need to set
*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.
For your convenience we provide :ref:`CMake presets <cmake_presets>`
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
(``-C ../cmake/presets/basic.cmake``). This step would only be needed
@ -155,22 +155,23 @@ specific CMake version is given when running ``cmake --help``.
Multi-configuration build systems
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Throughout this manual it is mostly assumed that LAMMPS is being built
Throughout this manual, it is mostly assumed that LAMMPS is being built
on a Unix-like operating system with "make" as the underlying "builder",
since this is the most common case. In this case the build "configuration"
is chose using ``-D CMAKE_BUILD_TYPE=<configuration>`` with ``<configuration>``
being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel".
Some build tools, however, can also use or even require to have a so-called
multi-configuration build system setup. For those the built type (or
configuration) is chosen at compile time using the same build files. E.g.
with:
since this is the most common case. In this case the build
"configuration" is chose using ``-D CMAKE_BUILD_TYPE=<configuration>``
with ``<configuration>`` being one of "Release", "Debug",
"RelWithDebInfo", or "MinSizeRel". Some build tools, however, can also
use or even require having a so-called multi-configuration build system
setup. For a multi-configuration build, the built type (or
configuration) is selected at compile time using the same build
files. E.g. with:
.. code-block:: bash
cmake --build build-multi --config Release
In that case the resulting binaries are not in the build folder directly
but in sub-directories corresponding to the build type (i.e. Release in
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:
@ -184,7 +185,7 @@ particular applicable to compiling packages that require additional libraries
that would be downloaded and compiled by CMake. The "windows" preset file
tries to keep track of which packages can be compiled natively with the
MSVC compilers out-of-the box. Not all of those external libraries are
portable to Windows either.
portable to Windows, either.
Installing CMake

94
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@ -46,7 +46,7 @@ It can be enabled for all C++ code with the following CMake flag
With this flag enabled all source files will be processed twice, first to
be compiled and then to be analyzed. Please note that the analysis can be
significantly more time consuming than the compilation itself.
significantly more time-consuming than the compilation itself.
----------
@ -140,36 +140,62 @@ of the LAMMPS project on GitHub.
The unit testing facility is integrated into the CMake build process
of the LAMMPS source code distribution itself. It can be enabled by
setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
It requires the `YAML <http://pyyaml.org/>`_ library and development
It requires the `YAML <https://pyyaml.org/>`_ library and development
headers (if those are not found locally a recent version will be
downloaded and compiled along with LAMMPS and the test program) to
compile and will download and compile a specific recent version of the
`Googletest <https://github.com/google/googletest/>`_ C++ test framework
for implementing the tests.
.. admonition:: Software version requirements for testing
:class: note
The compiler and library version requirements for the testing
framework are more strict than for the main part of LAMMPS. For
example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
(version 4.8.x) are not sufficient. The CMake configuration will try
to detect incompatible versions and either skip incompatible tests or
stop with an error. Also the number of tests will depend on
installed LAMMPS packages, development environment, operating system,
and configuration settings.
After compilation is complete, the unit testing is started in the build
folder using the ``ctest`` command, which is part of the CMake software.
The output of this command will be looking something like this::
The output of this command will be looking something like this:
[...]$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: MolPairStyle:hybrid-overlay
1/109 Test #1: MolPairStyle:hybrid-overlay ......... Passed 0.02 sec
Start 2: MolPairStyle:hybrid
2/109 Test #2: MolPairStyle:hybrid ................. Passed 0.01 sec
Start 3: MolPairStyle:lj_class2
[...]
Start 107: PotentialFileReader
107/109 Test #107: PotentialFileReader ................ Passed 0.04 sec
Start 108: EIMPotentialFileReader
108/109 Test #108: EIMPotentialFileReader ............. Passed 0.03 sec
Start 109: TestSimpleCommands
109/109 Test #109: TestSimpleCommands ................. Passed 0.02 sec
.. code-block:: console
100% tests passed, 0 tests failed out of 26
$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: RunLammps
1/563 Test #1: RunLammps .......................................... Passed 0.28 sec
Start 2: HelpMessage
2/563 Test #2: HelpMessage ........................................ Passed 0.06 sec
Start 3: InvalidFlag
3/563 Test #3: InvalidFlag ........................................ Passed 0.06 sec
Start 4: Tokenizer
4/563 Test #4: Tokenizer .......................................... Passed 0.05 sec
Start 5: MemPool
5/563 Test #5: MemPool ............................................ Passed 0.05 sec
Start 6: ArgUtils
6/563 Test #6: ArgUtils ........................................... Passed 0.05 sec
[...]
Start 561: ImproperStyle:zero
561/563 Test #561: ImproperStyle:zero ................................. Passed 0.07 sec
Start 562: TestMliapPyUnified
562/563 Test #562: TestMliapPyUnified ................................. Passed 0.16 sec
Start 563: TestPairList
563/563 Test #563: TestPairList ....................................... Passed 0.06 sec
Total Test time (real) = 25.57 sec
100% tests passed, 0 tests failed out of 563
Label Time Summary:
generated = 0.85 sec*proc (3 tests)
noWindows = 4.16 sec*proc (2 tests)
slow = 78.33 sec*proc (67 tests)
unstable = 28.23 sec*proc (34 tests)
Total Test time (real) = 132.34 sec
The ``ctest`` command has many options, the most important ones are:
@ -200,11 +226,13 @@ Fortran) and testing different aspects of the LAMMPS software and its features.
The tests will adapt to the compilation settings of LAMMPS, so that tests
will be skipped if prerequisite features are not available in LAMMPS.
.. note::
.. admonition:: Work in Progress
:class: note
The unit test framework was added in spring 2020 and is under active
development. The coverage is not complete and will be expanded over
time.
time. Preference is given to parts of the code base that are easy to
test or commonly used.
Tests for styles of the same kind of style (e.g. pair styles or bond
styles) are performed with the same test executable using different
@ -238,9 +266,9 @@ the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
since this will skip the MPI initialization for each test run.
Below is an example command and output:
.. parsed-literal::
.. code-block:: console
[tests]$ test_pair_style mol-pair-lj_cut.yaml
$ test_pair_style mol-pair-lj_cut.yaml
[==========] Running 6 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 6 tests from PairStyle
@ -495,6 +523,8 @@ The following options are available.
These should help to make source and documentation files conforming
to some the coding style preferences of the LAMMPS developers.
.. _clang-format:
Clang-format support
--------------------
@ -520,7 +550,7 @@ commands like the following:
.. code-block:: bash
$ clang-format -i some_file.cpp
clang-format -i some_file.cpp
The following target are available for both, GNU make and CMake:
@ -529,3 +559,19 @@ The following target are available for both, GNU make and CMake:
make format-src # apply clang-format to all files in src and the package folders
make format-tests # apply clang-format to all files in the unittest tree
----------
.. _gh-cli:
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.
The capabilities of the ``gh`` command is continually expanding, so
please see the documentation at https://cli.github.com/manual/

