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Merge branch 'lammps:develop' into develop

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This commit is contained in:
Gabriel Alkuino
2024-09-17 13:47:55 -04:00
committed by GitHub
parent ae80dba958 805c2ae131
commit 3effab8024
972 changed files with 128340 additions and 24979 deletions
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19
.github/CODEOWNERS vendored
View File

@ -50,6 +50,7 @@ src/PTM/* @pmla
src/QMMM/* @akohlmey
src/REACTION/* @jrgissing
src/REAXFF/* @hasanmetin @stanmoore1
src/RHEO/* @jtclemm
src/SCAFACOS/* @rhalver
src/SNAP/* @athomps
src/SPIN/* @julient31
@ -65,6 +66,9 @@ src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMMAND/geturl.* @akohlmey
src/EXTRA-COMMAND/group_ndx.* @akohlmey
src/EXTRA-COMMAND/ndx_group.* @akohlmey
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
@ -95,9 +99,10 @@ src/fix.* @sjplimp
src/force.* @sjplimp
src/group.* @sjplimp
src/improper.* @sjplimp
src/info.* @akohlmey
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/library.* @sjplimp
src/library.* @sjplimp @akohlmey
src/main.cpp @sjplimp
src/min_*.* @sjplimp
src/memory.* @sjplimp
@ -105,12 +110,12 @@ src/modify.* @sjplimp @stanmoore1
src/molecule.* @sjplimp
src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp
src/npair*.* @sjplimp
src/ntopo*.* @sjplimp
src/nstencil*.* @sjplimp
src/neighbor.* @sjplimp
src/nbin*.* @sjplimp
src/neigh_*.* @sjplimp
src/npair*.* @sjplimp @jtclemm
src/ntopo*.* @sjplimp @jtclemm
src/nstencil*.* @sjplimp @jtclemm
src/neighbor.* @sjplimp @jtclemm
src/nbin*.* @sjplimp @jtclemm
src/neigh_*.* @sjplimp @jtclemm
src/output.* @sjplimp
src/pair.* @sjplimp
src/rcb.* @sjplimp

89
.github/workflows/check-vla.yml vendored Normal file
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@ -0,0 +1,89 @@
# GitHub action to build LAMMPS on Linux with gcc and -Werror=vla
name: "Check for Variable Length Arrays"
on:
push:
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build with -Werror=vla
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
- name: Install extra packages
run: |
sudo apt-get install -y ccache \
libeigen3-dev \
libgsl-dev \
libcurl4-openssl-dev \
mold \
mpi-default-bin \
mpi-default-dev \
ninja-build \
python3-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-vla-ccache-${{ github.sha }}
restore-keys: linux-vla-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -S cmake -B build \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER=g++ \
-D CMAKE_C_COMPILER=gcc \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D CMAKE_BUILD_TYPE=Debug \
-D CMAKE_CXX_FLAGS_DEBUG="-Og -g -Werror=vla" \
-D DOWNLOAD_POTENTIALS=off \
-D BUILD_MPI=on \
-D BUILD_SHARED_LIBS=off \
-D BUILD_TOOLS=off \
-D ENABLE_TESTING=off \
-D MLIAP_ENABLE_ACE=on \
-D MLIAP_ENABLE_PYTHON=off \
-D PKG_AWPMD=on \
-D PKG_GPU=on \
-D GPU_API=opencl \
-D PKG_LATBOLTZ=on \
-D PKG_MDI=on \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=off \
-D PKG_MOLFILE=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s

51
.github/workflows/compile-msvc.yml vendored
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@ -1,5 +1,5 @@
# GitHub action to build LAMMPS on Windows with Visual C++
name: "Native Windows Compilation and Unit Tests"
# GitHub action to test LAMMPS on Windows with Visual C++
name: "Windows Unit Tests"
on:
push:
@ -11,11 +11,17 @@ on:
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Windows Compilation Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: windows-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
@ -23,36 +29,41 @@ jobs:
with:
fetch-depth: 2
- name: Enable MSVC++
uses: lammps/setup-msvc-dev@v3
with:
arch: x64
- name: Install Ccache
run: |
choco install ccache ninja -y
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: win-unit-ccache-${{ github.sha }}
restore-keys: win-unit-ccache-
- name: Select Python version
uses: actions/setup-python@v5
with:
python-version: '3.11'
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m pip install numpy
python3 -m pip install pyyaml
nuget install MSMPIsdk
nuget install MSMPIDIST
cmake -C cmake/presets/windows.cmake \
-D DOWNLOAD_POTENTIALS=off \
-D PKG_PYTHON=on \
-D WITH_PNG=off \
-D WITH_JPEG=off \
-S cmake -B build \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on \
-D ENABLE_TESTING=on
cmake --build build --config Release --parallel 2
cmake -C cmake\presets\windows.cmake -D CMAKE_CXX_COMPILER=cl -D CMAKE_CXX_COMPILER_LAUNCHER=ccache -D CMAKE_C_COMPILER=cl -D CMAKE_C_COMPILER_LAUNCHER=ccache -D CMAKE_Fortran_COMPILER="" -D DOWNLOAD_POTENTIALS=off -D PKG_PYTHON=on -D WITH_PNG=off -D WITH_JPEG=off -S cmake -B build -D BUILD_SHARED_LIBS=on -D ENABLE_TESTING=on -D CMAKE_BUILD_TYPE=Release -G Ninja
cmake --build build
ccache -s
- name: Run LAMMPS executable
shell: bash
run: |
./build/Release/lmp.exe -h
./build/Release/lmp.exe -in bench/in.lj
build\lmp.exe -h
build\lmp.exe -in bench\in.lj
- name: Run Unit Tests
working-directory: build
shell: bash
run: ctest -V -C Release -E FixTimestep:python_move_nve
run: ctest -V -E FixTimestep:python_move_nve

108
.github/workflows/full-regression.yml vendored Normal file
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@ -0,0 +1,108 @@
# GitHub action to build LAMMPS on Linux and run regression tests
name: "Full Regression Test"
on:
push:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build LAMMPS
# restrict to official LAMMPS repository
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 8
matrix:
idx: [ 0, 1, 2, 3, 4, 5, 6, 7 ]
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
show-progress: false
- name: Install extra packages
run: |
sudo apt-get install -y ccache ninja-build libeigen3-dev \
libgsl-dev libcurl4-openssl-dev python3-dev \
mpi-default-bin mpi-default-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-full-ccache-${{ github.sha }}
restore-keys: linux-full-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install numpy pyyaml junit_xml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=off \
-D DOWNLOAD_POTENTIALS=off \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Full Regression Tests
shell: bash
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_serial.yaml \
--examples-top-level=examples --analyze --num-workers=8
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_serial.yaml \
--list-input=input-list-${{ matrix.idx }}.txt \
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log
tar -cvf full-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
- name: Upload artifacts
uses: actions/upload-artifact@v4
with:
name: full-regression-test-artifact-${{ matrix.idx }}
path: full-regression-test-${{ matrix.idx }}.tar
merge:
runs-on: ubuntu-latest
needs: build
steps:
- name: Merge Artifacts
uses: actions/upload-artifact/merge@v4
with:
name: merged-full-regresssion-artifact
pattern: full-regression-test-artifact-*

117
.github/workflows/quick-regression.yml vendored Normal file
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@ -0,0 +1,117 @@
# GitHub action to build LAMMPS on Linux and run selected regression tests
name: "Quick Regression Test"
on:
pull_request:
branches:
- develop
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Build LAMMPS
# restrict to official LAMMPS repository
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 4
matrix:
idx: [ 0, 1, 2, 3 ]
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 0
show-progress: false
- name: Install extra packages
run: |
sudo apt-get install -y ccache ninja-build libeigen3-dev \
libgsl-dev libcurl4-openssl-dev python3-dev \
mpi-default-bin mpi-default-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-quick-ccache-${{ github.sha }}
restore-keys: linux-quick-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install numpy pyyaml junit_xml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=off \
-D DOWNLOAD_POTENTIALS=off \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Regression Tests for Modified Styles
shell: bash
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_quick.yaml \
--examples-top-level=examples \
--quick-reference=tools/regression-tests/reference.yaml \
--quick --quick-branch=origin/develop --quick-max=100 --num-workers=4
if [ -f input-list-${{ matrix.idx }}.txt ]
then \
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_quick.yaml \
--list-input=input-list-${{ matrix.idx }}.txt \
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log
fi
tar -cvf quick-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
- name: Upload artifacts
uses: actions/upload-artifact@v4
with:
name: quick-regression-test-artifact-${{ matrix.idx }}
path: quick-regression-test-${{ matrix.idx }}.tar
merge:
runs-on: ubuntu-latest
needs: build
steps:
- name: Merge Artifacts
uses: actions/upload-artifact/merge@v4
with:
name: merged-quick-regresssion-artifact
pattern: quick-regression-test-artifact-*

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

86
.github/workflows/unittest-linux.yml vendored Normal file
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@ -0,0 +1,86 @@
# GitHub action to build LAMMPS on Linux and run standard unit tests
name: "Unittest for Linux /w LAMMPS_BIGBIG"
on:
push:
branches:
- develop
pull_request:
branches:
- develop
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Linux Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
- name: Install extra packages
run: |
sudo apt-get install -y ccache \
libeigen3-dev \
libgsl-dev \
libcurl4-openssl-dev \
mold \
ninja-build \
python3-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-unit-ccache-${{ github.sha }}
restore-keys: linux-unit-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_SIZES=bigbig \
-D DOWNLOAD_POTENTIALS=off \
-D ENABLE_TESTING=on \
-D MLIAP_ENABLE_ACE=on \
-D MLIAP_ENABLE_PYTHON=off \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Tests
working-directory: build
shell: bash
run: ctest -V

4
.github/workflows/unittest-macos.yml vendored
View File

@ -11,6 +11,10 @@ on:
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: MacOS Unit Test

23
cmake/CMakeLists.txt
View File

@ -12,6 +12,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about requiring execute permission for find_program
# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
@ -469,13 +474,13 @@ if(BUILD_OMP)
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
endif()
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
endif()
endif()
endif()
@ -567,7 +572,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO EXTRA-COMMAND)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -887,7 +892,7 @@ endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)
find_package(ClangFormat 8.0)
find_package(ClangFormat 11.0)
if(ClangFormat_FOUND)
add_custom_target(format-src
@ -960,6 +965,9 @@ message(STATUS "<<< Compilers and Flags: >>>
C++ Standard: ${CMAKE_CXX_STANDARD}
C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines: ${DEFINES}")
if(CMAKE_CXX_COMPILER_LAUNCHER)
message(STATUS " Launcher: ${CMAKE_CXX_COMPILER_LAUNCHER}")
endif()
get_target_property(OPTIONS lammps COMPILE_OPTIONS)
if(OPTIONS)
message(" Options: ${OPTIONS}")
@ -978,6 +986,9 @@ if(_index GREATER -1)
Type: ${CMAKE_C_COMPILER_ID}
Version: ${CMAKE_C_COMPILER_VERSION}
C Flags: ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
if(CMAKE_C_COMPILER_LAUNCHER)
message(STATUS " Launcher: ${CMAKE_C_COMPILER_LAUNCHER}")
endif()
endif()
message(STATUS "<<< Linker flags: >>>")
message(STATUS "Executable name: ${LAMMPS_BINARY}")

48
cmake/Modules/Documentation.cmake
View File

@ -4,6 +4,8 @@
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
option(BUILD_DOC_VENV "Build LAMMPS documentation virtual environment" ON)
mark_as_advanced(BUILD_DOC_VENV)
# Current Sphinx versions require at least Python 3.8
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
@ -18,14 +20,6 @@ if(BUILD_DOC)
find_package(Doxygen 1.8.10 REQUIRED)
file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
add_custom_command(
OUTPUT docenv
COMMAND ${VIRTUALENV} docenv
)
set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
set(SPHINX_STATIC_DIR ${SPHINX_CONFIG_DIR}/_static)
@ -44,14 +38,32 @@ if(BUILD_DOC)
# configure paths in conf.py, since relative paths change when file is copied
configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
add_custom_command(
OUTPUT ${DOC_BUILD_DIR}/requirements.txt
DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
)
if(BUILD_DOC_VENV)
add_custom_command(
OUTPUT docenv
COMMAND ${VIRTUALENV} docenv
)
set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
add_custom_command(
OUTPUT ${DOC_BUILD_DIR}/requirements.txt
DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
)
set(DOCENV_DEPS docenv ${DOC_BUILD_DIR}/requirements.txt)
if(NOT TARGET Sphinx::sphinx-build)
add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${DOCENV_BINARY_DIR}/sphinx-build")
endif()
else()
find_package(Sphinx)
endif()
set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
@ -97,8 +109,8 @@ if(BUILD_DOC)
endif()
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
DEPENDS ${DOC_SOURCES} ${DOCENV_DEPS} ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
COMMAND Sphinx::sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF
COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp

3
cmake/Modules/FindClangFormat.cmake
View File

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

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

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

8
cmake/Modules/LAMMPSUtils.cmake
View File

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

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

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

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

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

17
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -127,7 +127,7 @@ if(PKG_KSPACE)
${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT)
set(FFT_KOKKOS_VALUES KISS FFTW3 MKL NVPL HIPFFT CUFFT MKL_GPU)
set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
@ -137,10 +137,8 @@ if(PKG_KSPACE)
message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
elseif(FFT_KOKKOS STREQUAL "KISS")
message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "CUFFT")
find_package(CUDAToolkit REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
target_link_libraries(lammps PRIVATE CUDA::cufft)
endif()
elseif(Kokkos_ENABLE_HIP)
@ -152,10 +150,21 @@ if(PKG_KSPACE)
elseif(FFT_KOKKOS STREQUAL "HIPFFT")
include(DetectHIPInstallation)
find_package(hipfft REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
target_link_libraries(lammps PRIVATE hip::hipfft)
endif()
elseif(FFT_KOKKOS STREQUAL "MKL_GPU")
if(NOT Kokkos_ENABLE_SYCL)
message(FATAL_ERROR "Using MKL_GPU FFT currently requires the SYCL backend of Kokkos.")
endif()
find_package(MKL REQUIRED)
target_link_libraries(lammps PRIVATE mkl_sycl_dft mkl_intel_ilp64 mkl_tbb_thread mkl_core tbb)
elseif(FFT_KOKKOS STREQUAL "MKL")
find_package(MKL REQUIRED)
elseif(FFT_KOKKOS STREQUAL "NVPL")
find_package(nvpl_fft REQUIRED)
target_link_libraries(lammps PRIVATE nvpl::fftw)
endif()
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_${FFT_KOKKOS})
endif()
if(PKG_ML-IAP)

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

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

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

@ -1,5 +1,11 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
# PACE library support for ML-PACE package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)

19
cmake/Modules/Packages/PLUMED.cmake
View File

@ -1,5 +1,10 @@
# Plumed2 support for PLUMED package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
@ -27,9 +32,9 @@ endif()
# Note: must also adjust check for supported API versions in
# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-src-2.9.2.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
@ -81,6 +86,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
DEPENDS plumed_build
COMMENT "Copying Plumed files"
)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
endif()
else()
@ -155,6 +163,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
@ -169,7 +180,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
endif()
endif()
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

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

@ -1,2 +1,2 @@
find_package(GSL 2.7 REQUIRED)
find_package(GSL 2.6 REQUIRED)
target_link_libraries(lammps PRIVATE GSL::gsl)

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

Binary file not shown.