567
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@ -12,11 +12,11 @@ in addition to
- Traditional make
* - .. code-block:: bash
$ cmake -D PKG_NAME=yes
cmake -D PKG_NAME=yes
- .. code-block:: bash
- .. code-block:: console
$ make yes-name
make yes-name
as described on the :doc:`Build_package <Build_package>` page.
@ -28,26 +28,28 @@ You may need to tell LAMMPS where it is found on your system.
This is the list of packages that may require additional steps.
.. this list must be kept in sync with its counterpart in Build_package.rst
.. table_from_list::
:columns: 6
* :ref:`ADIOS <adios>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COLVARS <colvar>`
* :ref:`COMPRESS <compress>`
* :ref:`ELECTRODE <electrode>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`INTEL <intel>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`LEPTON <lepton>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`MESONT <mesont>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
@ -124,8 +126,10 @@ CMake build
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_50
# value = sm_XX (see below, default is sm_50)
-D GPU_DEBUG=value # enable debug code in the GPU package library, mostly useful for developers
# value = yes or no (default)
-D HIP_PATH=value # value = path to HIP installation. Must be set if GPU_API=HIP
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
@ -147,7 +151,9 @@ CMake build
* sm_60 or sm_61 for Pascal (supported since CUDA 8)
* sm_70 for Volta (supported since CUDA 9)
* sm_75 for Turing (supported since CUDA 10)
* sm_80 for Ampere (supported since CUDA 11)
* sm_80 or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
* sm_89 for Lovelace (supported since CUDA 11.8)
* sm_90 for Hopper (supported since CUDA 12.0)
A more detailed list can be found, for example,
at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
@ -174,15 +180,25 @@ way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
The GPU library has some multi-thread support using OpenMP. If LAMMPS is built
with ``-D BUILD_OMP=on`` this will also be enabled.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
should only use this option in preparations to run on Aurora system at ANL.
.. code:: bash
# AMDGPU target (ROCm <= 4.0)
export HIP_PLATFORM=hcc
export HIP_PATH=/path/to/HIP/install
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
@ -191,6 +207,7 @@ and the linker to work correctly.
# AMDGPU target (ROCm >= 4.1)
export HIP_PLATFORM=amd
export HIP_PATH=/path/to/HIP/install
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
@ -199,10 +216,20 @@ and the linker to work correctly.
# CUDA target (not recommended, use GPU_ARCH=cuda)
# !!! DO NOT set CMAKE_CXX_COMPILER !!!
export HIP_PLATFORM=nvcc
export HIP_PATH=/path/to/HIP/install
export CUDA_PATH=/usr/local/cuda
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
make -j 4
.. code:: bash
# SPIR-V target (Intel GPUs)
export HIP_PLATFORM=spirv
export HIP_PATH=/path/to/HIP/install
export CMAKE_CXX_COMPILER=<hipcc/clang++>
cmake -D PKG_GPU=on -D GPU_API=HIP ..
make -j 4
Traditional make
^^^^^^^^^^^^^^^^
@ -215,15 +242,15 @@ LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ ,
Makefile you use.
You can also build the library in one step from the ``lammps/src`` dir,
using a command like these, which simply invoke the ``lib/gpu/Install.py``
using a command like these, which simply invokes the ``lib/gpu/Install.py``
script with the specified args:
.. code-block:: bash
$ make lib-gpu # print help message
$ make lib-gpu args="-b" # build GPU library with default Makefile.linux
$ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
$ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
make lib-gpu # print help message
make lib-gpu args="-b" # build GPU library with default Makefile.linux
make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
Note that this procedure starts with a Makefile.machine in lib/gpu, as
specified by the "-m" switch. For your convenience, machine makefiles
@ -249,10 +276,13 @@ To enable GPU binning via CUDA performance primitives set the Makefile variable
most modern GPUs.
To support the CUDA multiprocessor server you can set the define
``-DCUDA_PROXY``. Please note that in this case you must **not** use
``-DCUDA_MPS_SUPPORT``. Please note that in this case you must **not** use
the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
to empty.
The GPU library has some multi-thread support using OpenMP. You need to add
the compiler flag that enables OpenMP to the ``CUDR_OPTS`` Makefile variable.
If the library build is successful, 3 files should be created:
``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
``lib/gpu/Makefile.lammps``\ . The latter has settings that enable LAMMPS
@ -263,7 +293,7 @@ your machine are not correct, the LAMMPS build will fail, and
.. note::
If you re-build the GPU library in ``lib/gpu``, you should always
un-install the GPU package in ``lammps/src``, then re-install it and
uninstall the GPU package in ``lammps/src``, then re-install it and
re-build LAMMPS. This is because the compilation of files in the GPU
package uses the library settings from the ``lib/gpu/Makefile.machine``
used to build the GPU library.
@ -295,7 +325,7 @@ detailed information is available at:
In addition to installing the KIM API, it is also necessary to install the
library of KIM models (interatomic potentials).
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models
@ -331,18 +361,18 @@ minutes to hours) to build. Of course you only need to do that once.)
You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``. You can also do
this in one step from the lammps/src directory, using a command like
these, which simply invoke the ``lib/kim/Install.py`` script with
these, which simply invokes the ``lib/kim/Install.py`` script with
the specified args.
.. code-block:: bash
$ make lib-kim # print help message
$ make lib-kim args="-b " # (re-)install KIM API lib with only example models
$ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
$ make lib-kim args="-b -a everything" # install KIM API lib with all models
$ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
$ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
$ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
make lib-kim # print help message
make lib-kim args="-b " # (re-)install KIM API lib with only example models
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
When using the "-b " option, the KIM library is built using its native
cmake build system. The ``lib/kim/Install.py`` script supports a
@ -354,7 +384,7 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash
$ CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b " # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b " # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
Settings for debugging OpenKIM web queries discussed below need to
be applied by adding them to the ``LMP_INC`` variable through
@ -413,7 +443,7 @@ Enabling the extra unit tests have some requirements,
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see
`Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
@ -464,6 +494,9 @@ They must be specified in uppercase.
* - **Arch-ID**
- **HOST or GPU**
- **Description**
* - NATIVE
- HOST
- Local machine
* - AMDAVX
- HOST
- AMD 64-bit x86 CPU (AVX 1)
@ -503,9 +536,21 @@ They must be specified in uppercase.
* - BDW
- HOST
- Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
* - SKL
- HOST
- Intel Skylake Client CPU
* - SKX
- HOST
- Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
- Intel Skylake Xeon Server CPU (AVX512)
* - ICL
- HOST
- Intel Ice Lake Client CPU (AVX512)
* - ICX
- HOST
- Intel Ice Lake Xeon Server CPU (AVX512)
* - SPR
- HOST
- Intel Sapphire Rapids Xeon Server CPU (AVX512)
* - KNC
- HOST
- Intel Knights Corner Xeon Phi
@ -566,6 +611,12 @@ They must be specified in uppercase.
* - AMPERE86
- GPU
- NVIDIA Ampere generation CC 8.6 GPU
* - ADA89
- GPU
- NVIDIA Ada Lovelace generation CC 8.9 GPU
* - HOPPER90
- GPU
- NVIDIA Hopper generation CC 9.0 GPU
* - VEGA900
- GPU
- AMD GPU MI25 GFX900
@ -577,7 +628,10 @@ They must be specified in uppercase.
- AMD GPU MI100 GFX908
* - VEGA90A
- GPU
- AMD GPU
- AMD GPU MI200 GFX90A
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
* - INTEL_DG1
- GPU
- Intel Iris XeMAX GPU
@ -592,9 +646,12 @@ They must be specified in uppercase.
- Intel GPU Gen12LP
* - INTEL_XEHP
- GPU
- Intel GPUs Xe-HP
- Intel GPU Xe-HP
* - INTEL_PVC
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 3.5.0 of the Kokkos library.
This list was last updated for version 3.7.1 of the Kokkos library.
.. tabs::
@ -626,20 +683,11 @@ This list was last updated for version 3.5.0 of the Kokkos library.
-D Kokkos_ARCH_GPUARCH=yes # GPUARCH = GPU from list above
-D Kokkos_ENABLE_CUDA=yes
-D Kokkos_ENABLE_OPENMP=yes
-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper
This will also enable executing FFTs on the GPU, either via the
internal KISSFFT library, or - by preference - with the cuFFT
library bundled with the CUDA toolkit, depending on whether CMake
can identify its location. The *wrapper* value for
``CMAKE_CXX_COMPILER`` variable is the path to the CUDA nvcc
compiler wrapper provided in the Kokkos library:
``lib/kokkos/bin/nvcc_wrapper``\ . The setting should include the
full path name to the wrapper, e.g.
.. code-block:: bash
-D CMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper
can identify its location.
For AMD or NVIDIA GPUs using HIP, set these variables:
@ -774,51 +822,52 @@ will thus always enable it.
----------
.. _latte:
.. _lepton:
LATTE package
-------------------------
LEPTON package
--------------
To build with this package, you must download and build the LATTE
library.
To build with this package, you must build the Lepton library which is
included in the LAMMPS source distribution in the ``lib/lepton`` folder.
.. tabs::
.. tab:: CMake build
.. code-block:: bash
This is the recommended build procedure for using Lepton in
LAMMPS. No additional settings are normally needed besides
``-D PKG_LEPTON=yes``.
-D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes
-D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location)
If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
and built inside the CMake build directory. If the LATTE library
is already on your system (in a location CMake cannot find it),
``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
file, not the directory the library file is in.
On x86 hardware the Lepton library will also include a just-in-time
compiler for faster execution. This is auto detected but can
be explicitly disabled by setting ``-D LEPTON_ENABLE_JIT=no``
(or enabled by setting it to yes).
.. tab:: Traditional make
You can download and build the LATTE library manually if you
prefer; follow the instructions in ``lib/latte/README``\ . You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invokes the
``lib/latte/Install.py`` script with the specified args:
Before building LAMMPS, one must build the Lepton library in lib/lepton.
This can be done manually in the same folder by using or adapting
one of the provided Makefiles: for example, ``Makefile.serial`` for
the GNU C++ compiler, or ``Makefile.mpi`` for the MPI compiler wrapper.
The Lepton library is written in C++-11 and thus the C++ compiler
may need to be instructed to enable support for that.
In general, it is safer to use build setting consistent with the
rest of LAMMPS. This is best carried out from the LAMMPS src
directory using a command like these, which simply invokes the
``lib/lepton/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-latte # print help message
$ make lib-latte args="-b" # download and build in lib/latte/LATTE-master
$ make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
$ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
make lib-lepton # print help message
make lib-lepton args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-lepton args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
Note that 3 symbolic (soft) links, ``includelink`` and ``liblink``
and ``filelink.o``, are created in ``lib/latte`` to point to
required folders and files in the LATTE home directory. When
LAMMPS itself is built it will use these links. You should also
check that the ``Makefile.lammps`` file you create is appropriate
for the compiler you use on your system to build LATTE.
The "machine" argument of the "-m" flag is used to find a
Makefile.machine to use as build recipe.
The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a``
----------
@ -905,17 +954,17 @@ more details.
You can download and build the MS-CG library manually if you
prefer; follow the instructions in ``lib/mscg/README``\ . You can
also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/mscg/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-mscg # print help message
$ make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make serial"
$ make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make mpi"
$ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
make lib-mscg # print help message
make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make serial"
make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
# with the settings compatible with "make mpi"
make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
will be created in ``lib/mscg`` to point to the MS-CG
@ -962,15 +1011,15 @@ POEMS package
``lib/poems``\ . You can do this manually if you prefer; follow
the instructions in ``lib/poems/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/poems/Install.py`` script with the
which simply invokes the ``lib/poems/Install.py`` script with the
specified args:
.. code-block:: bash
$ make lib-poems # print help message
$ make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
$ make lib-poems args="-m icc" # build with Intel icc compiler
make lib-poems # print help message
make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-poems args="-m icc" # build with Intel icc compiler
The build should produce two files: ``lib/poems/libpoems.a`` and
``lib/poems/Makefile.lammps``. The latter is copied from an
@ -1025,7 +1074,7 @@ VORONOI package
-----------------------------
To build with this package, you must download and build the
`Voro++ library <http://math.lbl.gov/voro++>`_ or install a
`Voro++ library <https://math.lbl.gov/voro++/>`_ or install a
binary package provided by your operating system.
.. tabs::
@ -1051,15 +1100,15 @@ binary package provided by your operating system.
You can download and build the Voro++ library manually if you
prefer; follow the instructions in ``lib/voronoi/README``. You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/voronoi/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-voronoi # print help message
$ make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
$ make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
$ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
make lib-voronoi # print help message
make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
Note that 2 symbolic (soft) links, ``includelink`` and
``liblink``, are created in lib/voronoi to point to the Voro++
@ -1100,13 +1149,13 @@ systems.
.. code-block:: bash
$ make yes-adios
make yes-adios
otherwise, set ADIOS2_DIR environment variable when turning on the package:
.. code-block:: bash
$ ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed
ADIOS2_DIR=path make yes-adios # path is where ADIOS 2.x is installed
----------
@ -1130,15 +1179,15 @@ The ATC package requires the MANYBODY package also be installed.
``lib/atc``. You can do this manually if you prefer; follow the
instructions in ``lib/atc/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/atc/Install.py`` script with the
which simply invokes the ``lib/atc/Install.py`` script with the
specified args:
.. code-block:: bash
$ make lib-atc # print help message
$ make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-atc args="-m icc" # build with Intel icc compiler
make lib-atc # print help message
make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-atc args="-m icc" # build with Intel icc compiler
The build should produce two files: ``lib/atc/libatc.a`` and
``lib/atc/Makefile.lammps``. The latter is copied from an
@ -1157,17 +1206,17 @@ The ATC package requires the MANYBODY package also be installed.
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU Fortran compiler
----------
.. _awpmd:
AWPMD package
------------------
-------------
.. tabs::
@ -1181,15 +1230,15 @@ AWPMD package
``lib/awpmd``. You can do this manually if you prefer; follow the
instructions in ``lib/awpmd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/awpmd/Install.py`` script with the
which simply invokes the ``lib/awpmd/Install.py`` script with the
specified args:
.. code-block:: bash
$ make lib-awpmd # print help message
$ make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
$ make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-awpmd args="-m icc" # build with Intel icc compiler
make lib-awpmd # print help message
make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-awpmd args="-m icc" # build with Intel icc compiler
The build should produce two files: ``lib/awpmd/libawpmd.a`` and
``lib/awpmd/Makefile.lammps``. The latter is copied from an
@ -1208,21 +1257,20 @@ AWPMD package
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
----------
.. _colvars:
.. _colvar:
COLVARS package
---------------------------------------
---------------
This package includes the `Colvars library
<https://colvars.github.io/>`_ into the LAMMPS distribution, which can
be built for the most part with all major versions of the C++ language.
This package enables the use of the `Colvars <https://colvars.github.io/>`_
module included in the LAMMPS source distribution.
.. tabs::
@ -1235,42 +1283,45 @@ be built for the most part with all major versions of the C++ language.
.. tab:: Traditional make
Before building LAMMPS, one must build the Colvars library in lib/colvars.
As with other libraries distributed with LAMMPS, the Colvars library
needs to be built before building the LAMMPS program with the COLVARS
package enabled.
This can be done manually in the same folder by using or adapting
one of the provided Makefiles: for example, ``Makefile.g++`` for
the GNU C++ compiler. C++11 compatibility may need to be enabled
for some older compilers (as is done in the example makefile).
In general, it is safer to use build setting consistent with the
rest of LAMMPS. This is best carried out from the LAMMPS src
directory using a command like these, which simply invoke the
``lib/colvars/Install.py`` script with the specified args:
From the LAMMPS ``src`` directory, this is most easily and safely done
via one of the following commands, which implicitly rely on the
``lib/colvars/Install.py`` script with optional arguments:
.. code-block:: bash
$ make lib-colvars # print help message
$ make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
$ make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
make lib-colvars # print help message
make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled
The "machine" argument of the "-m" flag is used to find a
Makefile.machine to use as build recipe. If it does not already
exist in ``lib/colvars``, it will be auto-generated by using
compiler flags consistent with those parsed from the core LAMMPS
makefiles.
``Makefile.machine`` file to use as build recipe. If such recipe does
not already exist in ``lib/colvars``, suitable settings will be
auto-generated consistent with those used in the core LAMMPS makefiles.
.. versionchanged:: 8Feb2023
Please note that Colvars uses the Lepton library, which is now
included with the LEPTON package; if you use anything other than
the ``make lib-colvars`` command, please make sure to :ref:`build
Lepton beforehand <lepton>`.
Optional flags may be specified as environment variables:
.. code-block:: bash
$ COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
$ COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
COLVARS_DEBUG=yes make lib-colvars args="-m machine" # Build with debug code (much slower)
COLVARS_LEPTON=no make lib-colvars args="-m machine" # Build without Lepton (included otherwise)
The build should produce two files: the library ``lib/colvars/libcolvars.a``
(which also includes Lepton objects if enabled) and the specification file
``lib/colvars/Makefile.lammps``. The latter is auto-generated, and normally does
not need to be edited.
The build should produce two files: the library
``lib/colvars/libcolvars.a`` and the specification file
``lib/colvars/Makefile.lammps``. The latter is auto-generated,
and normally does not need to be edited.
----------
@ -1285,27 +1336,53 @@ This package depends on the KSPACE package.
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_KSPACE=yes`` and ``-D
PKG_ELECTRODE=yes``.
.. code-block:: bash
-D PKG_ELECTRODE=yes # enable the package itself
-D PKG_KSPACE=yes # the ELECTRODE package requires KSPACE
-D USE_INTERNAL_LINALG=value #
Features in the ELECTRODE package are dependent on code in the
KSPACE package so the latter one *must* be enabled.
The ELECTRODE package also requires LAPACK (and BLAS) and CMake
can identify their locations and pass that info to the ELECTRODE
build script. But on some systems this may cause problems when
linking or the dependency is not desired. Try enabling
``USE_INTERNAL_LINALG`` in those cases to use the bundled linear
algebra library and work around the limitation.
.. tab:: Traditional make
The package is activated with ``make yes-KSPACE`` and ``make
yes-ELECTRODE``
Note that the ``Makefile.lammps`` file has settings for the BLAS and
LAPACK linear algebra libraries. As explained in ``lib/awpmd/README``
these can either exist on your system, or you can use the files provided
in ``lib/linalg``. In the latter case you also need to build the library
in ``lib/linalg`` with a command like these:
Before building LAMMPS, you must configure the ELECTRODE support
libraries and settings in ``lib/electrode``. You can do this
manually, if you prefer, or do it in one step from the
``lammps/src`` dir, using a command like these, which simply
invokes the ``lib/electrode/Install.py`` script with the specified
args:
.. code-block:: bash
$ make lib-linalg # print help message
$ make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
$ make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
$ make lib-linalg args="-m gfortran" # build with GNU Fortran compiler
make lib-electrode # print help message
make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
Note that the ``Makefile.lammps`` file has settings for the BLAS
and LAPACK linear algebra libraries. These can either exist on
your system, or you can use the files provided in ``lib/linalg``.
In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
----------
@ -1342,13 +1419,56 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
.. code-block:: bash
$ make lib-pace # print help message
$ make lib-pace args="-b" # download and build the default version in lib/pace
make lib-pace # print help message
make lib-pace args="-b" # download and build the default version in lib/pace
You should not need to edit the ``lib/pace/Makefile.lammps`` file.
----------
.. _ml-pod:
ML-POD package
-----------------------------
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_ML-POD=yes``.
.. tab:: Traditional make
Before building LAMMPS, you must configure the ML-POD support
settings in ``lib/mlpod``. You can do this manually, if you
prefer, or do it in one step from the ``lammps/src`` dir, using a
command like the following, which simply invoke the
``lib/mlpod/Install.py`` script with the specified args:
.. code-block:: bash
make lib-mlpod # print help message
make lib-mlpod args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-mlpod args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
make lib-mlpod args="-m mpi -e linalg" # same as above but use the bundled linalg lib
Note that the ``Makefile.lammps`` file has settings to use the BLAS
and LAPACK linear algebra libraries. These can either exist on
your system, or you can use the files provided in ``lib/linalg``.
In the latter case you also need to build the library in
``lib/linalg`` with a command like these:
.. code-block:: bash
make lib-linalg # print help message
make lib-linalg args="-m serial" # build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m g++" # build with GNU C++ compiler
The package itself is activated with ``make yes-ML-POD``.
----------
.. _plumed:
PLUMED package
@ -1442,10 +1562,10 @@ LAMMPS build.
.. code-block:: bash
$ make lib-plumed # print help message
$ make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
$ make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
$ make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
make lib-plumed # print help message
make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
# /usr/local and use shared linkage mode
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
@ -1458,8 +1578,8 @@ LAMMPS build.
.. code-block:: bash
$ make yes-plumed
$ make machine
make yes-plumed
make machine
Once this compilation completes you should be able to run LAMMPS
in the usual way. For shared linkage mode, libplumed.so must be
@ -1506,13 +1626,13 @@ the HDF5 library.
``lib/h5md``. You can do this manually if you prefer; follow the
instructions in ``lib/h5md/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/h5md/Install.py`` script with the
which simply invokes the ``lib/h5md/Install.py`` script with the
specified args:
.. code-block:: bash
$ make lib-h5md # print help message
$ make lib-h5md args="-m h5cc" # build with h5cc compiler
make lib-h5md # print help message
make lib-h5md args="-m h5cc" # build with h5cc compiler
The build should produce two files: ``lib/h5md/libch5md.a`` and
``lib/h5md/Makefile.lammps``. The latter is copied from an
@ -1562,14 +1682,14 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
You can download and build the *n2p2* library manually if you prefer;
follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
one step from the ``lammps/src`` dir, using a command like these, which
simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
simply invokes the ``lib/hdnnp/Install.py`` script with the specified args:
.. code-block:: bash
$ make lib-hdnnp # print help message
$ make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-...
$ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
$ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
make lib-hdnnp # print help message
make lib-hdnnp args="-b" # download and build in lib/hdnnp/n2p2-...
make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
@ -1669,56 +1789,14 @@ MDI package
.. code-block:: bash
$ python Install.py -m gcc # build using gcc compiler
$ python Install.py -m icc # build using icc compiler
python Install.py -m gcc # build using gcc compiler
python Install.py -m icc # build using icc compiler
The build should produce two files: ``lib/mdi/includelink/mdi.h``
and ``lib/mdi/liblink/libmdi.so``\ .
----------
.. _mesont:
MESONT package
-------------------------
This package includes a library written in Fortran 90 in the
``lib/mesont`` folder, so a working Fortran 90 compiler is required to
compile it. Also, the files with the force field data for running the
bundled examples are not included in the source distribution. Instead
they will be downloaded the first time this package is installed.
.. tabs::
.. tab:: CMake build
No additional settings are needed besides ``-D PKG_MESONT=yes``
.. tab:: Traditional make
Before building LAMMPS, you must build the *mesont* library in
``lib/mesont``\ . You can also do it in one step from the
``lammps/src`` dir, using a command like these, which simply
invoke the ``lib/mesont/Install.py`` script with the specified
args:
.. code-block:: bash
$ make lib-mesont # print help message
$ make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
$ make lib-mesont args="-m ifort" # build with Intel icc compiler
The build should produce two files: ``lib/mesont/libmesont.a`` and
``lib/mesont/Makefile.lammps``\ . The latter is copied from an
existing ``Makefile.lammps.\*`` and has settings needed to build
LAMMPS with the *mesont* library (though typically the settings
contain only the Fortran runtime library). If necessary, you can
edit/create a new ``lib/mesont/Makefile.machine`` file for your
system, which should define an ``EXTRAMAKE`` variable to specify a
corresponding ``Makefile.lammps.machine`` file.
----------
.. _molfile:
MOLFILE package
@ -1819,6 +1897,22 @@ OPENMP package
For other platforms and compilers, please consult the
documentation about OpenMP support for your compiler.
.. admonition:: Adding OpenMP support on macOS
:class: note
Apple offers the `Xcode package and IDE
<https://developer.apple.com/xcode/>`_ for compiling software on
macOS, so you have likely installed it to compile LAMMPS. Their
compiler is based on `Clang <https://clang.llvm.org/>`_, but while it
is capable of processing OpenMP directives, the necessary header
files and OpenMP runtime library are missing. The `R developers
<https://www.r-project.org/>`_ have figured out a way to build those
in a compatible fashion. One can download them from
`https://mac.r-project.org/openmp/
<https://mac.r-project.org/openmp/>`_. Simply adding those files as
instructed enables the Xcode C++ compiler to compile LAMMPS with ``-D
BUILD_OMP=yes``.
----------
.. _qmmm:
@ -1868,15 +1962,15 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
``lib/qmmm``. You can do this manually if you prefer; follow the
first two steps explained in ``lib/qmmm/README``. You can also do
it in one step from the ``lammps/src`` dir, using a command like
these, which simply invoke the ``lib/qmmm/Install.py`` script with
these, which simply invokes the ``lib/qmmm/Install.py`` script with
the specified args:
.. code-block:: bash
$ make lib-qmmm # print help message
$ make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
$ make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
$ make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
make lib-qmmm # print help message
make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler
The build should produce two files: ``lib/qmmm/libqmmm.a`` and
``lib/qmmm/Makefile.lammps``. The latter is copied from an
@ -1913,14 +2007,25 @@ within CMake will download the non-commercial use version.
.. code-block:: bash
-D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes
-D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location)
-D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
# value = no (default) or yes
CMake will try to download and build the QUIP library from GitHub, if it is not
found on the local machine. This requires to have git installed. It will use the same compilers
and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the
Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
and installed QUIP library and CMake cannot find it.
CMake will try to download and build the QUIP library from GitHub,
if it is not found on the local machine. This requires to have git
installed. It will use the same compilers and flags as used for
compiling LAMMPS. Currently this is only supported for the GNU
and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
want to use a previously compiled and installed QUIP library and
CMake cannot find it.
The QUIP library requires LAPACK (and BLAS) and CMake can identify
their locations and pass that info to the QUIP build script. But
on some systems this triggers a (current) limitation of CMake and
the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
those cases to use the bundled linear algebra library and work around
the limitation.
.. tab:: Traditional make
@ -1965,7 +2070,7 @@ To build with this package, you must download and build the
You can download and build the ScaFaCoS library manually if you
prefer; follow the instructions in ``lib/scafacos/README``. You
can also do it in one step from the ``lammps/src`` dir, using a
command like these, which simply invoke the
command like these, which simply invokes the
``lib/scafacos/Install.py`` script with the specified args:
.. code-block:: bash
@ -2009,14 +2114,14 @@ Eigen3 is a template library, so you do not need to build it.
You can download the Eigen3 library manually if you prefer; follow
the instructions in ``lib/smd/README``. You can also do it in one
step from the ``lammps/src`` dir, using a command like these,
which simply invoke the ``lib/smd/Install.py`` script with the
which simply invokes the ``lib/smd/Install.py`` script with the
specified args:
.. code-block:: bash
$ make lib-smd # print help message
$ make lib-smd args="-b" # download to lib/smd/eigen3
$ make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
make lib-smd # print help message
make lib-smd args="-b" # download to lib/smd/eigen3
make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
Note that a symbolic (soft) link named ``includelink`` is created
in ``lib/smd`` to point to the Eigen dir. When LAMMPS builds it