5
cmake/packaging/build_linux_tgz.sh
View File

@ -2,9 +2,10 @@
APP_NAME=lammps-gui
DESTDIR=${PWD}/../LAMMPS_GUI
VERSION="$1"
echo "Delete old files, if they exist"
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz
rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
@ -71,7 +72,7 @@ do \
done
pushd ..
tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI
tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
popd
echo "Cleanup dir"

9
cmake/packaging/build_macos_dmg.sh
View File

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

5
cmake/packaging/build_windows_cross_zip.sh
View File

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

4
cmake/presets/clang.cmake
View File

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

18
cmake/presets/kokkos-sycl-intel.cmake Normal file
View File

@ -0,0 +1,18 @@
# preset that enables KOKKOS and selects SYCL compilation with OpenMP
# enabled as well. Also sets some performance related compiler flags.
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SYCL ON CACHE BOOL "" FORCE)
# hide deprecation warnings temporarily for stable release
set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
set(CMAKE_CXX_COMPILER icpx CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
# Silence everything
set(CMAKE_CXX_FLAGS "-w" CACHE STRING "" FORCE)
set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-max-parallel-link-jobs=32 -fsycl-targets=spir64_gen -Xsycl-target-backend \"-device 12.60.7\" " CACHE STRING "" FORCE)
set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)

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

18
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "27 June 2024" "2024-06-27"
.TH LAMMPS "1" "29 August 2024" "2024-08-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 27 June 2024
\- Molecular Dynamics Simulator. Version 29 August 2024
.SH SYNOPSIS
.B lmp
@ -226,6 +226,20 @@ arguments of the "dump" command. See the
.B LAMMPS
manual for details on either of the two commands.
.TP
\fB\-r2info <restart file> <keyword> ...\fR or
\fB\-restart2info <restart file> <keyword> ...\fR
Write information about the <restart file> previously written by
.B LAMMPS
to the screen and immediately exit. Following <restart file>
argument, additional keywords for the
.B LAMMPS
"info" command may be added to increase the amount of information
written. By default "system" "group" "fix" "compute" are already
set. See the
.B LAMMPS
manual for details on the "info" command.
.TP
.TP
\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
Specify a file for
.B LAMMPS

4
doc/msi2lmp.1
View File

@ -1,4 +1,4 @@
.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
.TH MSI2LMP "1" "v3.9.11" "2024-09-06"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS
@ -101,7 +101,7 @@ msi2lmp decane -c 0 -f oplsaa
.SH COPYRIGHT
© 2003--2022 Sandia Corporation
© 2003--2024 Sandia Corporation
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as

458
doc/src/Bibliography.rst
View File

@ -1,6 +1,12 @@
Bibliography
************
**(Abascal1)**
Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
**(Abascal2)**
Abascal, J Chem Phys, 123, 234505 (2005)
**(Ackland)**
Ackland, Jones, Phys Rev B, 73, 054104 (2006).
@ -22,21 +28,24 @@ Bibliography
**(Agnolin and Roux 2007)**
Agnolin, I. & Roux, J-N. (2007). Internal states of model isotropic granular packings. I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
**(Ahrens-Iwers2022)**
Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).
**(Ahrens-Iwers)**
Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
**(Aktulga)**
Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).
**(Albe)**
J.\ Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
**(Albe)**
**(Albe1)**
K.\ Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
**(Allen)**
Allen and Germano, Mol Phys 104, 3225-3235 (2006).
**(Allen)**
Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
**(AllenTildesley)**
Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987)
@ -49,6 +58,9 @@ Bibliography
**(Anderson)**
Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006).
**(Appshaw)**
Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
**(Avendano)**
C.\ Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
@ -58,7 +70,7 @@ Bibliography
**(Babadi)**
Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
**(Babadi)**
**(Babadi2)**
Babadi and Ejtehadi, EPL, 77 (2007) 23002.
**(Baczewski)**
@ -73,23 +85,23 @@ Bibliography
**(Ballenegger)**
Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009).
**(Banna)**
Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).
**(Barrat)**
Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
**(Barrett)**
Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
**(Barros)**
Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014)
**(Bartok)**
Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
**(Bartok2010)**
Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
**(Bartok_2010)**
AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010).
**(Bartok2013)**
Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013).
**(Bartok_PhD)**
A Bartok-Partay, PhD Thesis, University of Cambridge, (2010).
@ -97,36 +109,51 @@ Bibliography
**(Baskes)**
Baskes, Phys Rev B, 46, 2727-2742 (1992).
**(Baskes2)**
Baskes, Phys Rev B, 75, 094113 (2007).
**(Beck)**
Beck, Molecular Physics, 14, 311 (1968).
**(Becton)**
Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).
**(Behler and Parrinello 2007)**
Behler, J.; Parrinello, M. Phys. Rev. Lett. 2007, 98 (14), 146401.
**(Bennet)**
Bennet, J Comput Phys, 22, 245 (1976)
**(Berardi)**
Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
**(Berendsen)**
Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
**(Berendsen)**
Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
**(Berendsen2)**
Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
**(Bessarab)**
Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015).
**(Beutler)**
Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994).
**(Bialke)**
J.\ Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
**(Bird)**
G.\ A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994).
**(Bitzek)**
Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006).
**(Bolintineanu1)**
Bolintineanu, Lechman, Plimpton, Grest, Phys Rev E, 86, 066703 (2012).
**(Bolintineanu2)**
Bolintineanu, Grest, Lechman, Pierce, Plimpton, Schunk, Comp Particle Mechanics, 1, 321-356 (2014).
**(Bomont)**
Bomont, Bretonnet, J. Chem. Phys. 124, 054504 (2006).
**(Bond)**
Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
@ -134,7 +161,7 @@ Bibliography
Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
**(BoreschKarplus)**
Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
Boresch and Karplus, J Phys Chem A, 103, 103 (1999).
**(Botu1)**
V.\ Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
@ -169,8 +196,11 @@ Bibliography
**(Buck)**
Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006).
**(Bulacu)**
Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
**(Bussi)**
G.\ Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
**(Bussi1)**
Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
@ -178,20 +208,20 @@ Bibliography
**(Bussi2)**
Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
**(COMB)**
**(COMB_1)**
J.\ Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
**(COMB_2)**
T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
**(COMB3)**
T.\ Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013).
**(COMB_1)**
J.\ Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
**(Calhoun)**
A.\ Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
**(Campana)**
C.\ Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
C.\ Campana and M. H. Muser, Phys. Rev. B [74], 075420 (2006).
**(Cao1)**
J.\ Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@ -215,6 +245,9 @@ Bibliography
Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
**(Ceriotti)**
M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
**(Ceriotti1)**
Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, 1170-80 (2010)
**(Ceriotti2)**
@ -232,6 +265,18 @@ Bibliography
**(Clarke)**
Clarke and Smith, J Chem Phys, 84, 2290 (1986).
**(Clavier)**
G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
**(Clemmer)**
Clemmer and Robbins, Phys. Rev. Lett. (2022).
**(Clemmer1)**
Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).
**(Clemmer2)**
Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
**(Coleman)**
Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).
@ -244,8 +289,17 @@ Bibliography
**(Cornell)**
Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
**(Cundall, 1987)**
Cundall, P. A. Distinct Element Models of Rock and Soil
**(Curk1)**
T. Curk, J. Yuan, and E. Luijten, JCP 156 (2022).
**(Curk2)**
T. Curk and E. Luijten, PRL 126 (2021)
**(Cusentino)**
Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
**(Daivis and Todd)**
Daivis and Todd, J Chem Phys, 124, 194103 (2006).
@ -268,6 +322,15 @@ Bibliography
**(Daw2)**
M.\ S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
**(de Buyl)**
de Buyl, Colberg and Hofling, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
**(Deissenbeck)**
Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
**(de Koning)**
de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
**(DeVane)**
Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
@ -277,12 +340,24 @@ Bibliography
**(Destree)**
M.\ Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, J Chem Phys, 112, 9632 (2000).
**(Dickel)**
Dickel, Francis, and Barrett, Computational Materials Science 171 (2020): 109157.
**(Dietz)**
Dietz and Hoy, J. Chem Phys, 156, 014103 (2022).
**(Dobson)**
Dobson, J Chem Phys, 141, 184103 (2014).
**(Drautz)**
Drautz, Phys Rev B, 99, 014104 (2019).
**(Duffy)**
D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007).
**(Dufils)**
Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
**(Dullweber)**
Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997).
@ -295,6 +370,9 @@ Bibliography
**(Dunweg)**
Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
**(EcheverriRestrepo)**
Echeverri Restrepo, Andric, Comput Mater Sci, 218, 111978 (2023).
**(EDIP)**
J F Justo et al, Phys Rev B 58, 2539 (1998).
@ -304,12 +382,21 @@ Bibliography
**(Elliott)**
Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
**(Ellis)**
Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)
**(Emmrich)**
Emmrich, Weckner, Commun. Math. Sci., 5, 851-864 (2007),
**(Elstner)**
M.\ Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).
**(Erdmann)**
U.\ Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000.
**(Eshelby)**
J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
**(Espanol and Revenga)**
Espanol, Revenga, Physical Review E, 67, 026705 (2003).
@ -328,9 +415,18 @@ Bibliography
**(Faken)**
Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
**(Falk)**
Falk and Langer PRE, 57, 7192 (1998).
**(Fath)**
Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
**(Feng1)**
Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C. 127(18), 8704-8713 (2023).
**(Feng2)**
Z. Feng, ..., and W. Ouyang, Langmuir 39(50), 18198-18207 (2023).
**(Fennell)**
C.\ J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006).
@ -367,18 +463,36 @@ Bibliography
**(Frenkel)**
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(GLE4MD)**
`https://gle4md.org/ <https://gle4md.org/>`_
**(Fu)**
Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
**(Gao)**
Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
**(Gingrich)**
Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
**(Gissinger2017)**
Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
**(Gissinger2020)**
Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
**(Gissinger)**
Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
Jacob R. Gissinger, Scott R. Zavada, Joseph G. Smith, Josh Kemppainen, Ivan Gallegos, Gregory M. Odegard, Emilie J. Siochi, and Kristopher E. Wise, Carbon, 202, 336-347 (2023).
**(Gissinger2024)**
J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
**(Gloor)**
Gloor, J Chem Phys, 123, 134703 (2005)
**(Glosli)**
Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006).
**(Goff)**
Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).
**(Goldman1)**
Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
@ -412,6 +526,9 @@ Bibliography
**(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
**(Gupta)**
Gupta ,Phys Rev. B, 23, 6265-6270 (1981).
**(Hardy)**
David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006).
@ -433,6 +550,9 @@ Bibliography
**(Henrich)**
O.\ Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
**(Herman)**
M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
**(Hess)**
Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
@ -454,24 +574,42 @@ Bibliography
**(Hoover)**
Hoover, Phys Rev A, 31, 1695 (1985).
**(Huang)**
Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013).
**(Huang2014)**
X. Huang, "Exploring critical-state behavior using DEM", Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316
**(Hu)**
Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).
**(Hu)**
Hu, J. Chem. Theory Comput. 10, 5254 (2014).
**(Hummer)**
Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
**(Hunt)**
Hunt, Mol Simul, 42, 347 (2016).
**(Ikeshoji)**
Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
**(Ikeshoji2)**
Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
**(Ilie)**
Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
**(In 't Veld)**
In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
**(IPI)**
`https://ipi-code.org/ <https://ipi-code.org/>`
**(IPI-CPC)**
Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
**(Ikeshoji)**
Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
**(In 't Veld)**
In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
**(Isele-Holder)**
Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
@ -490,6 +628,9 @@ Bibliography
**(Izvekov)**
Izvekov, Voth, J Chem Phys 123, 134105 (2005).
**(Jadhao)**
Jadhao, Solis, Olvera de la Cruz, J Chem Phys, 138, 054119 (2013)
**(Janssens)**
Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006).
@ -502,6 +643,15 @@ Bibliography
**(Jiang)**
Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
**(Jiang1)**
Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
**(Jiang2)**
J.-W. Jiang, Nanotechnology 26, 315706 (2015).
**(Jiang3)**
J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
**(Johnson et al, 1971)**
Johnson, K. L., Kendall, K., & Roberts, A. D. (1971). Surface energy and the contact of elastic solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
@ -571,21 +721,24 @@ Bibliography
**(Lamoureux)**
Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
**(Larentzos)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
**(Landsgesell)**
J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, Macromolecules 53, 3007-3020 (2020).
**(Larentzos1)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting
J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014).
**(Larentzos2)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014).
**(Larsen)**
Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
**(Lebedeva et al.)**
**(Lebedeva1)**
I.\ V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
**(Lebedeva2)**
I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
**(Lechman)**
Lechman, et al, in preparation (2010).
@ -595,6 +748,9 @@ Bibliography
**(Lee2)**
Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001).
**(Lee2020)**
C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.
**(Lenart)**
Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007).
@ -619,8 +775,11 @@ Bibliography
**(Li2015_JCP)**
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI:10.1063/1.4923254.
**(Liang)**
Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)
**(Lisal)**
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).
**(Liu1)**
L.\ Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011).
@ -637,6 +796,15 @@ Bibliography
**(Luding, 2008)**
Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235.
**(Lysogorskiy)**
Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
**(Lysogorskiy21)**
Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
**(Lysogorskiy23)**
Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022).
**(Maaravi)**
T.\ Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
@ -655,12 +823,18 @@ Bibliography
**(Maginn)**
Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007).
**(Mahoney)**
Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
**(Malolepsza)**
Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015).
**(Mandadapu)**
Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
**(Mandelli_1)**
D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019).
**(Maras)**
Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016).
@ -676,6 +850,9 @@ Bibliography
**(Martyna1994)**
Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
**(Martyna2)**
G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
**(Mason)**
J.\ K. Mason, Acta Cryst A65, 259 (2009).
@ -715,6 +892,9 @@ Bibliography
**(Mie)**
G.\ Mie, Ann Phys, 316, 657 (1903).
**(Milano)**
G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).
**(Miller1)**
T.\ F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
@ -745,12 +925,18 @@ Bibliography
**(Mitchell2011a)**
Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011).
**(Miyazaki)**
Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).
**(Mniszewski)**
S.\ M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015).
**(Monaghan)**
Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983).
**(Monti)**
Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022).
**(Moore)**
Moore, J Chem Phys, 144, 104501 (2016).
@ -770,7 +956,7 @@ Bibliography
Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
**(Moustafa)**
Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
**(Muller-Plathe1)**
Muller-Plathe, J Chem Phys, 106, 6082 (1997).
@ -790,9 +976,6 @@ Bibliography
**(Neelov)**
Neelov, Holm, J Chem Phys 132, 234103 (2010)
**(Negre2016)**
C.\ F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016).
**(Nelson)**
Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
@ -802,12 +985,24 @@ Bibliography
**(Neyts)**
E.\ C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013).
**(Nguyen2023)**
Nguyen, Physical Review B, 107(14), 144103, (2023).
**(Nguyen2024)**
Nguyen, Journal of Computational Physics, 113102, (2024).
**(Nguyen and Rohskopf)**
Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
**(Nguyen and Sema)**
Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
**(NguyenTD)**
Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Comput Phys Commun 241, 80-19 (2019)
**(Nicholson and Rutledge)**
Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).
**(Nicklas)**
The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
**(Niklasson2002)**
A.\ M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
@ -820,6 +1015,9 @@ Bibliography
**(Niklasson2017)**
A.\ M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
**(Nitol)**
Nitol, Dickel, and Barrett, Computational Materials Science 188 (2021): 110207.
**(Noid)**
Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008).
@ -841,6 +1039,9 @@ Bibliography
**(O'Connor)**
O'Connor et al., J. Chem. Phys. 142, 024903 (2015).
**(O'Hearn)**
O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
**(Okabe)**
T.\ Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
@ -850,6 +1051,8 @@ Bibliography
**(Omelyan)**
Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001).
**(OPLS-AA96)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
**(Oppelstrup)**
Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published.
@ -871,14 +1074,17 @@ Bibliography
**(Ouyang2)**
W.\ Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
**(PASS)**
PASS webpage: https://www.sdu.dk/en/DPASS
**(Ouyang_1)**
W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
**(PLUMED)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Ouyang6)**
W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).
**(Pavlov)**
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
**(Ouyang7)**
W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
**(Palkar)**
Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
@ -889,21 +1095,33 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Parks)**
Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
**(Parrinello1981)**
**(Parrinello)**
Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
**(PASS)**
PASS webpage: https://www.sdu.dk/en/DPASS
**(Paula Leite2016)**
Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).
**(Paula Leite2017)**
Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, 32115 (2017).
**(Pavlov1)**
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
**(Pavlov2)**
Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)
**(Pearlman)**
Pearlman, J Chem Phys, 98, 1487 (1994)
**(Pedersen)**
Pedersen, J. Chem. Phys., 139, 104102 (2013).
**(Pedone)**
A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)
**(Peng)**
Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996).
@ -925,6 +1143,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Pettifor_3)**
D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002).
**(PFC)**
PFC Particle Flow Code 6.0 Documentation. Itasca Consulting Group.
**(Phillips)**
C.\ L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011).
@ -934,9 +1155,21 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Pisarev)**
V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014).
**(Plimpton)**
Plimpton and Knight, JPDC, 147, 184-195 (2021).
**(PLUMED)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Pollock)**
Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
**(Ponder)**
Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
**(Popov1)**
A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
**(Price1)**
Price and Brooks, J Chem Phys, 121, 10096 (2004).
@ -976,6 +1209,12 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Rick)**
S.\ W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994).
**(Rick2)**
S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
**(Roberts)**
R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
**(Rohart)**
Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).
@ -1012,9 +1251,18 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Sadigh)**
B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
**(Sadigh1)**
B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
**(Sadigh2)**
B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)
**(Safran)**
Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003).
**(Salanne)**
Salanne, Rotenberg, Jahn, Vuilleumier, Simon, Christian and Madden, Theor Chem Acc, 131, 1143 (2012).
**(Salerno)**
Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
@ -1024,9 +1272,18 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Sanyal2)**
Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
**(Scalfi)**
Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
**(Schelling)**
Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
**(Scherer1)**
C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018).
**(Scherer2)**
C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020).
**(Schlitter1)**
Schlitter, Swegat, Mulders, "Distance-type reaction coordinates for modelling activated processes", J Molecular Modeling, 7, 171-177 (2001).
@ -1045,21 +1302,36 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Schroeder)**
Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).
**(Seleson 2010)**
Seleson, Parks, Int J Mult Comp Eng 9(6), pp. 689-706, 2011.
**(Semaev)**
Semaev, Cryptography and Lattices, 181 (2001).
**(Seo)**
Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
**(Sheppard)**
Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008). See ref 1 in this paper for original reference to Qmin in Jonsson, Mills, Jacobsen.
**(Shi)**
Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
**(Shinoda)**
Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
**(Shinoda)**
Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
**(Shire)**
Shire, Hanley and Stratford, Comp. Part. Mech., (2020).
**(Sides)**
Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004).
**(Siepmann)**
Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
**(Silbert)**
Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001).
@ -1069,12 +1341,21 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Silling 2000)**
Silling, J Mech Phys Solids, 48, 175-209 (2000).
**(Silling 2005)**
Silling Askari, Computer and Structures, 83, 1526-1535 (2005).
**(Silling 2007)**
Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
**(Singh)**
Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
**(Singraber, Behler and Dellago 2019)**
Singraber, A.; Behler, J.; Dellago, C. J., Chem. Theory Comput. 2019, 15 (3), 1827-1840
**(Singraber et al 2019)**
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput. 2019, 15 (5), 3075-3092.
**(Sirk1)**
Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012.
@ -1087,6 +1368,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Snodin)**
B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
**(Son)**
Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).
**(Srivastava)**
Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).
@ -1096,6 +1380,12 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Steinhardt)**
P.\ Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
**(Steward)**
Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
**(Stewart2018)**
J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
**(Stiles)**
Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982).
@ -1153,12 +1443,21 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Tainter 2015)**
Tainter, Shi, and Skinner, 11, 2268 (2015)
**(Tang and Toennies)**
J Chem Phys, 80, 3726 (1984).
**(Tee)**
Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
**(Templeton2010)**
Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
**(Templeton2011)**
Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
**(tenWolde)**
P.\ R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
**(Tersoff_1)**
J.\ Tersoff, Phys Rev B, 37, 6991 (1988).
@ -1201,6 +1500,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Tranchida)**
Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).
**(Tribello)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Tsuji et al, 1992)**
Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3),
@ -1219,6 +1521,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Tuckerman4)**
Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997).
**(Tyagi)**
Tyagi, Suzen, Sega, Barbosa, Kantorovich, Holm, J Chem Phys, 132, 154112 (2010)
**(Ulomek)**
Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007
@ -1228,6 +1533,15 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Valone)**
Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
**(vanWijk)**
M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)
**(Van Workum)**
K. Van Workum et al., J. Chem. Phys. 125 144506 (2006)
**(Vargas and McCarthy 2001)**
Vargas, W.L. and McCarthy, J.J. (2001).
**(Varshalovich)**
Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987).
@ -1240,6 +1554,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Veld)**
In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
**(Verstraelen)**
Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).
**(Volkov1)**
Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
@ -1264,6 +1581,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Wang et al, 2015)**
Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015). Rolling and sliding in 3-D discrete element models. Particuology, 23, 49-55.
**(Wang2020)**
X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020).
**(Wang1)**
J.\ Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).
@ -1303,6 +1623,9 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Wicaksono2)**
Wicaksono, figshare, https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
**(Winkler)**
Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).
**(Wirnsberger)**
Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015).
@ -1315,9 +1638,27 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Wood)**
Wood and Thompson, J Chem Phys, 148, 241721, (2018)
**(Xie23)**
Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7
**(Yade-DEM)**
V. Smilauer et al. (2021), Yade Documentation 3rd ed.
**(Yanxon2020)**
Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020).
**(Yeh)**
Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
**(Yuan2010a)**
Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
**(Yuan2010b)**
Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010).
**(Zagaceta2020)**
Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020).
**(ZBL)**
J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press.
@ -1387,17 +1728,6 @@ D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Jo
**(Zimmerman2010)**
Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
**(de Buyl)**
de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
**(de Koning)**
de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
**(electronic stopping)**
Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
**(tenWolde)**
P.\ R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
**(vanWijk)**
M.\ M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)