45
doc/src/Build_link.rst
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@ -1,33 +1,32 @@
Link LAMMPS as a library to another code
========================================
LAMMPS is designed as a library of C++ objects that can be
integrated into other applications including Python scripts.
The files ``src/library.cpp`` and ``src/library.h`` define a
C-style API for using LAMMPS as a library. See the
:doc:`Howto_library` page
for a description of the interface and how to use it for your needs.
LAMMPS is designed as a library of C++ objects that can be integrated
into other applications, including Python scripts. The files
``src/library.cpp`` and ``src/library.h`` define a C-style API for using
LAMMPS as a library. See the :doc:`Howto_library` page for a
description of the interface and how to use it for your needs.
The :doc:`Build_basics` page explains how to build
LAMMPS as either a shared or static library. This results in a file
in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
in case of building a static library. In case of a shared library
the name is the same only that the suffix is going to be either ``.so``
or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS.
In some cases the ``.so`` file may be a symbolic link to a file with
the suffix ``.so.0`` (or some other number).
The :doc:`Build_basics` page explains how to build LAMMPS as either a
shared or static library. This results in a file in the compilation
folder called ``liblammps.a`` or ``liblammps_<name>.a`` in case of
building a static library. In case of a shared library, the name is the
same only that the suffix is going to be either ``.so`` or ``.dylib`` or
``.dll`` instead of ``.a`` depending on the OS. In some cases, the
``.so`` file may be a symbolic link to a file with the suffix ``.so.0``
(or some other number).
.. note::
Care should be taken to use the same MPI library for the calling code
and the LAMMPS library unless LAMMPS is to be compiled without (real)
MPI support using the include STUBS MPI library.
and the LAMMPS library, unless LAMMPS is to be compiled without (real)
MPI support using the included STUBS MPI library.
Link with LAMMPS as a static library
------------------------------------
The calling application can link to LAMMPS as a static library with
compilation and link commands as in the examples shown below. These
compilation and link commands, as in the examples shown below. These
are examples for a code written in C in the file ``caller.c``.
The benefit of linking to a static library is, that the resulting
executable is independent of that library since all required
@ -142,10 +141,10 @@ Link with LAMMPS as a shared library
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 to be specified when
linking 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:
library file. Thus, those libraries need not be specified when linking
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:
.. tabs::
@ -209,7 +208,7 @@ You can verify whether all required shared libraries are found with the
.. code-block:: bash
$ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
linux-vdso.so.1 (0x00007ffe729e0000)
liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
@ -222,7 +221,7 @@ If a required library is missing, you would get a 'not found' entry:
.. code-block:: bash
$ ldd caller
ldd caller
linux-vdso.so.1 (0x00007ffd672fe000)
liblammps.so => not found
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)

62
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View File

@ -20,21 +20,22 @@ with :doc:`CMake <Build_cmake>`. The makefiles of the traditional
make based build process and the scripts they are calling expect a few
additional tools to be available and functioning.
* a working C/C++ compiler toolchain supporting the C++11 standard; on
Linux these are often the GNU compilers. Some older compilers
* A working C/C++ compiler toolchain supporting the C++11 standard; on
Linux, these are often the GNU compilers. Some older compiler versions
require adding flags like ``-std=c++11`` to enable the C++11 mode.
* a Bourne shell compatible "Unix" shell program (often this is ``bash``)
* a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* python (optional, required for ``make lib-<pkg>`` in the src folder).
python scripts are currently tested with python 2.7 and 3.6. The procedure
for :doc:`building the documentation <Build_manual>` requires python 3.5 or later.
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* Python (optional, required for ``make lib-<pkg>`` in the src
folder). Python scripts are currently tested with python 2.7 and
3.6 to 3.11. The procedure for :doc:`building the documentation
<Build_manual>` *requires* Python 3.5 or later.
Getting started
^^^^^^^^^^^^^^^
To include LAMMPS packages (i.e. optional commands and styles) you must
enable (or "install") them first, as discussed on the :doc:`Build
package <Build_package>` page. If a packages requires (provided or
package <Build_package>` page. If a package requires (provided or
external) libraries, you must configure and build those libraries
**before** building LAMMPS itself and especially **before** enabling
such a package with ``make yes-<package>``. :doc:`Building LAMMPS with
@ -56,36 +57,36 @@ Compilation can take a long time, since LAMMPS is a large project with
many features. If your machine has multiple CPU cores (most do these
days), you can speed this up by compiling sources in parallel with
``make -j N`` (with N being the maximum number of concurrently executed
tasks). Also installation of the `ccache <https://ccache.dev/>`_ (=
Compiler Cache) software may speed up repeated compilation even more,
e.g. during code development.
tasks). Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
Cache) software may speed up repeated compilation even more, e.g. during
code development, especially when repeatedly switching between branches.
After the initial build, whenever you edit LAMMPS source files, or add
or remove new files to the source directory (e.g. by installing or
uninstalling packages), you must re-compile and relink the LAMMPS
executable with the same ``make <machine>`` command. The makefile's
dependency tracking should insure that only the necessary subset of
files are re-compiled. If you change settings in the makefile, you have
to recompile *everything*. To delete all objects you can use ``make
dependency tracking should ensure that only the necessary subset of
files is re-compiled. If you change settings in the makefile, you have
to recompile *everything*. To delete all objects, you can use ``make
clean-<machine>``.
.. note::
Before the actual compilation starts, LAMMPS will perform several
steps to collect information from the configuration and setup that
is then embedded into the executable. When you build LAMMPS for
the first time, it will also compile a tool to quickly assemble
a list of dependencies, that are required for the make program to
correctly detect which parts need to be recompiled after changes
were made to the sources.
steps to collect information from the configuration and setup that is
then embedded into the executable. When you build LAMMPS for the
first time, it will also compile a tool to quickly determine a list
of dependencies. Those are required for the make program to
correctly detect, which files need to be recompiled or relinked
after changes were made to the sources.
Customized builds and alternate makefiles
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The ``src/MAKE`` directory tree contains the ``Makefile.<machine>``
files included in the LAMMPS distribution. Typing ``make example`` uses
``Makefile.example`` from one of those folders, if available. Thus the
``make serial`` and ``make mpi`` lines above use
``Makefile.example`` from one of those folders, if available. The
``make serial`` and ``make mpi`` lines above, for example, use
``src/MAKE/Makefile.serial`` and ``src/MAKE/Makefile.mpi``,
respectively. Other makefiles are in these directories:
@ -106,17 +107,18 @@ a new name, please edit the first line with the description and machine
name, so you will not confuse yourself, when looking at the machine
summary.
Makefiles you may wish to try include these (some require a package
first be installed). Many of these include specific compiler flags
for optimized performance. Please note, however, that some of these
customized machine Makefile are contributed by users. Since both
compilers, OS configurations, and LAMMPS itself keep changing, their
settings may become outdated:
Makefiles you may wish to try out, include those listed below (some
require a package first be installed). Many of these include specific
compiler flags for optimized performance. Please note, however, that
some of these customized machine Makefile are contributed by users, and
thus may have modifications specific to the systems of those users.
Since compilers, OS configurations, and LAMMPS itself keep changing,
their settings may become outdated, too:
.. code-block:: bash
make mac # build serial LAMMPS on a Mac
make mac_mpi # build parallel LAMMPS on a Mac
make mac # build serial LAMMPS on macOS
make mac_mpi # build parallel LAMMPS on macOS
make intel_cpu # build with the INTEL package optimized for CPUs
make knl # build with the INTEL package optimized for KNLs
make opt # build with the OPT package optimized for CPUs