86
doc/src/Build_basics.rst
View File

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

12
doc/src/Build_cmake.rst
View File

@ -131,20 +131,20 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
configuration step. The cache file contains all current CMake settings.
To modify settings, enable or disable features, you need to set
*variables* with either the *-D* command line flag (``-D
*variables* with either the ``-D`` command line flag (``-D
VARIABLE1_NAME=value``) or change them in the text mode of the graphical
user interface. The *-D* flag can be used several times in one command.
user interface. The ``-D`` flag can be used several times in one command.
For your convenience, we provide :ref:`CMake presets <cmake_presets>`
that combine multiple settings to enable optional LAMMPS packages or use
a different compiler tool chain. Those are loaded with the *-C* flag
a different compiler tool chain. Those are loaded with the ``-C`` flag
(``-C ../cmake/presets/basic.cmake``). This step would only be needed
once, as the settings from the preset files are stored in the
``CMakeCache.txt`` file. It is also possible to customize the build
by adding one or more *-D* flags to the CMake command line.
by adding one or more ``-D`` flags to the CMake command line.
Generating files for alternate build tools (e.g. Ninja) and project files
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
command line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
@ -171,7 +171,7 @@ files. E.g. with:
In that case the resulting binaries are not in the build folder directly
but in subdirectories corresponding to the build type (i.e. Release in
the example from above). Similarly, for running unit tests the
configuration is selected with the *-C* flag:
configuration is selected with the ``-C`` flag:
.. code-block:: bash

172
doc/src/Build_development.rst
View File

@ -138,12 +138,27 @@ during development:
The status of this automated testing can be viewed on `https://ci.lammps.org
<https://ci.lammps.org>`_.
The scripts and inputs for integration, run, and regression testing
are maintained in a
`separate repository <https://github.com/lammps/lammps-testing>`_
of the LAMMPS project on GitHub. A few tests are also run as GitHub
Actions and their configuration files are in the ``.github/workflows/``
folder of the LAMMPS git tree.
The scripts and inputs for integration, run, and legacy regression
testing are maintained in a `separate repository
<https://github.com/lammps/lammps-testing>`_ of the LAMMPS project on
GitHub. A few tests are also run as GitHub Actions and their
configuration files are in the ``.github/workflows/`` folder of the
LAMMPS git tree.
Regression tests can also be performed locally with the :ref:`regression
tester tool <regression>`. The tool checks if a given LAMMPS binary run
with selected input examples produces thermo output that is consistent
with the provided log files. The script can be run in one pass over all
available input files, but it can also first create multiple lists of
inputs or folders that can then be run with multiple workers
concurrently to speed things up. Another mode allows to do a quick
check of inputs that contain commands that have changes in the current
checkout branch relative to a git branch. This works similar to the two
pass mode, but will select only shorter runs and no more than 100 inputs
that are chosen randomly. This ensures that this test runs
significantly faster compared to the full test run. These test runs can
also be performed with instrumented LAMMPS binaries (see previous
section).
The unit testing facility is integrated into the CMake build process of
the LAMMPS source code distribution itself. It can be enabled by
@ -153,7 +168,12 @@ development headers to compile (if those are not found locally a recent
version of that library will be downloaded and compiled along with
LAMMPS and the test programs) and will download and compile a specific
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
test framework that is used to implement the tests.
test framework that is used to implement the tests. Those unit tests
may be combined with memory access and leak checking with valgrind
(see below for how to enable it). In that case, running so-called
death tests will create a lot of false positives and thus they can be
disabled by configuring compilation with the additional setting
``-D SKIP_DEATH_TESTS=on``.
.. admonition:: Software version and LAMMPS configuration requirements
:class: note
@ -176,24 +196,24 @@ The output of this command will be looking something like this:
$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: RunLammps
1/563 Test #1: RunLammps .......................................... Passed 0.28 sec
1/563 Test #1: RunLammps .................................. Passed 0.28 sec
Start 2: HelpMessage
2/563 Test #2: HelpMessage ........................................ Passed 0.06 sec
2/563 Test #2: HelpMessage ................................ Passed 0.06 sec
Start 3: InvalidFlag
3/563 Test #3: InvalidFlag ........................................ Passed 0.06 sec
3/563 Test #3: InvalidFlag ................................ Passed 0.06 sec
Start 4: Tokenizer
4/563 Test #4: Tokenizer .......................................... Passed 0.05 sec
4/563 Test #4: Tokenizer .................................. Passed 0.05 sec
Start 5: MemPool
5/563 Test #5: MemPool ............................................ Passed 0.05 sec
5/563 Test #5: MemPool .................................... Passed 0.05 sec
Start 6: ArgUtils
6/563 Test #6: ArgUtils ........................................... Passed 0.05 sec
6/563 Test #6: ArgUtils ................................... Passed 0.05 sec
[...]
Start 561: ImproperStyle:zero
561/563 Test #561: ImproperStyle:zero ................................. Passed 0.07 sec
561/563 Test #561: ImproperStyle:zero ......................... Passed 0.07 sec
Start 562: TestMliapPyUnified
562/563 Test #562: TestMliapPyUnified ................................. Passed 0.16 sec
562/563 Test #562: TestMliapPyUnified ......................... Passed 0.16 sec
Start 563: TestPairList
563/563 Test #563: TestPairList ....................................... Passed 0.06 sec
563/563 Test #563: TestPairList ............................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 563
@ -208,24 +228,25 @@ The output of this command will be looking something like this:
The ``ctest`` command has many options, the most important ones are:
.. list-table::
:widths: 20 80
* - Option
- Function
* - -V
* - ``-V``
- verbose output: display output of individual test runs
* - -j <num>
* - ``-j <num>``
- parallel run: run <num> tests in parallel
* - -R <regex>
* - ``-R <regex>``
- run subset of tests matching the regular expression <regex>
* - -E <regex>
* - ``-E <regex>``
- exclude subset of tests matching the regular expression <regex>
* - -L <regex>
* - ``-L <regex>``
- run subset of tests with a label matching the regular expression <regex>
* - -LE <regex>
* - ``-LE <regex>``
- exclude subset of tests with a label matching the regular expression <regex>
* - -N
* - ``-N``
- dry-run: display list of tests without running them
* - -T memcheck
* - ``-T memcheck``
- run tests with valgrind memory checker (if available)
In its full implementation, the unit test framework will consist of multiple
@ -331,16 +352,17 @@ paths in the individual source files.
The force style test programs have a common set of options:
.. list-table::
:widths: 25 75
* - Option
- Function
* - -g <newfile>
* - ``-g <newfile>``
- regenerate reference data in new YAML file
* - -u
* - ``-u``
- update reference data in the original YAML file
* - -s
* - ``-s``
- print error statistics for each group of comparisons
* - -v
* - ``-v``
- verbose output: also print the executed LAMMPS commands
The ``ctest`` tool has no mechanism to directly pass flags to the individual
@ -354,10 +376,10 @@ set in an environment variable ``TEST_ARGS``. Example:
To add a test for a style that is not yet covered, it is usually best
to copy a YAML file for a similar style to a new file, edit the details
of the style (how to call it, how to set its coefficients) and then
run test command with either the *-g* and the replace the initial
test file with the regenerated one or the *-u* option. The *-u* option
run test command with either the ``-g`` and the replace the initial
test file with the regenerated one or the ``-u`` option. The ``-u`` option
will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested
so using ``-g`` is recommended unless the YAML file is fully tested
and working.
Some of the force style tests are rather slow to run and some are very
@ -507,27 +529,51 @@ After post-processing with ``gen_coverage_html`` the results are in
a folder ``coverage_html`` and can be viewed with a web browser.
The images below illustrate how the data is presented.
.. list-table::
.. only:: not latex
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
.. list-table::
Top of the overview page
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
Top of the overview page
Styles with good coverage
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
Styles with good coverage
Top of individual source page
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Top of individual source page
Source page with branches
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Source page with branches
.. only:: latex
.. figure:: JPG/coverage-overview-top.png
:width: 60%
Top of the overview page
.. figure:: JPG/coverage-overview-manybody.png
:width: 60%
Styles with good coverage
.. figure:: JPG/coverage-file-top.png
:width: 60%
Top of individual source page
.. figure:: JPG/coverage-file-branches.png
:width: 60%
Source page with branches
Coding style utilities
----------------------
@ -599,11 +645,35 @@ The following target are available for both, GNU make and CMake:
GitHub command line interface
-----------------------------
GitHub is developing a `tool for the command line
<https://cli.github.com>`_ that interacts with the GitHub website via a
command called ``gh``. This can be extremely convenient when working
with a Git repository hosted on GitHub (like LAMMPS). It is thus highly
recommended to install it when doing LAMMPS development.
GitHub has developed a `command line tool <https://cli.github.com>`_
to interact with the GitHub website via a command called ``gh``.
This is extremely convenient when working with a Git repository hosted
on GitHub (like LAMMPS). It is thus highly recommended to install it
when doing LAMMPS development. To use ``gh`` you must be within a git
checkout of a repository and you must obtain an authentication token
to connect your checkout with a GitHub user. This is done with the
command: ``gh auth login`` where you then have to follow the prompts.
Here are some examples:
The capabilities of the ``gh`` command is continually expanding, so
please see the documentation at https://cli.github.com/manual/
.. list-table::
:header-rows: 1
:widths: 34 66
* - Command
- Description
* - ``gh pr list``
- List currently open pull requests
* - ``gh pr checks 404``
- Shows the status of all checks for pull request #404
* - ``gh pr view 404``
- Shows the description and recent comments for pull request #404
* - ``gh co 404``
- Check out the branch from pull request #404; set up for pushing changes
* - ``gh issue list``
- List currently open issues
* - ``gh issue view 430 --comments``
- Shows the description and all comments for issue #430
The capabilities of the ``gh`` command are continually expanding, so
for more details please see the documentation at https://cli.github.com/manual/
or use ``gh --help`` or ``gh <command> --help`` for embedded help.