69
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@ -2,7 +2,7 @@ Build the LAMMPS documentation
==============================
Depending on how you obtained LAMMPS and whether you have built the
manual yourself, this directory has a number of sub-directories and
manual yourself, this directory has a number of subdirectories and
files. Here is a list with descriptions:
.. code-block:: bash
@ -33,7 +33,7 @@ various tools and files. Some of them have to be installed (see below). For
the rest the build process will attempt to download and install them into
a python virtual environment and local folders.
A current version of the manual (latest patch release, that is the state
A current version of the manual (latest feature release, that is the state
of the *release* branch) is is available online at:
`https://docs.lammps.org/ <https://docs.lammps.org/>`_.
A version of the manual corresponding to the ongoing development (that is
@ -48,18 +48,15 @@ Build using GNU make
The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
can be translated to different output format using the `Sphinx
<sphinx_>`_ document generator tool. It also incorporates programmer
documentation extracted from the LAMMPS C++ sources through the `Doxygen
<https://doxygen.nl>`_ program. Currently the translation to HTML, PDF
(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
readers) are supported. For that to work a Python 3 interpreter, the
``doxygen`` tools and internet access to download additional files and
tools are required. This download is usually only required once or
after the documentation folder is returned to a pristine state with
``make clean-all``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _sphinx: https://www.sphinx-doc.org
<https://www.sphinx-doc.org/>`_ document generator tool. It also
incorporates programmer documentation extracted from the LAMMPS C++
sources through the `Doxygen <https://doxygen.nl/>`_ program. Currently
the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
and MOBI (for Amazon Kindle(tm) readers) are supported. For that to work a
Python interpreter version 3.8 or later, the ``doxygen`` tools and
internet access to download additional files and tools are required.
This download is usually only required once or after the documentation
folder is returned to a pristine state with ``make clean-all``.
For the documentation build a python virtual environment is set up in
the folder ``doc/docenv`` and various python packages are installed into
@ -90,6 +87,7 @@ folder. The following ``make`` commands are available:
make anchor_check # check for duplicate anchor labels
make style_check # check for complete and consistent style lists
make package_check # check for complete and consistent package lists
make link_check # check for broken or outdated URLs
make spelling # spell-check the manual
----------
@ -128,38 +126,29 @@ common setups:
.. code-block:: bash
sudo apt-get install python-virtualenv git doxygen
sudo apt-get install git doxygen
.. tab:: RHEL or CentOS (Version 7.x)
.. code-block:: bash
sudo yum install python3-virtualenv git doxygen
sudo yum install git doxygen
.. tab:: Fedora or RHEL/CentOS (8.x or later)
.. code-block:: bash
sudo dnf install python3-virtualenv git doxygen
sudo dnf install git doxygen
.. tab:: MacOS X
.. tab:: macOS
*Python 3*
Download the latest Python 3 MacOS X package from
If Python 3 is not available on your macOS system, you can
download the latest Python 3 macOS package from
`https://www.python.org <https://www.python.org>`_ and install it.
This will install both Python 3 and pip3.
*virtualenv*
Once Python 3 is installed, open a Terminal and type
.. code-block:: bash
pip3 install virtualenv
This will install virtualenv from the Python Package Index.
Prerequisites for PDF
---------------------
@ -179,7 +168,7 @@ math expressions transparently into embedded images.
For converting the generated ePUB file to a MOBI format file (for e-book
readers, like Kindle, that cannot read ePUB), you also need to have the
``ebook-convert`` tool from the "calibre" software
installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
Typing ``make mobi`` will first create the ePUB file and then convert
it. On the Kindle readers in particular, you also have support for PDF
files, so you could download and view the PDF version as an alternative.
@ -219,9 +208,20 @@ be multiple tests run automatically:
- A test that only standard, printable ASCII text characters are used.
This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
thus prints all offending lines with filename and line number
prepended to the screen. Special characters like the Angstrom
:math:`\mathrm{\mathring{A}}` should be typeset with embedded math
(like this ``:math:`\mathrm{\mathring{A}}```\ ).
prepended to the screen. Special characters like Greek letters
(:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
(:math:`x^2~~\mathrm{U}_{LJ}`), mathematical expressions
(:math:`\frac{1}{2}\mathrm{N}~~x\to\infty`), or the Angstrom symbol
(:math:`\AA`) should be typeset with embedded LaTeX (like this
``:math:`\alpha \sigma \epsilon```, ``:math:`x^2 \mathrm{E}_{LJ}```,
``:math:`\frac{1}{2}\mathrm{N} x\to\infty```, or ``:math:`\AA```\ ).
- Embedded LaTeX is rendered in HTML output with `MathJax
<https://www.mathjax.org/>`_ and in PDF output by passing the embedded
text to LaTeX. Some care has to be taken, though, since there are
limitations which macros and features can be used in either mode, so
it is recommended to always check whether any new or changed
documentation does translate and render correctly with either output.
- A test whether all styles are documented and listed in their
respective overview pages. A typical output with warnings looks like this:
@ -252,6 +252,5 @@ manual with ``make spelling``. This requires `a library called enchant
positives* (e.g. keywords, names, abbreviations) those can be added to
the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
.. _lws: https://www.lammps.org
.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html