565
doc/src/Build_extras.rst
View File

@ -7,6 +7,8 @@ in addition to
.. list-table::
:align: center
:header-rows: 1
:widths: 50 50
:width: 80%
* - CMake build
- Traditional make
@ -14,7 +16,7 @@ in addition to
cmake -D PKG_NAME=yes
- .. code-block:: console
- .. code-block:: bash
make yes-name
@ -73,7 +75,7 @@ COMPRESS package
To build with this package you must have the `zlib compression library
<https://zlib.net>`_ available on your system to build dump styles with
a '/gz' suffix. There are also styles using the
a ``/gz`` suffix. There are also styles using the
`Zstandard <https://facebook.github.io/zstd/>`_ library which have a
'/zstd' suffix. The zstd library version must be at least 1.4. Older
versions use an incompatible API and thus LAMMPS will fail to compile.
@ -95,7 +97,7 @@ versions use an incompatible API and thus LAMMPS will fail to compile.
<https://www.freedesktop.org/wiki/Software/pkg-config/>`_ tool to
identify the necessary flags to compile with this library, so the
corresponding ``libzstandard.pc`` file must be in a folder where
pkg-config can find it, which may require adding it to the
``pkg-config`` can find it, which may require adding it to the
``PKG_CONFIG_PATH`` environment variable.
.. tab:: Traditional make
@ -115,7 +117,7 @@ GPU package
To build with this package, you must choose options for precision and
which GPU hardware to build for. The GPU package currently supports
three different types of backends: OpenCL, CUDA and HIP.
three different types of back ends: OpenCL, CUDA and HIP.
CMake build
^^^^^^^^^^^
@ -127,46 +129,53 @@ CMake build
# 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)
-D GPU_DEBUG=value # enable debug code in the GPU package library, mostly useful for developers
-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_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
# default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for
# HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # use GPU binning on with CUDA (should be off for modern GPUs)
# enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
-D CUDPP_OPT=value # use GPU binning with CUDA (should be off for modern GPUs)
# enables CUDA Performance Primitives, must be "no" for
# CUDA_MPS_SUPPORT=yes
# value = yes or no (default)
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active
# nvidia-cuda-mps daemon
# value = yes or no (default)
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU architectures
-D CUDA_BUILD_MULTIARCH=value # enables building CUDA kernels for all supported GPU
# architectures
# value = yes (default) or no
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library,
# no local OpenCL headers/libs needed
# value = yes (default) or no
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
``GPU_ARCH`` settings for different GPU hardware is as follows:
* sm_30 for Kepler (supported since CUDA 5 and until CUDA 10.x)
* sm_35 or sm_37 for Kepler (supported since CUDA 5 and until CUDA 11.x)
* sm_50 or sm_52 for Maxwell (supported since CUDA 6)
* 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 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)
* ``sm_30`` for Kepler (supported since CUDA 5 and until CUDA 10.x)
* ``sm_35`` or ``sm_37`` for Kepler (supported since CUDA 5 and until CUDA 11.x)
* ``sm_50`` or ``sm_52`` for Maxwell (supported since CUDA 6)
* ``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`` 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>`_
CMake can detect which version of the CUDA toolkit is used and thus will
try to include support for **all** major GPU architectures supported by
this toolkit. Thus the GPU_ARCH setting is merely an optimization, to
this toolkit. Thus the ``GPU_ARCH`` setting is merely an optimization, to
have code for the preferred GPU architecture directly included rather
than having to wait for the JIT compiler of the CUDA driver to translate
it. This behavior can be turned off (e.g. to speed up compilation) by
setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
setting ``CUDA_ENABLE_MULTIARCH`` to ``no``.
When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
CUDA toolkit is required and a GPU architecture of Kepler or later,
@ -185,21 +194,21 @@ build, and link with a static OpenCL ICD loader library and standard
OpenCL headers. This 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`.
``USE_STATIC_OPENCL_LOADER`` to ``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.
``HCC_AMDGPU_TARGET`` (for ROCm <= 4.0) or ``CUDA_PATH`` are
necessary for ``hipcc`` and the linker to work correctly.
.. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
run HIP code on Intel GPUs via the OpenCL or Level Zero back ends. To use
CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
option in preparations to run on Aurora system at Argonne.
@ -257,28 +266,35 @@ 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
# print help message
make lib-gpu
# build GPU library with default Makefile.linux
make lib-gpu args="-b"
# create new Makefile.xk7.single, altered for single-precision
make lib-gpu args="-m xk7 -p single -o xk7.single"
# build GPU library with mixed precision and P100 using other settings in Makefile.mpi
make lib-gpu args="-m mpi -a sm_60 -p mixed -b"
Note that this procedure starts with a Makefile.machine in lib/gpu, as
specified by the "-m" switch. For your convenience, machine makefiles
specified by the ``-m`` switch. For your convenience, machine makefiles
for "mpi" and "serial" are provided, which have the same settings as
the corresponding machine makefiles in the main LAMMPS source
folder. In addition you can alter 4 important settings in the
Makefile.machine you start from via the corresponding -c, -a, -p, -e
Makefile.machine you start from via the corresponding ``-c``, ``-a``, ``-p``, ``-e``
switches (as in the examples above), and also save a copy of the new
Makefile if desired:
* ``CUDA_HOME`` = where NVIDIA CUDA software is installed on your system
* ``CUDA_ARCH`` = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
* ``CUDA_ARCH`` = ``sm_XX``, what GPU hardware you have, same as CMake ``GPU_ARCH`` above
* ``CUDA_PRECISION`` = precision (double, mixed, single)
* ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
* ``EXTRAMAKE`` = which ``Makefile.lammps.*`` file to copy to Makefile.lammps
The file Makefile.cuda is set up to include support for multiple
The file ``Makefile.cuda`` is set up to include support for multiple
GPU architectures as supported by the CUDA toolkit in use. This is done
through using the "--gencode " flag, which can be used multiple times and
through using the ``--gencode`` flag, which can be used multiple times and
thus support all GPU architectures supported by your CUDA compiler.
To enable GPU binning via CUDA performance primitives set the Makefile variable
@ -349,12 +365,16 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: bash
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off, value = off (default) or on
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer, value = no (default) or yes
-D KIM_EXTRA_UNITTESTS=value # enables extra unit tests, value = no (default) or yes
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build
# value = no (default) or yes
-D LMP_DEBUG_CURL=value # set libcurl verbose mode on/off
# value = off (default) or on
-D LMP_NO_SSL_CHECK=value # tell libcurl to not verify the peer
# value = no (default) or yes
-D KIM_EXTRA_UNITTESTS=value # enables extra unit tests
# value = no (default) or yes
If ``DOWNLOAD_KIM`` is set to *yes* (or *on*), the KIM API library
If ``DOWNLOAD_KIM`` is set to ``yes`` (or ``on``), the KIM API library
will be downloaded and built inside the CMake build directory. If
the KIM library is already installed on your system (in a location
where CMake cannot find it), you may need to set the
@ -362,7 +382,7 @@ minutes to hours) to build. Of course you only need to do that once.)
found, or run the command ``source kim-api-activate``.
Extra unit tests can only be available if they are explicitly requested
(``KIM_EXTRA_UNITTESTS`` is set to *yes* (or *on*)) and the prerequisites
(``KIM_EXTRA_UNITTESTS`` is set to ``yes`` (or ``on``)) and the prerequisites
are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for
more details on this.
@ -376,15 +396,28 @@ minutes to hours) to build. Of course you only need to do that once.)
.. 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
# print help message
make lib-kim
When using the "-b " option, the KIM library is built using its native
# (re-)install KIM API lib with only example models
make lib-kim args="-b"
# ditto plus one model
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"
# install KIM API lib with all models
make lib-kim args="-b -a everything"
# add one model or model driver
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
# use an existing KIM API installation at the provided location
make lib-kim args="-p <prefix>"
# ditto but add one model or driver
make lib-kim args="-p <prefix> -a EAM_Dynamo_Ackland_W__MO_141627196590_002"
When using the ``-b`` option, the KIM library is built using its native
cmake build system. The ``lib/kim/Install.py`` script supports a
``CMAKE`` environment variable if the cmake executable is named other
than ``cmake`` on your system. Additional environment variables may be
@ -394,7 +427,9 @@ 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
# (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"
Settings for debugging OpenKIM web queries discussed below need to
be applied by adding them to the ``LMP_INC`` variable through
@ -434,7 +469,7 @@ KIM Extra unit tests (CMake only)
During development, testing, or debugging, if
:doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
``KIM_EXTRA_UNITTESTS`` to ``yes`` (or ``on``).
Enabling the extra unit tests have some requirements,
@ -449,10 +484,12 @@ Enabling the extra unit tests have some requirements,
*conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
Conda. More detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
* It is also necessary to install
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
* It is also necessary to install the following KIM models:
* ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``
* ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``
* ``LennardJones612_UniversalShifted__MO_959249795837_003``
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
@ -639,6 +676,9 @@ They must be specified in uppercase.
* - AMD_GFX1100
- GPU
- AMD GPU RX7900XTX
* - AMD_GFX1103
- GPU
- AMD Phoenix APU with Radeon 740M/760M/780M/880M/890M
* - INTEL_GEN
- GPU
- SPIR64-based devices, e.g. Intel GPUs, using JIT
@ -713,20 +753,34 @@ This list was last updated for version 4.3.0 of the Kokkos library.
platform-appropriate vendor library: rocFFT on AMD GPUs or cuFFT on
NVIDIA GPUs.
To simplify compilation, five preset files are included in the
For Intel GPUs using SYCL, set these variables:
.. code-block:: bash
-D Kokkos_ARCH_HOSTARCH=yes # HOSTARCH = HOST from list above
-D Kokkos_ARCH_GPUARCH=yes # GPUARCH = GPU from list above
-D Kokkos_ENABLE_SYCL=yes
-D Kokkos_ENABLE_OPENMP=yes
-D FFT_KOKKOS=MKL_GPU
This will enable FFTs on the GPU using the oneMKL library.
To simplify compilation, six preset files are included in the
``cmake/presets`` folder, ``kokkos-serial.cmake``,
``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``. They will enable
the KOKKOS package and enable some hardware choices. For GPU
support those preset files must be customized to match the
hardware used. So to compile with CUDA device parallelization with
some common packages enabled, you can do the following:
``kokkos-hip.cmake``, ``kokkos-sycl-nvidia.cmake``, and
``kokkos-sycl-intel.cmake``. They will enable the KOKKOS
package and enable some hardware choices. For GPU support those
preset files must be customized to match the hardware used. So
to compile with CUDA device parallelization with some common
packages enabled, you can do the following:
.. code-block:: bash
mkdir build-kokkos-cuda
cd build-kokkos-cuda
cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake -C ../cmake/presets/basic.cmake \
-C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake --build .
.. tab:: Basic traditional make settings:
@ -754,9 +808,10 @@ This list was last updated for version 4.3.0 of the Kokkos library.
.. code-block:: make
KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is hosting the GPU
KOKKOS_CUDA_OPTIONS = "enable_lambda"
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
# hosting the GPU
# GPUARCH = GPU from list above
KOKKOS_CUDA_OPTIONS = "enable_lambda"
FFT_INC = -DFFT_CUFFT # enable use of cuFFT (optional)
FFT_LIB = -lcufft # link to cuFFT library
@ -784,10 +839,23 @@ This list was last updated for version 4.3.0 of the Kokkos library.
.. code-block:: make
KOKKOS_DEVICES = HIP
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is hosting the GPU
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
# hosting the GPU
# GPUARCH = GPU from list above
FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional)
FFT_LIB = -lhipfft # link to hipFFT library
FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional)
FFT_LIB = -lhipfft # link to hipFFT library
For Intel GPUs using SYCL:
.. code-block:: make
KOKKOS_DEVICES = SYCL
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
# hosting the GPU
# GPUARCH = GPU from list above
FFT_INC = -DFFT_KOKKOS_MKL_GPU # enable use of oneMKL for Intel GPUs (optional)
# link to oneMKL FFT library
FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -mkl_core -ltbb
Advanced KOKKOS compilation settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -871,11 +939,16 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
.. code-block:: bash
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")
# print help message
make lib-lepton
The "machine" argument of the "-m" flag is used to find a
# build with GNU g++ compiler (settings as with "make serial")
make lib-lepton args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-lepton args="-m mpi"
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``
@ -897,7 +970,8 @@ Eigen3 is a template library, so you do not need to build it.
.. code-block:: bash
-D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location)
-D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a
# custom location)
If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be
downloaded and inside the CMake build directory. If the Eigen3
@ -915,9 +989,14 @@ Eigen3 is a template library, so you do not need to build it.
.. code-block:: bash
make lib-machdyn # print help message
make lib-machdyn args="-b" # download to lib/machdyn/eigen3
make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3
# print help message
make lib-machdyn
# download to lib/machdyn/eigen3
make lib-machdyn args="-b"
# use existing Eigen installation in /usr/include/eigen3
make lib-machdyn args="-p /usr/include/eigen3"
Note that a symbolic (soft) link named ``includelink`` is created
in ``lib/machdyn`` to point to the Eigen dir. When LAMMPS builds it
@ -991,7 +1070,7 @@ OPT package
The compiler flag ``-restrict`` must be used to build LAMMPS with
the OPT package when using Intel compilers. It should be added to
the :code:`CCFLAGS` line of your ``Makefile.machine``. See
the ``CCFLAGS`` line of your ``Makefile.machine``. See
``src/MAKE/OPTIONS/Makefile.opt`` for an example.
----------
@ -1018,10 +1097,17 @@ POEMS package
.. 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
# print help message
make lib-poems
# build with GNU g++ compiler (settings as with "make serial")
make lib-poems args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-poems args="-m mpi"
# build with Intel Classic compiler
make lib-poems args="-m icc"
The build should produce two files: ``lib/poems/libpoems.a`` and
``lib/poems/Makefile.lammps``. The latter is copied from an
@ -1085,9 +1171,12 @@ binary package provided by your operating system.
.. code-block:: bash
-D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location)
-D DOWNLOAD_VORO=value # download Voro++ for build
# value = no (default) or yes
-D VORO_LIBRARY=path # Voro++ library file
# (only needed if at custom location)
-D VORO_INCLUDE_DIR=path # Voro++ include directory
# (only needed if at custom location)
If ``DOWNLOAD_VORO`` is set, the Voro++ library will be downloaded
and built inside the CMake build directory. If the Voro++ library
@ -1107,12 +1196,19 @@ binary package provided by your operating system.
.. 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
# print help message
make lib-voronoi
Note that 2 symbolic (soft) links, ``includelink`` and
# download and build the default version in lib/voronoi/voro++-<version>
make lib-voronoi args="-b"
# use existing Voro++ installation in $HOME/voro++
make lib-voronoi args="-p $HOME/voro++"
# download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
make lib-voronoi args="-b -v voro++0.4.6"
Note that two symbolic (soft) links, ``includelink`` and
``liblink``, are created in lib/voronoi to point to the Voro++
source dir. When LAMMPS builds in ``src`` it will use these
links. You should not need to edit the
@ -1186,10 +1282,17 @@ The ATC package requires the MANYBODY package also be installed.
.. 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
# print help message
make lib-atc
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-atc args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-atc args="-m mpi"
# build with Intel Classic compiler
make lib-atc args="-m icc"
The build should produce two files: ``lib/atc/libatc.a`` and
``lib/atc/Makefile.lammps``. The latter is copied from an
@ -1208,10 +1311,17 @@ 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 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
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU Fortran compiler
make lib-linalg args="-m g++"
----------
@ -1237,10 +1347,17 @@ AWPMD package
.. 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
# print help message
make lib-awpmd
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-awpmd args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-awpmd args="-m mpi"
# build with Intel Classic compiler
make lib-awpmd args="-m icc"
The build should produce two files: ``lib/awpmd/libawpmd.a`` and
``lib/awpmd/Makefile.lammps``. The latter is copied from an
@ -1259,10 +1376,17 @@ AWPMD package
.. 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
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
----------
@ -1295,10 +1419,17 @@ module included in the LAMMPS source distribution.
.. 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
# print help message
make lib-colvars
# build with GNU g++ compiler (settings as with "make serial")
make lib-colvars args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-colvars args="-m mpi"
# build with GNU g++ compiler and colvars debugging enabled
make lib-colvars args="-m g++-debug"
The "machine" argument of the "-m" flag is used to find a
``Makefile.machine`` file to use as build recipe. If such recipe does
@ -1317,8 +1448,11 @@ module included in the LAMMPS source distribution.
.. 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)
# Build with debug code (much slower)
COLVARS_DEBUG=yes make lib-colvars args="-m machine"
# Build without Lepton (included otherwise)
COLVARS_LEPTON=no make lib-colvars args="-m machine"
The build should produce two files: the library
``lib/colvars/libcolvars.a`` and the specification file
@ -1365,9 +1499,14 @@ This package depends on the KSPACE package.
.. code-block:: bash
make lib-electrode # print help message
make lib-electrode args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-electrode args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
# print help message
make lib-electrode
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-electrode args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-electrode args="-m mpi"
Note that the ``Makefile.lammps`` file has settings for the BLAS
@ -1378,10 +1517,17 @@ This package depends on the KSPACE package.
.. 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
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
The package itself is activated with ``make yes-KSPACE`` and
``make yes-ELECTRODE``
@ -1398,6 +1544,11 @@ in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
Instead of including the ML-PACE package directly into LAMMPS, it
is also possible to skip this step and build the ML-PACE package as
a plugin using the CMake script files in the ``examples/PACKAGE/pace/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
@ -1421,8 +1572,11 @@ 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
# print help message
make lib-pace
# download and build the default version in lib/pace
make lib-pace args="-b"
You should not need to edit the ``lib/pace/Makefile.lammps`` file.
@ -1449,10 +1603,17 @@ ML-POD package
.. 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
# print help message
make lib-mlpod
# build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
make lib-mlpod args="-m serial"
# build with default MPI compiler (settings as with "make mpi")
make lib-mlpod args="-m mpi"
# same as above but use the bundled linalg lib
make lib-mlpod args="-m mpi -e linalg"
Note that the ``Makefile.lammps`` file has settings to use the BLAS
and LAPACK linear algebra libraries. These can either exist on
@ -1462,10 +1623,17 @@ ML-POD package
.. 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
# print help message
make lib-linalg
# build with GNU C++ compiler (settings as with "make serial")
make lib-linalg args="-m serial"
# build with default MPI C++ compiler (settings as with "make mpi")
make lib-linalg args="-m mpi"
# build with GNU C++ compiler
make lib-linalg args="-m g++"
The package itself is activated with ``make yes-ML-POD``.
@ -1488,10 +1656,13 @@ within CMake will download the non-commercial use version.
.. code-block:: bash
-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
-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
@ -1562,6 +1733,11 @@ try a different one, switch to a different build system, consider a
global PLUMED installation or consider downloading PLUMED during the
LAMMPS build.
Instead of including the PLUMED package directly into LAMMPS, it
is also possible to skip this step and build the PLUMED package as
a plugin using the CMake script files in the ``examples/PACKAGE/plumed/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
@ -1575,17 +1751,20 @@ LAMMPS build.
.. code-block:: bash
-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime
-D DOWNLOAD_PLUMED=value # download PLUMED for build
# value = no (default) or yes
-D PLUMED_MODE=value # Linkage mode for PLUMED
# value = static (default), shared,
# or runtime
If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
If ``DOWNLOAD_PLUMED`` is set to ``yes``, the PLUMED library will be
downloaded (the version of PLUMED that will be downloaded is
hard-coded to a vetted version of PLUMED, usually a recent stable
release version) and built inside the CMake build directory. If
``DOWNLOAD_PLUMED`` is set to "no" (the default), CMake will try
to detect and link to an installed version of PLUMED. For this to
work, the PLUMED library has to be installed into a location where
the ``pkg-config`` tool can find it or the PKG_CONFIG_PATH
the ``pkg-config`` tool can find it or the ``PKG_CONFIG_PATH``
environment variable has to be set up accordingly. PLUMED should
be installed in such a location if you compile it using the
default make; make install commands.
@ -1614,14 +1793,21 @@ 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
# /usr/local and use shared linkage mode
# print help message
make lib-plumed
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
are created in lib/plumed that point to the location of the PLUMED
# download and build PLUMED in lib/plumed/plumed2
make lib-plumed args="-b"
# use existing PLUMED installation in $HOME/.local
make lib-plumed args="-p $HOME/.local"
# use existing PLUMED installation in /usr/local and
# use shared linkage mode
make lib-plumed args="-p /usr/local -m shared"
Note that two symbolic (soft) links, ``includelink`` and ``liblink``
are created in ``lib/plumed`` that point to the location of the PLUMED
build to use. A new file ``lib/plumed/Makefile.lammps`` is also
created with settings suitable for LAMMPS to compile and link
PLUMED using the desired linkage mode. After this step is
@ -1636,17 +1822,17 @@ LAMMPS build.
Once this compilation completes you should be able to run LAMMPS
in the usual way. For shared linkage mode, libplumed.so must be
found by the LAMMPS executable, which on many operating systems
means, you have to set the LD_LIBRARY_PATH environment variable
means, you have to set the ``LD_LIBRARY_PATH`` environment variable
accordingly.
Support for the different linkage modes in LAMMPS varies for
different operating systems, using the static linkage is expected
to be the most portable, and thus set to be the default.
If you want to change the linkage mode, you have to re-run "make
lib-plumed" with the desired settings **and** do a re-install if
the PLUMED package with "make yes-plumed" to update the
required makefile settings with the changes in the lib/plumed
If you want to change the linkage mode, you have to re-run ``make
lib-plumed`` with the desired settings **and** do a re-install if
the PLUMED package with ``make yes-plumed`` to update the
required makefile settings with the changes in the ``lib/plumed``
folder.
----------
@ -1720,8 +1906,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
.. code-block:: bash
-D DOWNLOAD_N2P2=value # download n2p2 for build, value = no (default) or yes
-D N2P2_DIR=path # n2p2 base directory (only needed if a custom location)
-D DOWNLOAD_N2P2=value # download n2p2 for build
# value = no (default) or yes
-D N2P2_DIR=path # n2p2 base directory
# (only needed if a custom location)
If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
built inside the CMake build directory. If the *n2p2* library is already
@ -1738,12 +1926,19 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
.. 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
# print help message
make lib-hdnnp
Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
# download and build in lib/hdnnp/n2p2-...
make lib-hdnnp args="-b"
# download and build specific version
make lib-hdnnp args="-b -v 2.1.4"
# use the existing n2p2 installation in /usr/local/n2p2
make lib-hdnnp args="-p /usr/local/n2p2"
Note that three symbolic (soft) links, ``includelink``, ``liblink`` and
``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
respectively. When LAMMPS is built in ``src`` it will use these links.
@ -1790,19 +1985,19 @@ code when using features from the INTEL package.
.. code-block:: make
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
For KNLs:
.. code-block:: make
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload -fno-alias -ansi-alias -restrict $(OPTFLAGS)
LINKFLAGS = -g -qopenmp $(OPTFLAGS)
LIB = -ltbbmalloc
In Long-range thread mode (LRT) a modified verlet style is used, that
operates the Kspace calculation in a separate thread concurrently to
@ -1831,7 +2026,8 @@ MDI package
.. code-block:: bash
-D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes
-D DOWNLOAD_MDI=value # download MDI Library for build
# value = no (default) or yes
.. tab:: Traditional make
@ -1860,7 +2056,8 @@ MOLFILE package
.. code-block:: bash
-D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile plugin headers are installed
-D MOLFILE_INCLUDE_DIR=path # (optional) path where VMD molfile
# plugin headers are installed
-D PKG_MOLFILE=yes
Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
@ -2019,10 +2216,17 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
.. 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
# print help message
make lib-qmmm
# build with GNU Fortran compiler (settings as in "make serial")
make lib-qmmm args="-m serial"
# build with default MPI compiler (settings as in "make mpi")
make lib-qmmm args="-m mpi"
# build with GNU Fortran compiler
make lib-qmmm args="-m gfortran"
The build should produce two files: ``lib/qmmm/libqmmm.a`` and
``lib/qmmm/Makefile.lammps``. The latter is copied from an
@ -2035,10 +2239,10 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
You can then install QMMM package and build LAMMPS in the usual
manner. After completing the LAMMPS build and compiling Quantum
ESPRESSO with external library support (via "make couple"), go
ESPRESSO with external library support (via ``make couple``), go
back to the ``lib/qmmm`` folder and follow the instructions in the
README file to build the combined LAMMPS/QE QM/MM executable
(pwqmmm.x) in the lib/qmmm folder.
(``pwqmmm.x``) in the ``lib/qmmm`` folder.
----------
@ -2108,11 +2312,16 @@ To build with this package, you must download and build the
.. code-block:: bash
make lib-scafacos # print help message
make lib-scafacos args="-b" # download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-p $HOME/scafacos # use existing ScaFaCoS installation in $HOME/scafacos
# print help message
make lib-scafacos
Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``, are
# download and build in lib/scafacos/scafacos-<version>
make lib-scafacos args="-b"
# use existing ScaFaCoS installation in $HOME/scafacos
make lib-scafacos args="-p $HOME/scafacos
Note that two symbolic (soft) links, ``includelink`` and ``liblink``, are
created in ``lib/scafacos`` to point to the ScaFaCoS src dir. When LAMMPS
builds in src it will use these links. You should not need to edit
the ``lib/scafacos/Makefile.lammps`` file.