54
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@ -4,13 +4,14 @@ Include packages in build
In LAMMPS, a package is a group of files that enable a specific set of
features. For example, force fields for molecular systems or
rigid-body constraints are in packages. In the src directory, each
package is a sub-directory with the package name in capital letters.
package is a subdirectory with the package name in capital letters.
An overview of packages is given on the :doc:`Packages <Packages>` doc
page. Brief overviews of each package are on the :doc:`Packages details <Packages_details>` page.
page. Brief overviews of each package are on the :doc:`Packages details
<Packages_details>` page.
When building LAMMPS, you can choose to include or exclude each
package. In general there is no need to include a package if you
package. Generally, there is no need to include a package if you
never plan to use its features.
If you get a run-time error that a LAMMPS command or style is
@ -30,23 +31,28 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
These links take you to the extra instructions for those select
packages:
.. this list must be kept in sync with its counterpart in Build_extras.rst
.. table_from_list::
:columns: 6
* :ref:`ADIOS <adios>`
* :ref:`ATC <atc>`
* :ref:`AWPMD <awpmd>`
* :ref:`COLVARS <colvars>`
* :ref:`COLVARS <colvar>`
* :ref:`COMPRESS <compress>`
* :ref:`ELECTRODE <electrode>`
* :ref:`GPU <gpu>`
* :ref:`H5MD <h5md>`
* :ref:`INTEL <intel>`
* :ref:`KIM <kim>`
* :ref:`KOKKOS <kokkos>`
* :ref:`LATTE <latte>`
* :ref:`LEPTON <lepton>`
* :ref:`MACHDYN <machdyn>`
* :ref:`MDI <mdi>`
* :ref:`ML-HDNNP <ml-hdnnp>`
* :ref:`ML-IAP <mliap>`
* :ref:`ML-PACE <ml-pace>`
* :ref:`ML-POD <ml-pod>`
* :ref:`ML-QUIP <ml-quip>`
* :ref:`MOLFILE <molfile>`
* :ref:`MSCG <mscg>`
@ -87,7 +93,7 @@ versus make.
If you switch between building with CMake and make builds, no
packages in the src directory can be installed when you invoke
``cmake``. CMake will give an error if that is not the case,
indicating how you can un-install all packages in the src dir.
indicating how you can uninstall all packages in the src dir.
.. tab:: Traditional make
@ -96,7 +102,7 @@ versus make.
cd lammps/src
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # un-install a package with name
make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed
Examples:
@ -112,13 +118,13 @@ versus make.
.. note::
You must always re-build LAMMPS (via make) after installing or
un-installing a package, for the action to take effect. The
uninstalling a package, for the action to take effect. The
included dependency tracking will make certain only files that
are required to be rebuilt are recompiled.
.. note::
You cannot install or un-install packages and build LAMMPS in a
You cannot install or uninstall packages and build LAMMPS in a
single make command with multiple targets, e.g. ``make
yes-colloid mpi``. This is because the make procedure creates
a list of source files that will be out-of-date for the build
@ -143,7 +149,7 @@ other files dependent on that package are also excluded.
if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE)
were pre-installed via the traditional make procedure in the ``src``
directory. That is no longer the case, so that CMake will build
as-is without needing to un-install those packages.
as-is without needing to uninstall those packages.
----------
@ -160,9 +166,9 @@ control flow constructs for more complex operations.
LAMMPS includes several of these files to define configuration
"presets", similar to the options that exist for the Make based
system. Using these files you can enable/disable portions of the
available packages in LAMMPS. If you need a custom preset you can take
one of them as a starting point and customize it to your needs.
system. Using these files, you can enable/disable portions of the
available packages in LAMMPS. If you need a custom preset, you can
make a copy of one of them and modify it to suit your needs.
.. code-block:: bash
@ -176,7 +182,7 @@ one of them as a starting point and customize it to your needs.
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
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers
Presets that have names starting with "windows" are specifically for
compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@ -220,7 +226,7 @@ The following commands are useful for managing package source files
and their installation when building LAMMPS via traditional make.
Just type ``make`` in lammps/src to see a one-line summary.
These commands install/un-install sets of packages:
These commands install/uninstall sets of packages:
.. code-block:: bash
@ -236,40 +242,40 @@ These commands install/un-install sets of packages:
make yes-ext # install packages that require external libraries
make no-ext # uninstall packages that require external libraries
which install/un-install various sets of packages. Typing ``make
which install/uninstall various sets of packages. Typing ``make
package`` will list all the these commands.
.. note::
Installing or un-installing a package for the make based build process
Installing or uninstalling a package for the make based build process
works by simply copying files back and forth between the main source
directory src and the sub-directories with the package name (e.g.
directory src and the subdirectories with the package name (e.g.
src/KSPACE, src/ATC), so that the files are included or excluded
when LAMMPS is built. Only source files in the src folder will be
compiled.
The following make commands help manage files that exist in both the
src directory and in package sub-directories. You do not normally
src directory and in package subdirectories. You do not normally
need to use these commands unless you are editing LAMMPS files or are
updating LAMMPS via git.
Type ``make package-status`` or ``make ps`` to show which packages are
currently installed. For those that are installed, it will list any
files that are different in the src directory and package
sub-directory.
subdirectory.
Type ``make package-installed`` or ``make pi`` to show which packages are
currently installed, without listing the status of packages that are
not installed.
Type ``make package-update`` or ``make pu`` to overwrite src files with
files from the package sub-directories if the package is installed. It
files from the package subdirectories if the package is installed. It
should be used after the checkout has been :doc:`updated or changed
withy git <Install_git>`, this will only update the files in the package
sub-directories, but not the copies in the src folder.
with git <Install_git>`, this will only update the files in the package
subdirectories, but not the copies in the src folder.
Type ``make package-overwrite`` to overwrite files in the package
sub-directories with src files.
subdirectories with src files.
Type ``make package-diff`` to list all differences between pairs of
files in both the source directory and the package directory.

85
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@ -1,8 +1,8 @@
Optional build settings
=======================
LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make.
LAMMPS can be built with several optional settings. Each subsection
explains how to do this for building both with CMake and make.
* `C++11 standard compliance`_ when building all of LAMMPS
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
@ -41,7 +41,7 @@ FFT library
When the KSPACE package is included in a LAMMPS build, the
:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
require use of an FFT library to compute 1d FFTs. The KISS FFT
library is included with LAMMPS but other libraries can be faster.
library is included with LAMMPS, but other libraries can be faster.
LAMMPS can use them if they are available on your system.
.. tabs::
@ -63,9 +63,9 @@ LAMMPS can use them if they are available on your system.
Usually these settings are all that is needed. If FFTW3 is
selected, then CMake will try to detect, if threaded FFTW
libraries are available and enable them by default. This setting
is independent of whether OpenMP threads are enabled and a
packages like KOKKOS or OPENMP is used. If CMake cannot detect
the FFT library, you can set these variables to assist:
is independent of whether OpenMP threads are enabled and a package
like KOKKOS or OPENMP is used. If CMake cannot detect the FFT
library, you can set these variables to assist:
.. code-block:: bash
@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system.
files in its default search path. You must specify ``FFT_LIB``
with the appropriate FFT libraries to include in the link.
The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
distribution. It is portable across all platforms. Depending on the size
of the FFTs and the number of processors used, the other libraries listed
here can be faster.
The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
included in the LAMMPS distribution. It is portable across all
platforms. Depending on the size of the FFTs and the number of
processors used, the other libraries listed here can be faster.
However, note that long-range Coulombics are only a portion of the
per-timestep CPU cost, FFTs are only a portion of long-range
Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
communication can be costly). A breakdown of these timings is printed
to the screen at the end of a run when using the
:doc:`kspace_style pppm <kspace_style>` command. The
:doc:`Screen and logfile output <Run_output>`
page gives more details. A more detailed (and time consuming)
report of the FFT performance is generated with the
per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
and 1d FFTs are only a portion of the FFT cost (parallel communication
can be costly). A breakdown of these timings is printed to the screen
at the end of a run when using the :doc:`kspace_style pppm
<kspace_style>` command. The :doc:`Screen and logfile output
<Run_output>` page gives more details. A more detailed (and time
consuming) report of the FFT performance is generated with the
:doc:`kspace_modify fftbench yes <kspace_modify>` command.
FFTW is a fast, portable FFT library that should also work on any
platform and can be faster than the KISS FFT library. You can
download it from `www.fftw.org <http://www.fftw.org>`_. LAMMPS requires
version 3.X; the legacy version 2.1.X is no longer supported.
platform and can be faster than the KISS FFT library. You can download
it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
3.X; the legacy version 2.1.X is no longer supported.
Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges
@ -142,18 +141,18 @@ 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).
Performing 3d FFTs in parallel can be time consuming due to data
access and required communication. This cost can be reduced by
performing single-precision FFTs instead of double precision. Single
precision means the real and imaginary parts of a complex datum are
4-byte floats. Double precision means they are 8-byte doubles. Note
that Fourier transform and related PPPM operations are somewhat less
sensitive to floating point truncation errors and thus the resulting
error is less than the difference in precision. Using the ``-DFFT_SINGLE``
setting trades off a little accuracy for reduced memory use and
parallel communication costs for transposing 3d FFT data.
Performing 3d FFTs in parallel can be time-consuming due to data access
and required communication. This cost can be reduced by performing
single-precision FFTs instead of double precision. Single precision
means the real and imaginary parts of a complex datum are 4-byte floats.
Double precision means they are 8-byte doubles. Note that Fourier
transform and related PPPM operations are somewhat less sensitive to
floating point truncation errors, and thus the resulting error is
generally less than the difference in precision. Using the
``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
use and parallel communication costs for transposing 3d FFT data.
When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW
When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
library a second time with support for single-precision.
For FFTW3, do the following, which should produce the additional
@ -178,11 +177,11 @@ ARRAY mode.
Size of LAMMPS integer types and size limits
--------------------------------------------
LAMMPS has a few integer data types which can be defined as either
4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
This has an impact on the size of a system that can be simulated
or how large counters can become before "rolling over".
The default setting of "smallbig" is almost always adequate.
LAMMPS uses a few custom integer data types, which can be defined as
either 4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
This has an impact on the size of a system that can be simulated, or how
large counters can become before "rolling over". The default setting of
"smallbig" is almost always adequate.
.. tabs::
@ -255,7 +254,7 @@ topology information, though IDs are enabled by default. The
:doc:`atom_modify id no <atom_modify>` command will turn them off. Atom
IDs are required for molecular systems with bond topology (bonds,
angles, dihedrals, etc). Similarly, some force or compute or fix styles
require atom IDs. Thus if you model a molecular system or use one of
require atom IDs. Thus, if you model a molecular system or use one of
those styles with more than 2 billion atoms, you need the "bigbig"
setting.
@ -265,7 +264,7 @@ systems and 500 million for systems with bonds (the additional
restriction is due to using the 2 upper bits of the local atom index
in neighbor lists for storing special bonds info).
Image flags store 3 values per atom in a single integer which count the
Image flags store 3 values per atom in a single integer, which count the
number of times an atom has moved through the periodic box in each
dimension. See the :doc:`dump <dump>` manual page for a discussion. If
an atom moves through the periodic box more than this limit, the value
@ -286,7 +285,7 @@ Output of JPG, 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
PNG image files. Likewise, the :doc:`dump movie <dump_image>` command
outputs movie files in a variety of movie formats. Using these options
requires the following settings:
@ -355,7 +354,7 @@ 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>`. Currently supported compression tools are:
:doc:`dump <dump>`. Supported compression tools are currently
``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
.. tabs::
@ -395,7 +394,7 @@ Memory allocation alignment
---------------------------------------
This setting enables the use of the "posix_memalign()" call instead of
"malloc()" when LAMMPS allocates large chunks or memory. Vector
"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
@ -497,7 +496,7 @@ Trigger selected floating-point exceptions
------------------------------------------
Many kinds of CPUs have the capability to detect when a calculation
results in an invalid math operation like a division by zero or calling
results in an invalid math operation, like a division by zero or calling
the square root with a negative argument. The default behavior on
most operating systems is to continue and have values for ``NaN`` (= not
a number) or ``Inf`` (= infinity). This allows software to detect and