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

2
doc/src/Build_make.rst
View File

@ -25,7 +25,7 @@ additional tools to be available and functioning.
require adding flags like ``-std=c++11`` to enable the C++11 mode.
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* Python (optional, required for ``make lib-<pkg>`` in the src
* Python (optional, required for ``make lib-<pkg>`` in the ``src``
folder). Python scripts are currently tested with python 2.7 and
3.6 to 3.11. The procedure for :doc:`building the documentation
<Build_manual>` *requires* Python 3.5 or later.

58
doc/src/Build_package.rst
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@ -100,10 +100,10 @@ versus make.
.. code-block:: bash
cd lammps/src
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed
make ps # check which packages are currently installed
make yes-name # install a package with name
make no-name # uninstall a package with name
make mpi # build LAMMPS with whatever packages are now installed
Examples:
@ -172,18 +172,41 @@ make a copy of one of them and modify it to suit your needs.
.. code-block:: bash
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake # enable just a few core packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake # enable most packages
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake # enable packages which download sources or potential files
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake # disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake # change settings to use the Clang compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake # change settings to use the GNU compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake # change settings to use the Intel compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake # change settings to use the PGI compilers by default
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS
# enable just a few core packages
cmake -C ../cmake/presets/basic.cmake [OPTIONS] ../cmake
# enable most packages
cmake -C ../cmake/presets/most.cmake [OPTIONS] ../cmake
# enable packages which download sources or potential files
cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake
# disable packages that do require extra libraries or tools
cmake -C ../cmake/presets/nolib.cmake [OPTIONS] ../cmake
# change settings to use the Clang compilers by default
cmake -C ../cmake/presets/clang.cmake [OPTIONS] ../cmake
# change settings to use the GNU compilers by default
cmake -C ../cmake/presets/gcc.cmake [OPTIONS] ../cmake
# change settings to use the Intel compilers by default
cmake -C ../cmake/presets/intel.cmake [OPTIONS] ../cmake
# change settings to use the PGI compilers by default
cmake -C ../cmake/presets/pgi.cmake [OPTIONS] ../cmake
# enable all packages
cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake
# disable all packages
cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake
# compile with MinGW cross-compilers
mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake
# compile serial multi-arch binaries on macOS
cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake
Presets that have names starting with "windows" are specifically for
compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@ -209,7 +232,8 @@ Example
# GPU package and configure it for using CUDA. You can run.
mkdir build
cd build
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
-D PKG_GPU=on -D GPU_API=cuda ../cmake
# to add another package, say BODY to the previous configuration you can run:
cmake -D PKG_BODY=on .

218
doc/src/Build_settings.rst
View File

@ -1,3 +1,7 @@
.. raw:: latex
\clearpage
Optional build settings
=======================
@ -8,7 +12,8 @@ explains how to do this for building both with CMake and make.
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
* `Size of LAMMPS integer types and size limits`_
* `Read or write compressed files`_
* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `Support for downloading files`_
* `Memory allocation alignment`_
* `Workaround for long long integers`_
* `Exception handling when using LAMMPS as a library`_ to capture errors
@ -19,7 +24,7 @@ explains how to do this for building both with CMake and make.
.. _cxx11:
C++11 standard compliance
------------------------------------------
-------------------------
A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
LAMMPS version 3 March 2020 is the last version compatible with the previous
@ -31,12 +36,16 @@ flags to enable C++11 compliance. Example for GNU c++ 4.8.x:
CCFLAGS = -g -O3 -std=c++11
Individual packages may require compliance with a later C++ standard
like C++14 or C++17. These requirements will be documented with the
:doc:`individual packages <Packages_details>`.
----------
.. _fft:
FFT library
---------------------
-----------
When the KSPACE package is included in a LAMMPS build, the
:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
@ -58,8 +67,10 @@ libraries and better pipelining for packing and communication.
.. code-block:: bash
-D FFT=value # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or KISS or CUFFT or HIPFFT, default is KISS
-D FFT=value # FFTW3 or MKL or NVPL or KISS,
# default is FFTW3 if found, else KISS
-D FFT_KOKKOS=value # FFTW3 or MKL or NVPL or KISS or CUFFT
# or HIPFFT or MKL_GPU, default is KISS
-D FFT_SINGLE=value # yes or no (default), no = double precision
-D FFT_PACK=value # array (default) or pointer or memcpy
-D FFT_USE_HEFFTE=value # yes or no (default), yes links to heFFTe
@ -67,11 +78,11 @@ libraries and better pipelining for packing and communication.
.. note::
When the Kokkos variant of a package is compiled and selected at run time,
the FFT library selected by the FFT_KOKKOS variable applies. Otherwise,
the FFT library selected by the ``FFT_KOKKOS`` variable applies. Otherwise,
the FFT library selected by the FFT variable applies.
The same FFT settings apply to both. FFT_KOKKOS must be compatible with the
The same FFT settings apply to both. ``FFT_KOKKOS`` must be compatible with the
Kokkos back end - for example, when using the CUDA back end of Kokkos,
you must use either CUFFT or KISS.
you must use either ``CUFFT`` or ``KISS``.
Usually these settings are all that is needed. If FFTW3 is
selected, then CMake will try to detect, if threaded FFTW
@ -89,8 +100,11 @@ libraries and better pipelining for packing and communication.
-D MKL_INCLUDE_DIR=path # ditto for Intel MKL library
-D FFT_MKL_THREADS=on # enable using threaded FFTs with MKL libraries
-D MKL_LIBRARY=path # path to MKL libraries
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock heFFTe back end
-D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
# heFFTe back end
-D Heffte_ROOT=path # path to an existing heFFTe installation
-D nvpl_fft_INCLUDE_DIR=path # path to NVPL FFT include files
-D nvpl_fft_LIBRARY_DIR=path # path to NVPL FFT libraries
.. note::
@ -108,30 +122,58 @@ libraries and better pipelining for packing and communication.
.. code-block:: make
FFT_INC = -DFFT_FFTW3 # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
# default is KISS if not specified
FFT_INC = -DFFT_KOKKOS_CUFFT # -DFFT_KOKKOS_{FFTW,FFTW3,MKL,CUFFT,HIPFFT,KISS}
# default is KISS if not specified
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT_PACK_ARRAY if not specified
FFT_INC = -DFFT_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), NVPL, or MKL
FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), NVPL, MKL, CUFFT,
# HIPFFT, or MKL_GPU
FFT_INC = -DFFT_SINGLE # do not specify for double precision
FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
FFT_INC = -DFFT_MKL_THREADS # enable using threaded FFTs with MKL libraries
FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
# default is FFT_PACK_ARRAY if not specified
.. code-block:: make
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
FFT_LIB = -lhipfft # hipFFT either precision
FFT_LIB = -lcufft # cuFFT either precision
FFT_LIB = -lfftw3 # FFTW3 double precision
FFT_LIB = -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler, serial interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compiler, serial interface
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core # MKL with GNU compiler, threaded interface
FFT_LIB = -lmkl_rt # MKL with automatic runtime selection of interface libs
FFT_INC = -I/usr/local/include
FFT_PATH = -L/usr/local/lib
# hipFFT either precision
FFT_LIB = -lhipfft
# cuFFT either precision
FFT_LIB = -lcufft
# MKL_GPU either precision
FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -lmkl_core -ltbb
# FFTW3 double precision
FFT_LIB = -lfftw3
# FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
FFT_LIB = -lfftw3 -lfftw3_omp
# FFTW3 single precision
FFT_LIB = -lfftw3 -lfftw3f
# serial MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
# serial MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
# threaded MKL with Intel compiler
FFT_LIB = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
# threaded MKL with GNU compiler
FFT_LIB = -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core
# MKL with automatic runtime selection of interface libs
FFT_LIB = -lmkl_rt
# threaded NVPL FFT
FFT_LIB = -lnvpl_fftw
As with CMake, you do not need to set paths in ``FFT_INC`` or
``FFT_PATH``, if the compiler can find the FFT header and library
@ -147,11 +189,11 @@ libraries and better pipelining for packing and communication.
FFT_PATH =
FFT_LIB = $(heffte_link) $(heffte_libs)
The heFFTe install path will contain `HeffteMakefile.in`.
which will define the `heffte_` include variables needed to link to heFFTe from
The heFFTe install path will contain ``HeffteMakefile.in``.
which will define the ``heffte_`` include variables needed to link to heFFTe from
an external project using traditional make.
The `-DFFT_HEFFTE` is required to switch to using heFFTe, while the optional `-DFFT_HEFFTE_FFTW`
selects the desired heFFTe back end, e.g., `-DFFT_HEFFTE_FFTW` or `-DFFT_HEFFTE_MKL`,
The ``-DFFT_HEFFTE`` is required to switch to using heFFTe, while the optional ``-DFFT_HEFFTE_FFTW``
selects the desired heFFTe back end, e.g., ``-DFFT_HEFFTE_FFTW`` or ``-DFFT_HEFFTE_MKL``,
omitting the variable will default to the `stock` back end.
The heFFTe `stock` back end is intended to be used for testing and debugging,
but is not performance optimized for large scale production runs.
@ -179,17 +221,22 @@ it from `www.fftw.org <https://www.fftw.org>`_. LAMMPS requires version
Building FFTW for your box should be as simple as ``./configure; make;
make install``. The install command typically requires root privileges
(e.g. invoke it via sudo), unless you specify a local directory with
the "--prefix" option of configure. Type ``./configure --help`` to see
the ``--prefix`` option of configure. Type ``./configure --help`` to see
various options.
The Intel MKL math library is part of the Intel compiler suite. It
can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
above).
The NVIDIA Performance Libraries (NVPL) FFT library is optimized for NVIDIA
Grace Armv9.0 architecture. You can download it from https://docs.nvidia.com/nvpl/
The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
AMD's HIP installations, respectively. These FFT libraries require the
Kokkos acceleration package to be enabled and the Kokkos back end to be
GPU-resident (i.e., HIP or CUDA).
GPU-resident (i.e., HIP or CUDA). Similarly, GPU offload of FFTs on
Intel GPUs with oneMKL currently requires the Kokkos acceleration
package to be enabled with the SYCL back end.
Performing 3d FFTs in parallel can be time-consuming due to data access
and required communication. This cost can be reduced by performing
@ -215,7 +262,7 @@ produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
Performing 3d FFTs requires communication to transpose the 3d FFT
grid. The data packing/unpacking for this can be done in one of 3
modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
modes (ARRAY, POINTER, MEMCPY) as set by the ``FFT_PACK`` syntax above.
Depending on the machine, the size of the FFT grid, the number of
processors used, one option may be slightly faster. The default is
ARRAY mode.
@ -232,6 +279,10 @@ and those variables will be passed into the heFFTe build.
----------
.. raw:: latex
\clearpage
.. _size:
Size of LAMMPS integer types and size limits
@ -272,7 +323,7 @@ LAMMPS system size restrictions
.. list-table::
:header-rows: 1
:widths: auto
:widths: 18 27 28 27
:align: center
* -
@ -341,8 +392,8 @@ in whichever ``lib/gpu/Makefile`` is used must be the same as above.
.. _graphics:
Output of JPG, PNG, and movie files
--------------------------------------------------
Output of JPEG, PNG, and movie files
------------------------------------
The :doc:`dump image <dump_image>` command has options to output JPEG or
PNG image files. Likewise, the :doc:`dump movie <dump_image>` command
@ -355,12 +406,13 @@ requires the following settings:
.. code-block:: bash
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB files, else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
-D WITH_JPEG=value # yes or no
# default = yes if CMake finds JPEG development files, else no
-D WITH_PNG=value # yes or no
# default = yes if CMake finds PNG and ZLIB development files,
# else no
-D WITH_FFMPEG=value # yes or no
# default = yes if CMake can find ffmpeg, else no
Usually these settings are all that is needed. If CMake cannot
find the graphics header, library, executable files, you can set
@ -382,8 +434,10 @@ requires the following settings:
LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG <other LMP_INC settings>
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
JPG_INC = -I/usr/local/include # path to jpeglib.h, png.h, zlib.h headers
# if make cannot find them
JPG_PATH = -L/usr/lib # paths to libjpeg.a, libpng.a, libz.a (.so)
# files if make cannot find them
JPG_LIB = -ljpeg -lpng -lz # library names
As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
@ -414,8 +468,8 @@ Read or write compressed files
If this option is enabled, large files can be read or written with
compression by ``gzip`` or similar tools by several LAMMPS commands,
including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
:doc:`dump <dump>`. Supported compression tools are currently
``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
:doc:`dump <dump>`. Supported compression tools and algorithms are currently
``gzip``, ``bzip2``, ``zstd``, ``xz``, ``lz4``, and ``lzma`` (via xz).
.. tabs::
@ -423,8 +477,8 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
.. code-block:: bash
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find the gzip program, else no
-D WITH_GZIP=value # yes or no
# default is yes if CMake can find the gzip program
.. tab:: Traditional make
@ -446,18 +500,64 @@ during a run.
available using a compression library instead, which is what the
:ref:`COMPRESS package <PKG-COMPRESS>` enables.
--------------------------------------------------
.. _libcurl:
Support for downloading files
-----------------------------
.. versionadded:: 29Aug2024
The :doc:`geturl command <geturl>` command uses the `the libcurl library
<https://curl.se/libcurl/>`_ to download files. This requires that
LAMMPS is compiled accordingly which needs the following settings:
.. tabs::
.. tab:: CMake build
.. code-block:: bash
-D WITH_CURL=value # yes or no
# default = yes if CMake finds CURL development files, else no
Usually these settings are all that is needed. If CMake cannot
find the graphics header, library, executable files, you can set
these variables:
.. code-block:: bash
-D CURL_INCLUDE_DIR=path # path to folder which contains curl.h header file
-D CURL_LIBRARY=path # path to libcurls.a (.so) file
.. tab:: Traditional make
.. code-block:: make
LMP_INC = -DLAMMPS_CURL <other LMP_INC settings>
CURL_INC = -I/usr/local/include # path to curl folder with curl.h
CURL_PATH = -L/usr/lib # paths to libcurl.a(.so) if make cannot find it
CURL_LIB = -lcurl # library names
As with CMake, you do not need to set ``CURL_INC`` or ``CURL_PATH``,
if make can find the libcurl header and library files in their
default system locations. You must specify ``CURL_LIB`` with a
paths or linker flags to link to libcurl.
----------
.. _align:
Memory allocation alignment
---------------------------------------
---------------------------
This setting enables the use of the "posix_memalign()" call instead of
"malloc()" when LAMMPS allocates large chunks of memory. Vector
This setting enables the use of the ``posix_memalign()`` call instead of
``malloc()`` when LAMMPS allocates large chunks of memory. Vector
instructions on CPUs may become more efficient, if dynamically allocated
memory is aligned on larger-than-default byte boundaries. On most
current operating systems, the "malloc()" implementation returns
current operating systems, the ``malloc()`` implementation returns
pointers that are aligned to 16-byte boundaries. Using SSE vector
instructions efficiently, however, requires memory blocks being aligned
on 64-byte boundaries.
@ -471,9 +571,9 @@ on 64-byte boundaries.
-D LAMMPS_MEMALIGN=value # 0, 8, 16, 32, 64 (default)
Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
"posix_memalign()" and revert to using the "malloc()" C-library
``posix_memalign()`` and revert to using the ``malloc()`` C-library
function instead. When compiling LAMMPS for Windows systems,
"malloc()" will always be used and this setting is ignored.
``malloc()`` will always be used and this setting is ignored.
.. tab:: Traditional make
@ -482,7 +582,7 @@ on 64-byte boundaries.
LMP_INC = -DLAMMPS_MEMALIGN=value # 8, 16, 32, 64
Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
allocated with the "malloc()" function call
allocated with the ``malloc()`` function call
instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
Windows different function calls with different semantics for
allocating aligned memory, that are not compatible with how LAMMPS

39
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@ -1,26 +1,30 @@
.. table_from_list::
:columns: 3
.. only:: html
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. table_from_list::
:columns: 5
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. raw:: latex
\clearpage
General commands
================
An alphabetic list of general LAMMPS commands. Note that style
commands with many variants, can be more easily accessed via the small
table above.
An alphabetic list of general LAMMPS commands.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`angle_coeff <angle_coeff>`
* :doc:`angle_style <angle_style>`
@ -54,6 +58,7 @@ table above.
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix_modify <fix_modify>`
* :doc:`geturl <geturl>`
* :doc:`group <group>`
* :doc:`if <if>`
* :doc:`improper_coeff <improper_coeff>`
@ -121,7 +126,7 @@ commands have accelerated versions. This is indicated by an
additional letter in parenthesis: k = KOKKOS.
.. table_from_list::
:columns: 5
:columns: 6
* :doc:`dynamical_matrix (k) <dynamical_matrix>`
* :doc:`group2ndx <group2ndx>`