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

13
doc/src/Commands_all.rst
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@ -10,17 +10,21 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
General commands
================
An alphabetic list of general LAMMPS commands.
An alphabetic list of general LAMMPS commands. Note that style
commands with many variants, can be more easily accessed via the small
table above.
.. table_from_list::
:columns: 5
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
* :doc:`angle_write <angle_write>`
* :doc:`atom_modify <atom_modify>`
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
@ -28,7 +32,6 @@ An alphabetic list of general LAMMPS commands.
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change_box <change_box>`
* :doc:`clear <clear>`
* :doc:`comm_modify <comm_modify>`
@ -43,6 +46,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`dielectric <dielectric>`
* :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`dihedral_write <dihedral_write>`
* :doc:`dimension <dimension>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`
@ -60,6 +64,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
* :doc:`labelmap <labelmap>`
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
@ -86,8 +91,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset_atom_ids <reset_atom_ids>`
* :doc:`reset_mol_ids <reset_mol_ids>`
* :doc:`reset_atoms <reset_atoms>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`
@ -123,6 +127,7 @@ additional letter in parenthesis: k = KOKKOS.
* :doc:`group2ndx <group2ndx>`
* :doc:`hyper <hyper>`
* :doc:`kim <kim_commands>`
* :doc:`fitpod <fitpod_command>`
* :doc:`mdi <mdi>`
* :doc:`ndx2group <group2ndx>`
* :doc:`neb <neb>`

11
doc/src/Commands_bond.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:
@ -41,8 +42,11 @@ OPT.
* :doc:`gaussian <bond_gaussian>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/restrain <bond_harmonic_restrain>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>`
* :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
* :doc:`lepton (o) <bond_lepton>`
* :doc:`mesocnt <bond_mesocnt>`
* :doc:`mm3 <bond_mm3>`
* :doc:`morse (o) <bond_morse>`
* :doc:`nonlinear (o) <bond_nonlinear>`
@ -74,6 +78,7 @@ OPT.
*
*
*
* :doc:`amoeba <angle_amoeba>`
* :doc:`charmm (iko) <angle_charmm>`
* :doc:`class2 (ko) <angle_class2>`
* :doc:`class2/p6 <angle_class2>`
@ -90,9 +95,11 @@ OPT.
* :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`gaussian <angle_gaussian>`
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`lepton (o) <angle_lepton>`
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`spica (o) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
@ -123,6 +130,7 @@ OPT.
* :doc:`fourier (io) <dihedral_fourier>`
* :doc:`harmonic (iko) <dihedral_harmonic>`
* :doc:`helix (o) <dihedral_helix>`
* :doc:`lepton (o) <dihedral_lepton>`
* :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
* :doc:`nharmonic (o) <dihedral_nharmonic>`
* :doc:`opls (iko) <dihedral_opls>`
@ -152,6 +160,7 @@ OPT.
*
*
*
* :doc:`amoeba <improper_amoeba>`
* :doc:`class2 (ko) <improper_class2>`
* :doc:`cossq (o) <improper_cossq>`
* :doc:`cvff (io) <improper_cvff>`

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

10
doc/src/Commands_compute.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================
@ -45,21 +46,25 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`com/chunk <compute_com_chunk>`
* :doc:`contact/atom <compute_contact_atom>`
* :doc:`coord/atom (k) <compute_coord_atom>`
* :doc:`count/type <compute_count_type>`
* :doc:`damage/atom <compute_damage_atom>`
* :doc:`dihedral <compute_dihedral>`
* :doc:`dihedral/local <compute_dihedral_local>`
* :doc:`dilatation/atom <compute_dilatation_atom>`
* :doc:`dipole <compute_dipole>`
* :doc:`dipole/chunk <compute_dipole_chunk>`
* :doc:`dipole/tip4p <compute_dipole>`
* :doc:`dipole/tip4p/chunk <compute_dipole_chunk>`
* :doc:`displace/atom <compute_displace_atom>`
* :doc:`dpd <compute_dpd>`
* :doc:`dpd/atom <compute_dpd_atom>`
* :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
* :doc:`efield/atom <compute_efield_atom>`
* :doc:`efield/wolf/atom <compute_efield_wolf_atom>`
* :doc:`entropy/atom <compute_entropy_atom>`
* :doc:`erotate/asphere <compute_erotate_asphere>`
* :doc:`erotate/rigid <compute_erotate_rigid>`
* :doc:`erotate/sphere <compute_erotate_sphere>`
* :doc:`erotate/sphere (k) <compute_erotate_sphere>`
* :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
* :doc:`event/displace <compute_event_displace>`
* :doc:`fabric <compute_fabric>`
@ -86,7 +91,6 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
* :doc:`ke/eff <compute_ke_eff>`
* :doc:`ke/rigid <compute_ke_rigid>`
* :doc:`mesont <compute_mesont>`
* :doc:`mliap <compute_mliap>`
* :doc:`momentum <compute_momentum>`
* :doc:`msd <compute_msd>`
@ -103,9 +107,11 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`pe/tally <compute_tally>`
* :doc:`plasticity/atom <compute_plasticity_atom>`
* :doc:`pressure <compute_pressure>`
* :doc:`pressure/alchemy <compute_pressure_alchemy>`
* :doc:`pressure/uef <compute_pressure_uef>`
* :doc:`property/atom <compute_property_atom>`
* :doc:`property/chunk <compute_property_chunk>`
* :doc:`property/grid <compute_property_grid>`
* :doc:`property/local <compute_property_local>`
* :doc:`ptm/atom <compute_ptm_atom>`
* :doc:`rdf <compute_rdf>`

57
doc/src/Commands_dump.rst Normal file
View File

@ -0,0 +1,57 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Dump commands
=============
An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
.. table_from_list::
:columns: 5
* :doc:`atom <dump>`
* :doc:`atom/adios <dump_adios>`
* :doc:`atom/gz <dump>`
* :doc:`atom/mpiio <dump>`
* :doc:`atom/zstd <dump>`
* :doc:`cfg <dump>`
* :doc:`cfg/gz <dump>`
* :doc:`cfg/mpiio <dump>`
* :doc:`cfg/uef <dump_cfg_uef>`
* :doc:`cfg/zstd <dump>`
* :doc:`custom <dump>`
* :doc:`custom/adios <dump_adios>`
* :doc:`custom/gz <dump>`
* :doc:`custom/mpiio <dump>`
* :doc:`custom/zstd <dump>`
* :doc:`dcd <dump>`
* :doc:`grid <dump>`
* :doc:`grid/vtk <dump>`
* :doc:`h5md <dump_h5md>`
* :doc:`image <dump_image>`
* :doc:`local <dump>`
* :doc:`local/gz <dump>`
* :doc:`local/zstd <dump>`
* :doc:`molfile <dump_molfile>`
* :doc:`movie <dump_image>`
* :doc:`netcdf <dump_netcdf>`
* :doc:`netcdf/mpiio <dump>`
* :doc:`vtk <dump_vtk>`
* :doc:`xtc <dump>`
* :doc:`xyz <dump>`
* :doc:`xyz/gz <dump>`
* :doc:`xyz/mpiio <dump>`
* :doc:`xyz/zstd <dump>`
* :doc:`yaml <dump>`

35
doc/src/Commands_fix.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============
@ -28,6 +29,9 @@ OPT.
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`alchemy <fix_alchemy>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`append/atoms <fix_append_atoms>`
* :doc:`atc <fix_atc>`
* :doc:`atom/swap <fix_atom_swap>`
@ -35,14 +39,12 @@ OPT.
* :doc:`ave/chunk <fix_ave_chunk>`
* :doc:`ave/correlate <fix_ave_correlate>`
* :doc:`ave/correlate/long <fix_ave_correlate_long>`
* :doc:`ave/grid <fix_ave_grid>`
* :doc:`ave/histo <fix_ave_histo>`
* :doc:`ave/histo/weight <fix_ave_histo>`
* :doc:`ave/time <fix_ave_time>`
* :doc:`aveforce <fix_aveforce>`
* :doc:`balance <fix_balance>`
* :doc:`brownian <fix_brownian>`
* :doc:`brownian/asphere <fix_brownian>`
* :doc:`brownian/sphere <fix_brownian>`
* :doc:`bocs <fix_bocs>`
* :doc:`bond/break <fix_bond_break>`
* :doc:`bond/create <fix_bond_create>`
@ -50,6 +52,9 @@ OPT.
* :doc:`bond/react <fix_bond_react>`
* :doc:`bond/swap <fix_bond_swap>`
* :doc:`box/relax <fix_box_relax>`
* :doc:`brownian <fix_brownian>`
* :doc:`brownian/asphere <fix_brownian>`
* :doc:`brownian/sphere <fix_brownian>`
* :doc:`charge/regulation <fix_charge_regulation>`
* :doc:`cmap <fix_cmap>`
* :doc:`colvars <fix_colvars>`
@ -62,13 +67,14 @@ OPT.
* :doc:`drude <fix_drude>`
* :doc:`drude/transform/direct <fix_drude_transform>`
* :doc:`drude/transform/inverse <fix_drude_transform>`
* :doc:`dt/reset <fix_dt_reset>`
* :doc:`dt/reset (k) <fix_dt_reset>`
* :doc:`edpd/source <fix_dpd_source>`
* :doc:`efield <fix_efield>`
* :doc:`efield/tip4p <fix_efield>`
* :doc:`ehex <fix_ehex>`
* :doc:`electrode/conp (i) <fix_electrode_conp>`
* :doc:`electrode/conq (i) <fix_electrode_conp>`
* :doc:`electrode/thermo (i) <fix_electrode_conp>`
* :doc:`electrode/conp (i) <fix_electrode>`
* :doc:`electrode/conq (i) <fix_electrode>`
* :doc:`electrode/thermo (i) <fix_electrode>`
* :doc:`electron/stopping <fix_electron_stopping>`
* :doc:`electron/stopping/fit <fix_electron_stopping>`
* :doc:`enforce2d (k) <fix_enforce2d>`
@ -88,6 +94,7 @@ OPT.
* :doc:`grem <fix_grem>`
* :doc:`halt <fix_halt>`
* :doc:`heat <fix_heat>`
* :doc:`heat/flow <fix_heat_flow>`
* :doc:`hyper/global <fix_hyper_global>`
* :doc:`hyper/local <fix_hyper_local>`
* :doc:`imd <fix_imd>`
@ -97,13 +104,13 @@ OPT.
* :doc:`langevin/drude <fix_langevin_drude>`
* :doc:`langevin/eff <fix_langevin_eff>`
* :doc:`langevin/spin <fix_langevin_spin>`
* :doc:`latte <fix_latte>`
* :doc:`lb/fluid <fix_lb_fluid>`
* :doc:`lb/momentum <fix_lb_momentum>`
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`
* :doc:`mdi/aimd <fix_mdi_aimd>`
* :doc:`mdi/qm <fix_mdi_qm>`
* :doc:`mdi/qmmm <fix_mdi_qmmm>`
* :doc:`meso/move <fix_meso_move>`
* :doc:`mol/swap <fix_mol_swap>`
* :doc:`momentum (k) <fix_momentum>`
@ -162,8 +169,9 @@ OPT.
* :doc:`orient/fcc <fix_orient>`
* :doc:`orient/eco <fix_orient_eco>`
* :doc:`pafi <fix_pafi>`
* :doc:`pair <fix_pair>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd <fix_pimd>`
* :doc:`pimd/nvt <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
* :doc:`plumed <fix_plumed>`
* :doc:`poems <fix_poems>`
@ -209,6 +217,7 @@ OPT.
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`sgcmc <fix_sgcmc>`
* :doc:`shake (k) <fix_shake>`
* :doc:`shardlow (k) <fix_shardlow>`
* :doc:`smd <fix_smd>`
@ -245,18 +254,19 @@ OPT.
* :doc:`tune/kspace <fix_tune_kspace>`
* :doc:`vector <fix_vector>`
* :doc:`viscosity <fix_viscosity>`
* :doc:`viscous <fix_viscous>`
* :doc:`viscous (k) <fix_viscous>`
* :doc:`viscous/sphere <fix_viscous_sphere>`
* :doc:`wall/body/polygon <fix_wall_body_polygon>`
* :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
* :doc:`wall/colloid <fix_wall>`
* :doc:`wall/ees <fix_wall_ees>`
* :doc:`wall/gran <fix_wall_gran>`
* :doc:`wall/gran (k) <fix_wall_gran>`
* :doc:`wall/gran/region <fix_wall_gran_region>`
* :doc:`wall/harmonic <fix_wall>`
* :doc:`wall/lj1043 <fix_wall>`
* :doc:`wall/lj126 <fix_wall>`
* :doc:`wall/lj93 (k) <fix_wall>`
* :doc:`wall/lepton <fix_wall>`
* :doc:`wall/morse <fix_wall>`
* :doc:`wall/piston <fix_wall_piston>`
* :doc:`wall/reflect (k) <fix_wall_reflect>`
@ -264,4 +274,5 @@ OPT.
* :doc:`wall/region <fix_wall_region>`
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
* :doc:`wall/table <fix_wall>`
* :doc:`widom <fix_widom>`

1
doc/src/Commands_kspace.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
KSpace solvers
==============

34
doc/src/Commands_pair.rst
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@ -10,6 +10,7 @@
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
@ -38,6 +39,7 @@ OPT.
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`amoeba (g) <pair_amoeba>`
* :doc:`atm <pair_atm>`
* :doc:`awpmd/cut <pair_awpmd>`
* :doc:`beck (go) <pair_beck>`
@ -53,6 +55,7 @@ OPT.
* :doc:`born/coul/msm (o) <pair_born>`
* :doc:`born/coul/wolf (go) <pair_born>`
* :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/poly (o) <pair_brownian>`
@ -91,8 +94,8 @@ OPT.
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/ext (k) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (k) <pair_dpd_ext>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (gko) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -124,6 +127,7 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`hippo (g) <pair_amoeba>`
* :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
* :doc:`ilp/tmd (t) <pair_ilp_tmd>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@ -131,6 +135,9 @@ OPT.
* :doc:`lcbop <pair_lcbop>`
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`lepton (o) <pair_lepton>`
* :doc:`lepton/coul (o) <pair_lepton>`
* :doc:`lepton/sphere (o) <pair_lepton>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
@ -161,16 +168,18 @@ OPT.
* :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
* :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
* :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
* :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
* :doc:`lj/cut/dipole/cut (gko) <pair_dipole>`
* :doc:`lj/cut/dipole/long (g) <pair_dipole>`
* :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
* :doc:`lj/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/sphere (o) <pair_lj_cut_sphere>`
* :doc:`lj/cut/thole/long (o) <pair_thole>`
* :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`
* :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
* :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`lj/expand (gko) <pair_lj_expand>`
* :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
* :doc:`lj/expand/coul/long (gk) <pair_lj_expand>`
* :doc:`lj/expand/sphere (o) <pair_lj_expand_sphere>`
* :doc:`lj/gromacs (gko) <pair_gromacs>`
* :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
* :doc:`lj/long/coul/long (iot) <pair_lj_long>`
@ -179,9 +188,9 @@ OPT.
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@ -194,14 +203,15 @@ OPT.
* :doc:`lubricateU/poly <pair_lubricateU>`
* :doc:`mdpd <pair_mesodpd>`
* :doc:`mdpd/rhosum <pair_mesodpd>`
* :doc:`meam <pair_meam>`
* :doc:`meam (k) <pair_meam>`
* :doc:`meam/ms (k) <pair_meam>`
* :doc:`meam/spline (o) <pair_meam_spline>`
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mesocnt <pair_mesocnt>`
* :doc:`mesont/tpm <pair_mesont_tpm>`
* :doc:`mesocnt/viscous <pair_mesocnt>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mliap <pair_mliap>`
* :doc:`mliap (k) <pair_mliap>`
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
@ -232,6 +242,8 @@ OPT.
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pod <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
@ -268,6 +280,7 @@ OPT.
* :doc:`spin/magelec <pair_spin_magelec>`
* :doc:`spin/neel <pair_spin_neel>`
* :doc:`srp <pair_srp>`
* :doc:`srp/react <pair_srp>`
* :doc:`sw (giko) <pair_sw>`
* :doc:`sw/angle/table <pair_sw_angle_table>`
* :doc:`sw/mod (o) <pair_sw>`
@ -289,6 +302,7 @@ OPT.
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`
* :doc:`ylz <pair_ylz>`
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`

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

87
doc/src/Commands_removed.rst
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@ -2,14 +2,17 @@ Removed commands and packages
=============================
This page lists LAMMPS commands and packages that have been removed from
the distribution and provides suggestions for alternatives or replacements.
LAMMPS has special dummy styles implemented, that will stop LAMMPS and
print a suitable error message in most cases, when a style/command is used
that has been removed.
the distribution and provides suggestions for alternatives or
replacements. LAMMPS has special dummy styles implemented, that will
stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
.. deprecated:: 11Dec2015
The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
since they were superseded by the more general and extensible "chunk
infrastructure". Here the system is partitioned in one of many possible
@ -17,10 +20,37 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
Reset_ids command
-----------------
Box command
-----------
The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
.. deprecated:: 22Dec2022
The *box* command has been removed and the LAMMPS code changed so it won't
be needed. If present, LAMMPS will ignore the command and print a warning.
Reset_ids, reset_atom_ids, reset_mol_ids commands
-------------------------------------------------
.. deprecated:: 22Dec2022
The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
been folded into the :doc:`reset_atoms <reset_atoms>` command. If
present, LAMMPS will replace the commands accordingly and print a
warning.
LATTE package
-------------
.. deprecated:: TBD
The LATTE package with the fix latte command was removed from LAMMPS.
This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package
<PKG-MDI>`. These fixes are compatible with several quantum software
packages, including LATTE. See the ``examples/QUANTUM`` dir and the
:doc:`MDI coupling HOWTO <Howto_mdi>` page. MDI supports running LAMMPS
with LATTE as a plugin library (similar to the way fix latte worked), as
well as on a different set of MPI processors.
MEAM package
------------
@ -30,18 +60,42 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
Fortran code of MEAM into C++, which removes several restrictions
(e.g. there can be multiple instances in hybrid pair styles) and allows
for some optimizations leading to better performance. The pair style
:doc:`meam <pair_meam>` has the exact same syntax.
:doc:`meam <pair_meam>` has the exact same syntax. For a transition
period the C++ version of MEAM was called USER-MEAMC so it could
coexist with the Fortran version.
Minimize style fire/old
-----------------------
.. deprecated:: 8Feb2023
Minimize style *fire/old* has been removed. Its functionality can be
reproduced with *fire* with specific options. Please see the
:doc:`min_modify command <min_modify>` documentation for details.
Pair style mesont/tpm, compute style mesont, atom style mesont
--------------------------------------------------------------
.. deprecated:: 8Feb2023
Pair style *mesont/tpm*, compute style *mesont*, and atom style
*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
The same functionality is available through
:doc:`pair style mesocnt <pair_mesocnt>`,
:doc:`bond style mesocnt <bond_mesocnt>` and
:doc:`angle style mesocnt <angle_mesocnt>`.
REAX package
------------
The REAX package has been removed since it was superseded by the
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF
package has been tested to yield equivalent results to the REAX package,
offers better performance, supports OpenMP multi-threading via OPENMP,
and GPU and threading parallelization through KOKKOS. The new pair styles
are not syntax compatible with the removed reax pair style, so input
files will have to be adapted.
:ref:`REAXFF package <PKG-REAXFF>`. The REAXFF package has been tested
to yield equivalent results to the REAX package, offers better
performance, supports OpenMP multi-threading via OPENMP, and GPU and
threading parallelization through KOKKOS. The new pair styles are not
syntax compatible with the removed reax pair style, so input files will
have to be adapted. The REAXFF package was originally called
USER-REAXC.
USER-CUDA package
-----------------
@ -60,5 +114,6 @@ restart2data tool
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For added
convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`

3
doc/src/Developer.rst
View File

@ -13,12 +13,15 @@ of time and requests from the LAMMPS user community.
Developer_org
Developer_code_design
Developer_parallel
Developer_atom
Developer_comm_ops
Developer_flow
Developer_write
Developer_notes
Developer_updating
Developer_plugins
Developer_unittest
Classes
Developer_platform
Developer_utils
Developer_grid

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