54
doc/src/Commands_bond.rst
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@ -1,21 +1,7 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
.. _bond:
Bond_style potentials
=====================
Bond styles
===========
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -23,7 +9,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
@ -33,6 +19,8 @@ OPT.
*
*
*
*
*
* :doc:`bpm/rotational <bond_bpm_rotational>`
* :doc:`bpm/spring <bond_bpm_spring>`
* :doc:`class2 (ko) <bond_class2>`
@ -60,8 +48,8 @@ OPT.
.. _angle:
Angle_style potentials
======================
Angle styles
============
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -69,11 +57,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid <angle_hybrid>`
* :doc:`hybrid (k) <angle_hybrid>`
*
*
*
*
*
@ -101,13 +91,13 @@ OPT.
* :doc:`mesocnt <angle_mesocnt>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`spica (o) <angle_spica>`
* :doc:`spica (ko) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
Dihedral_style potentials
=========================
Dihedral styles
===============
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -115,11 +105,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <dihedral_none>`
* :doc:`zero <dihedral_zero>`
* :doc:`hybrid <dihedral_hybrid>`
* :doc:`hybrid (k) <dihedral_hybrid>`
*
*
*
*
*
@ -144,8 +136,8 @@ OPT.
.. _improper:
Improper_style potentials
=========================
Improper styles
===============
All LAMMPS :doc:`improper_style <improper_style>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -153,11 +145,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <improper_none>`
* :doc:`zero <improper_zero>`
* :doc:`hybrid <improper_hybrid>`
* :doc:`hybrid (k) <improper_hybrid>`
*
*
*
*
*

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

20
doc/src/Commands_compute.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Compute commands
================
Compute styles
==============
An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
Some styles have accelerated versions. This is indicated by
@ -21,7 +7,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k =
KOKKOS, o = OPENMP, t = OPT.
.. table_from_list::
:columns: 5
:columns: 4
* :doc:`ackland/atom <compute_ackland_atom>`
* :doc:`adf <compute_adf>`

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

20
doc/src/Commands_fix.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============
Fix styles
==========
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -21,7 +7,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 5
:columns: 4
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`

16
doc/src/Commands_input.rst
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@ -10,14 +10,14 @@ for any commands that may be processed later. Commands may set an
internal variable, read in a file, or run a simulation. These actions
can be grouped into three categories:
a) commands that change a global setting (examples: timestep, newton,
echo, log, thermo, restart),
a) commands that change a global setting (examples: :doc:`timestep <timestep>`, :doc:`newton <newton>`,
:doc:`echo <echo>`, :doc:`log <log>`, :doc:`thermo <thermo>`, :doc:`restart <restart>`),
b) commands that add, modify, remove, or replace "styles" that are
executed during a "run" (examples: pair_style, fix, compute, dump,
thermo_style, pair_modify), and
executed during a "run" (examples: :doc:`pair_style <pair_style>`, :doc:`fix <fix>`, :doc:`compute <compute>`, :doc:`dump <dump>`,
:doc:`thermo_style <thermo_style>`, :doc:`pair_modify <pair_modify>`), and
c) commands that execute a "run" or perform some other computation or
operation (examples: print, run, minimize, temper, write_dump, rerun,
read_data, read_restart)
operation (examples: :doc:`print <print>`, :doc:`run <run>`, :doc:`minimize <minimize>`, :doc:`temper <temper>`, :doc:`write_dump <write_dump>`, :doc:`rerun <rerun>`,
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`)
Commands in category a) have default settings, which means you only
need to use the command if you wish to change the defaults.
@ -61,7 +61,7 @@ between commands in the c) category. The following rules apply:
<read_data>` command initializes the system by setting up the
simulation box and assigning atoms to processors. If default values
are not desired, the :doc:`processors <processors>` and
:doc:`boundary <boundary>` commands need to be used before read_data
:doc:`boundary <boundary>` commands need to be used before ``read_data``
to tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
@ -70,6 +70,6 @@ more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
You can use the :ref:`-skiprun <skiprun>` command line flag
to have LAMMPS skip the execution of any "run", "minimize", or similar
to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar
commands to check the entire input for correct syntax to avoid crashes
on typos or syntax errors in long runs.

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

26
doc/src/Commands_pair.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
Pair styles
===========
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -21,7 +7,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 3
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
@ -35,10 +21,6 @@ OPT.
*
*
*
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -195,7 +177,7 @@ OPT.
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/long (gko) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`

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

2
doc/src/Commands_removed.rst
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@ -171,7 +171,7 @@ instructions to install i-PI from PyPI via pip are provided.
LAMMPS shell
------------
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.

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

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

9
doc/src/Developer_code_design.rst
View File

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

2
doc/src/Developer_flow.rst
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@ -128,7 +128,7 @@ reflect particles off box boundaries in the :doc:`FixWallReflect class
The ``decide()`` method in the Neighbor class determines whether
neighbor lists need to be rebuilt on the current timestep (conditions
can be changed using the :doc:`neigh_modify every/delay/check
<neigh_modify>` command. If not, coordinates of ghost atoms are
<neigh_modify>` command). If not, coordinates of ghost atoms are
acquired by each processor via the ``forward_comm()`` method of the Comm
class. If neighbor lists need to be built, several operations within
the inner if clause of the pseudocode are first invoked. The

2
doc/src/Developer_grid.rst
View File

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

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

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

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

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

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

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

31
doc/src/Developer_unittest.rst
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@ -44,7 +44,7 @@ available:
.. list-table::
:header-rows: 1
:widths: auto
:widths: 32 18 50
:align: left
* - File name:
@ -227,12 +227,12 @@ Tests for the C-style library interface
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tests for validating the LAMMPS C-style library interface are in the
``unittest/c-library`` folder. They are implemented in either way used
for utility functions and for LAMMPS commands, but use the functions
``unittest/c-library`` folder. They are implemented either to be used
for utility functions or for LAMMPS commands, but use the functions
implemented in the ``src/library.cpp`` file as much as possible. There
may be some overlap with other tests, but only in as much as is required
to test the C-style library API. The tests are distributed over
multiple test programs which tries to match the grouping of the
multiple test programs which try to match the grouping of the
functions in the source code and :ref:`in the manual <lammps_c_api>`.
This group of tests also includes tests invoking LAMMPS in parallel
@ -258,7 +258,7 @@ Tests for the Python module and package
The ``unittest/python`` folder contains primarily tests for classes and
functions in the LAMMPS python module but also for commands in the
PYTHON package. These tests are only enabled, if the necessary
PYTHON package. These tests are only enabled if the necessary
prerequisites are detected or enabled during configuration and
compilation of LAMMPS (shared library build enabled, Python interpreter
found, Python development files found).
@ -272,7 +272,7 @@ Tests for the Fortran interface
Tests for using the Fortran module are in the ``unittest/fortran``
folder. Since they are also using the GoogleTest library, they require
to also implement test wrappers in C++ that will call fortran functions
implementing test wrappers in C++ that will call fortran functions
which provide a C function interface through ISO_C_BINDINGS that will in
turn call the functions in the LAMMPS Fortran module.
@ -293,7 +293,7 @@ The ``unittest/formats`` folder contains test programs for reading and
writing files like data files, restart files, potential files or dump files.
This covers simple things like the file i/o convenience functions in the
``utils::`` namespace to complex tests of atom styles where creating and
deleting of atoms with different properties is tested in different ways
deleting atoms with different properties is tested in different ways
and through script commands or reading and writing of data or restart files.
Tests for styles computing or modifying forces
@ -411,7 +411,7 @@ With this scheme a large fraction of the code of any tested pair style
will be executed and consistent results are required for different
settings and between different accelerated pair style variants and the
base class, as well as for computing individual pairs through the
``Pair::single()`` where supported.
``Pair::single()`` method where supported.
The ``test_pair_style`` tester is used with 4 categories of test inputs:
@ -443,7 +443,7 @@ file for a style that is similar to one to be tested. The file name should
follow the naming conventions described above and after copying the file,
the first step is to replace the style names where needed. The coefficient
values do not have to be meaningful, just in a reasonable range for the
given system. It does not matter if some forces are large, for as long as
given system. It does not matter if some forces are large, as long as
they do not diverge.
The template input files define a large number of index variables at the top
@ -535,7 +535,7 @@ The are by default no unit tests for newly added features (e.g. pair, fix,
or compute styles) unless your pull request also includes tests for the
added features. If you are modifying some features, you may see failures
for existing tests, if your modifications have some unexpected side effects
or your changes render the existing text invalid. If you are adding an
or your changes render the existing test invalid. If you are adding an
accelerated version of an existing style, then only tests for INTEL,
KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
Tests for the GPU package are time consuming and thus are only run
@ -543,7 +543,7 @@ Tests for the GPU package are time consuming and thus are only run
to the pull request. After the test has started, it is often best to
remove the label since every PR activity will re-trigger the test (that
is a limitation of triggering a test with a label). Support for unit
tests with using KOKKOS with GPU acceleration is currently not supported.
tests when using KOKKOS with GPU acceleration is currently not supported.
When you see a failed build on GitHub, click on ``Details`` to be taken
to the corresponding LAMMPS Jenkins CI web page. Click on the "Exit"
@ -589,11 +589,10 @@ While the epsilon (relative precision) for a single, `IEEE 754 compliant
point operation is at about 2.2e-16, the achievable precision for the
tests is lower due to most numbers being sums over intermediate results
and the non-associativity of floating point math leading to larger
errors. In some cases specific properties of the tested style. As a
rule of thumb, the test epsilon can often be in the range 5.0e-14 to
1.0e-13. But for "noisy" force kernels, e.g. those a larger amount of
arithmetic operations involving `exp()`, `log()` or `sin()` functions,
and also due to the effect of compiler optimization or differences
errors. As a rule of thumb, the test epsilon can often be in the range
5.0e-14 to 1.0e-13. But for "noisy" force kernels, e.g. those a larger
amount of arithmetic operations involving `exp()`, `log()` or `sin()`
functions, and also due to the effect of compiler optimization or differences
between compilers or platforms, epsilon may need to be further relaxed,
sometimes epsilon can be relaxed to 1.0e-12. If interpolation or lookup
tables are used, epsilon may need to be set to 1.0e-10 or even higher.

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

2
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@ -622,7 +622,7 @@ classes:
of a dense, symmetric, real matrix.
#. The "PEigenDense" class only calculates the principal eigenvalue
(ie. the largest or smallest eigenvalue), and its corresponding
(i.e. the largest or smallest eigenvalue), and its corresponding
eigenvector. However it is much more efficient than "Jacobi" when
applied to large matrices (larger than 13x13). PEigenDense also can
understand complex-valued Hermitian matrices.

1
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@ -12,3 +12,4 @@ details are provided for writing code for LAMMPS.
Developer_write_pair
Developer_write_fix
Developer_write_command

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

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

35
doc/src/Developer_write_pair.rst
View File

@ -160,7 +160,7 @@ message and before the include guards for the class definition:
#endif
This block of between ``#ifdef PAIR_CLASS`` and ``#else`` will be
This block between ``#ifdef PAIR_CLASS`` and ``#else`` will be
included by the ``Force`` class in ``force.cpp`` to build a map of
"factory functions" that will create an instance of these classes and
return a pointer to it. The map connects the name of the pair style,
@ -371,9 +371,9 @@ but moving this to a separate function allows users to change global
settings like the default cutoff without having to reissue all
pair_coeff commands or re-read the ``Pair Coeffs`` sections from the
data file. In the ``settings()`` function, also the arrays for storing
parameters, to define cutoffs, track with pairs of parameters have been
explicitly set are allocated and, if needed, initialized. In this case,
the memory allocation and initialization is moved to a function
parameters, to define cutoffs, track which pairs of parameters have been
explicitly set and allocated and, if needed, initialized. In this case,
the memory allocation and initialization are moved to a function
``allocate()``.
.. code-block:: c++
@ -588,17 +588,20 @@ loop atoms are also initialized.
jnum = numneigh[i];
The inner loop (index *j*) processes the neighbor lists. The neighbor
list code encodes in the upper 2 bits whether a pair is a regular pair
of neighbor (= 0) or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3)
:doc:`"special" neighbor <special_bonds>`. The ``sbmask()`` inline
function extracts those bits and converts them into a number. This
number is used to look up the corresponding scaling factor for the
non-bonded interaction from the ``force->special_lj`` array and stores
it in the `factor_lj` variable. Due to the additional bits, the value
of *j* would be out of range when accessing data from per-atom arrays,
so we apply the NEIGHMASK constant with a bit-wise and operation to mask
them out. This step *must* be done, even if a pair style does not use
special bond scaling of forces and energies to avoid segmentation faults.
list code encodes extra information using the upper 3 bits. The 2
highest bits encode whether a pair is a regular pair of neighbor (= 0)
or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3) :doc:`"special" neighbor
<special_bonds>`. The next highest bit encodes whether the pair stores
data in a ``fix neigh/history`` instance (an undocumented internal fix
style). The ``sbmask()`` inline function extracts those bits and
converts them into a number. This number is used to look up the
corresponding scaling factor for the non-bonded interaction from the
``force->special_lj`` array and stores it in the `factor_lj` variable.
Due to the additional bits, the value of *j* would be out of range when
accessing data from per-atom arrays, so we apply the NEIGHMASK constant
with a bit-wise and operation to mask them out. This step *must* be
done, even if a pair style does not use special bond scaling of forces
and energies to avoid segmentation faults.
With the corrected *j* index, it is now possible to compute the distance
of the pair. For efficiency reasons, the square root is only taken
@ -891,7 +894,7 @@ through *multiple* :doc:`pair_coeff commands <pair_coeff>`. Pair styles
that require a single "pair_coeff \* \*" command line are not compatible
with reading their parameters from data files. For pair styles like
*born/gauss* that do support writing to data files, the potential
parameters will be read from the data file, if present and
parameters will be read from the data file, if present, and
:doc:`pair_coeff commands <pair_coeff>` may not be needed.
The member variable ``writedata`` should be set to 1 in the constructor,

3
doc/src/Errors_common.rst
View File

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

22
doc/src/Errors_messages.rst
View File

@ -96,13 +96,13 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
are too far apart to make a valid angle.
*Angle atoms %d %d %d missing on proc %d at step %ld*
One or more of 3 atoms needed to compute a particular angle are
One or more of three atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
*Angle atoms missing on proc %d at step %ld*
One or more of 3 atoms needed to compute a particular angle are
One or more of three atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
@ -1932,7 +1932,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Self-explanatory.
*Compute chunk/atom fix array is accessed out-of-range*
the index for the array is out of bounds.
The index for the array is out of bounds.
*Compute chunk/atom fix does not calculate a per-atom array*
Self-explanatory.
@ -6073,9 +6073,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*New atom IDs exceed maximum allowed ID*
See the setting for tagint in the src/lmptype.h file.
*New bond exceeded bonds per atom in create_bonds*
See the read_data command for info on using the "extra/bond/per/atom"
keyword to allow for additional bonds to be formed
*New bond exceeded bonds per atom in create\_bonds*
See the read_data command for info on using the "extra/bond/per/atom"
keyword to allow for additional bonds to be formed
*New bond exceeded bonds per atom in fix bond/create*
See the read_data command for info on using the "extra/bond/per/atom"
@ -7310,12 +7310,12 @@ keyword to allow for additional bonds to be formed
atom has moved too far.
*Restrain atoms %d %d %d missing on proc %d at step %ld*
The 3 atoms in a restrain angle specified by the fix restrain
The three atoms in a restrain angle specified by the fix restrain
command are not all accessible to a processor. This probably means an
atom has moved too far.
*Restrain atoms %d %d missing on proc %d at step %ld*
The 2 atoms in a restrain bond specified by the fix restrain
The two atoms in a restrain bond specified by the fix restrain
command are not all accessible to a processor. This probably means an
atom has moved too far.
@ -7406,7 +7406,7 @@ keyword to allow for additional bonds to be formed
*Shake angles have different bond types*
All 3-atom angle-constrained SHAKE clusters specified by the fix shake
command that are the same angle type, must also have the same bond
types for the 2 bonds in the angle.
types for the two bonds in the angle.
*Shake atoms %d %d %d %d missing on proc %d at step %ld*
The 4 atoms in a single shake cluster specified by the fix shake
@ -7414,12 +7414,12 @@ keyword to allow for additional bonds to be formed
an atom has moved too far.
*Shake atoms %d %d %d missing on proc %d at step %ld*
The 3 atoms in a single shake cluster specified by the fix shake
The three atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.
*Shake atoms %d %d missing on proc %d at step %ld*
The 2 atoms in a single shake cluster specified by the fix shake
The two atoms in a single shake cluster specified by the fix shake
command are not all accessible to a processor. This probably means
an atom has moved too far.

6
doc/src/Errors_warnings.rst
View File

@ -23,7 +23,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
adjusted to match the user-specified accuracy.
*Angle atoms missing at step %ld*
One or more of 3 atoms needed to compute a particular angle are
One or more of three atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
@ -233,7 +233,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
style.
*Fix langevin gjf using random gaussians is not implemented with kokkos*
This will most likely cause errors in kinetic fluctuations.
This will most likely cause errors in kinetic fluctuations.
*Fix property/atom mol or charge w/out ghost communication*
A model typically needs these properties defined for ghost atoms.
@ -324,7 +324,7 @@ This will most likely cause errors in kinetic fluctuations.
Specifically they are further apart than half a periodic box length.
Or they are more than a box length apart in a non-periodic dimension.
This is usually due to the initial data file not having correct image
flags for the 2 atoms in a bond that straddles a periodic boundary.
flags for the two atoms in a bond that straddles a periodic boundary.
They should be different by 1 in that case. This is a warning because
inconsistent image flags will not cause problems for dynamics or most
LAMMPS simulations. However they can cause problems when such atoms

4
doc/src/Fortran.rst
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@ -1077,7 +1077,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. list-table::
:header-rows: 1
:widths: auto
:widths: 21 20 40 19
* - Style
- Type
@ -1167,7 +1167,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. list-table::
:header-rows: 1
:widths: auto
:widths: 20 19 11 11 21 18
* - Style
- Type

4
doc/src/Howto_bioFF.rst
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@ -43,7 +43,7 @@ have potential energy function of the form
}} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}
The terms are computed by bond styles (relationship between 2 atoms),
The terms are computed by bond styles (relationship between two atoms),
angle styles (between 3 atoms) , dihedral/improper styles (between 4
atoms), pair styles (non-covalently bonded pair interactions) and
special bonds. The CMAP term (see :doc:`fix cmap <fix_cmap>` command for
@ -73,7 +73,7 @@ with additional switching or shifting functions that ramp the energy
and/or force smoothly to zero between an inner :math:`(a)` and outer
:math:`(b)` cutoff. The older styles with *charmm* (not *charmmfsw* or
*charmmfsh*\ ) in their name compute the LJ and Coulombic interactions
with an energy switching function (esw) S(r) which ramps the energy
with an energy switching function (esw) :math:`S(r)` which ramps the energy
smoothly to zero between the inner and outer cutoff. This can cause
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which

2
doc/src/Howto_bpm.rst
View File

@ -17,6 +17,8 @@ producing fracture. The examples/bpm directory has sample input scripts
for simulations of the fragmentation of an impacted plate and the
pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
for more general information on the approach and the LAMMPS implementation.
Example movies illustrating some of these capabilities are found at
https://www.lammps.org/movies.html#bpmpackage.
----------

2
doc/src/Howto_cmake.rst
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@ -348,7 +348,7 @@ Some common LAMMPS specific variables
* - ``FFT``
- select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
* - ``FFT_KOKKOS``
- select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default)
- select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``MKL_GPU``, ``KISS`` (default)
* - ``FFT_SINGLE``
- select whether to use single precision FFTs (default: ``off``)
* - ``WITH_JPEG``

2
doc/src/Howto_coreshell.rst
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@ -178,7 +178,7 @@ the pairs. This can be done by using the *bias* keyword of the
To maintain the correct polarizability of the core/shell pairs, the
kinetic energy of the internal motion shall remain nearly constant.
Therefore the choice of spring force and mass ratio need to ensure
much faster relative motion of the 2 atoms within the core/shell pair
much faster relative motion of the two atoms within the core/shell pair
than their center-of-mass velocity. This allows the shells to
effectively react instantaneously to the electrostatic environment and
limits energy transfer to or from the core/shell oscillators.

2
doc/src/Howto_couple.rst
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@ -36,7 +36,7 @@ the context of your application.
steps, invoke the command, etc.
In this scenario, the other code can be called as a library, as in
1., or it could be a stand-alone code, invoked by a system() call
1., or it could be a stand-alone code, invoked by a ``system()`` call
made by the command (assuming your parallel machine allows one or
more processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS through files that the

8
doc/src/Howto_diffusion.rst
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@ -1,8 +1,8 @@
Calculate diffusion coefficients
================================
The diffusion coefficient D of a material can be measured in at least
2 ways using various options in LAMMPS. See the examples/DIFFUSE
The diffusion coefficient :math:`D` of a material can be measured in at least
2 ways using various options in LAMMPS. See the ``examples/DIFFUSE``
directory for scripts that implement the 2 methods discussed here for
a simple Lennard-Jones fluid model.
@ -12,7 +12,7 @@ of the MSD versus time is proportional to the diffusion coefficient.
The instantaneous MSD values can be accumulated in a vector via the
:doc:`fix vector <fix_vector>` command, and a line fit to the vector to
compute its slope via the :doc:`variable slope <variable>` function, and
thus extract D.
thus extract :math:`D`.
The second method is to measure the velocity auto-correlation function
(VACF) of the system, via the :doc:`compute vacf <compute_vacf>`
@ -20,4 +20,4 @@ command. The time-integral of the VACF is proportional to the
diffusion coefficient. The instantaneous VACF values can be
accumulated in a vector via the :doc:`fix vector <fix_vector>` command,
and time integrated via the :doc:`variable trap <variable>` function,
and thus extract D.
and thus extract :math:`D`.

30
doc/src/Howto_elastic.rst
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@ -4,21 +4,27 @@ Calculate elastic constants
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
stress and strain tensors in the limit of infinitesimal deformation.
In tensor notation, this is expressed as s_ij = C_ijkl \* e_kl, where
the repeated indices imply summation. s_ij are the elements of the
symmetric stress tensor. e_kl are the elements of the symmetric strain
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has 3\^4=81 elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
most 7\*6/2 = 21 distinct elements.
In tensor notation, this is expressed as
.. math::
s_{ij} = C_{ijkl} e_{kl}
where
the repeated indices imply summation. :math:`s_{ij}` are the elements of the
symmetric stress tensor. :math:`e_{kl}` are the elements of the symmetric strain
tensor. :math:`C_{ijkl}` are the elements of the fourth rank tensor of elastic
constants. In three dimensions, this tensor has :math:`3^4=81` elements. Using
Voigt notation, the tensor can be written as a 6x6 matrix, where :math:`C_{ij}`
is now the derivative of :math:`s_i` w.r.t. :math:`e_j`. Because :math:`s_i` is itself a
derivative w.r.t. :math:`e_i`, it follows that :math:`C_{ij}` is also symmetric, with at
most :math:`\frac{7 \times 6}{2}` = 21 distinct elements.
At zero temperature, it is easy to estimate these derivatives by
deforming the simulation box in one of the six directions using the
:doc:`change_box <change_box>` command and measuring the change in the
stress tensor. A general-purpose script that does this is given in the
examples/ELASTIC directory described on the :doc:`Examples <Examples>`
``examples/ELASTIC`` directory described on the :doc:`Examples <Examples>`
doc page.
Calculating elastic constants at finite temperature is more
@ -33,7 +39,7 @@ the :doc:`compute born/matrix <compute_born_matrix>` command,
which works for any bonded or non-bonded potential in LAMMPS.
The most expensive part of the calculation is the sampling of
the stress fluctuations. Several examples of this method are
provided in the examples/ELASTIC_T/BORN_MATRIX directory
provided in the ``examples/ELASTIC_T/BORN_MATRIX`` directory
described on the :doc:`Examples <Examples>` doc page.
A second way is to measure
@ -43,7 +49,7 @@ the systematic and statistical errors in this method, the magnitude of
the deformation must be chosen judiciously, and care must be taken to
fully equilibrate the deformed cell before sampling the stress
tensor. An example of this method is provided in the
examples/ELASTIC_T/DEFORMATION directory
``examples/ELASTIC_T/DEFORMATION`` directory
described on the :doc:`Examples <Examples>` doc page.
Another approach is to sample the triclinic cell fluctuations

16
doc/src/Howto_kappa.rst
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@ -1,20 +1,22 @@
Calculate thermal conductivity
==============================
The thermal conductivity kappa of a material can be measured in at
least 4 ways using various options in LAMMPS. See the examples/KAPPA
The thermal conductivity :math:`\kappa` of a material can be measured in at
least 4 ways using various options in LAMMPS. See the ``examples/KAPPA``
directory for scripts that implement the 4 methods discussed here for
a simple Lennard-Jones fluid model. Also, see the :doc:`Howto viscosity <Howto_viscosity>` page for an analogous discussion
for viscosity.
The thermal conductivity tensor kappa is a measure of the propensity
The thermal conductivity tensor :math:`\mathbf{\kappa}` is a measure of the propensity
of a material to transmit heat energy in a diffusive manner as given
by Fourier's law
J = -kappa grad(T)
.. math::
where J is the heat flux in units of energy per area per time and
grad(T) is the spatial gradient of temperature. The thermal
J = -\kappa \cdot \text{grad}(T)
where :math:`J` is the heat flux in units of energy per area per time and
:math:`\text{grad}(T)` is the spatial gradient of temperature. The thermal
conductivity thus has units of energy per distance per time per degree
K and is often approximated as an isotropic quantity, i.e. as a
scalar.
@ -49,7 +51,7 @@ details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the heat flux
to kappa. The heat flux can be calculated from the fluctuations of
to :math:`\kappa`. The heat flux can be calculated from the fluctuations of
per-atom potential and kinetic energies and per-atom stress tensor in
a steady-state equilibrated simulation. This is in contrast to the
two preceding non-equilibrium methods, where energy flows continuously

549
doc/src/Howto_lammps_gui.rst
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@ -1,5 +1,5 @@
Using the LAMMPS-GUI
====================
Using LAMMPS-GUI
================
This document describes **LAMMPS-GUI version 1.6**.
@ -16,54 +16,127 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
.. note::
Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux (Ubuntu
20.04LTS or later and compatible), macOS (version 11 aka Big Sur or
later), and Windows (version 10 or later) :ref:`are available
<lammps_gui_install>` for download. None-MPI LAMMPS executables of
the same LAMMPS version are included in these packages as well. The
source code for the LAMMPS-GUI is included in the LAMMPS source code
Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
(Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
Sur or later), and Windows (version 10 or later) :ref:`are available
<lammps_gui_install>` for download. Non-MPI LAMMPS executables (as
``lmp``) for running LAMMPS from the command line and :doc:`some
LAMMPS tools <Tools>` compiled executables are also included.
The source code for LAMMPS-GUI is included in the LAMMPS source code
distribution and can be found in the ``tools/lammps-gui`` folder. It
can be compiled alongside LAMMPS when :doc:`compiling with CMake
<Build_cmake>`.
LAMMPS-GUI tries to provide an experience similar to what people
traditionally would do to run LAMMPS using a command line window
but just rolled into a single executable:
traditionally would have running LAMMPS using a command line window and
the console LAMMPS executable but just rolled into a single executable:
- editing LAMMPS input files with a text editor
- writing & editing LAMMPS input files with a text editor
- run LAMMPS on those input file with selected command line flags
- use or extract data from the created files and visualize it with
either a molecular visualization program or a plotting program
- extract data from the created files and visualize it with and
external software
That procedure is quite effective for people proficient in using the
command line, as that allows them to use tools for the individual steps
that they are most comfortable with. It is often *required* to adopt
this workflow when running LAMMPS simulations on high-performance
that they are most comfortable with. In fact, it is often *required* to
adopt this workflow when running LAMMPS simulations on high-performance
computing facilities.
The main benefit of using the LAMMPS-GUI application instead is that
many basic tasks can be done directly from the GUI without switching to
a text console window or using external programs, let alone writing
scripts to extract data from the generated output. It also integrates
well with graphical desktop environments.
The main benefit of using LAMMPS-GUI is that many basic tasks can be
done directly from the GUI **without** switching to a text console
window or using external programs, let alone writing scripts to extract
data from the generated output. It also integrates well with graphical
desktop environments where the `.lmp` filename extension can be
registered with LAMMPS-GUI as the executable to launch when double
clicking on such files. Also, LAMMPS-GUI has support for drag-n-drop,
i.e. an input file can be selected and then moved and dropped on the
LAMMPS-GUI executable, and LAMMPS-GUI will launch and read the file into
its buffer. In many cases LAMMPS-GUI will be integrated into the
graphical desktop environment and can be launched like other
applications.
LAMMPS-GUI thus makes it easier for beginners to get started running
simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
since you only need to learn how to use a single program for most tasks
and thus time can be saved and people can focus on learning LAMMPS. It
is also designed to keep the barrier low when you decide to switch to a
full featured, standalone programming editor and more sophisticated
visualization and analysis tools, and run LAMMPS from the command line
or a batch script.
and thus time can be saved and people can focus on learning LAMMPS.
The tutorials at https://lammpstutorials.github.io/ are specifically
updated for use with LAMMPS-GUI.
Another design goal is to keep the barrier low when replacing part of
the functionality of LAMMPS-GUI with external tools. That said, LAMMPS-GUI
has some unique functionality that is not found elsewhere:
- auto-adapting to features available in the integrated LAMMPS library
- interactive visualization using the :doc:`dump image <dump_image>`
command with the option to copy-paste the resulting settings
- automatic slide show generation from dump image out at runtime
- automatic plotting of thermodynamics data at runtime
- inspection of binary restart files
The following text provides a detailed tour of the features and
functionality of the LAMMPS-GUI. Suggestions for new features and
functionality of LAMMPS-GUI. Suggestions for new features and
reports of bugs are always welcome. You can use the :doc:`the same
channels as for LAMMPS itself <Errors_bugs>` for that purpose.
-----
Installing Pre-compiled LAMMPS-GUI Packages
-------------------------------------------
LAMMPS-GUI is available as pre-compiled binary packages for Linux
x86\_64, macOS 11 and later, and Windows 10 and later. Alternately, it
can be compiled from source.
Windows 10 and later
^^^^^^^^^^^^^^^^^^^^
After downloading the ``LAMMPS-Win10-64bit-GUI-<version>.exe`` installer
package, you need to execute it, and start the installation process.
Since those packages are currently unsigned, you have to enable "Developer Mode"
in the Windows System Settings to run the installer.
MacOS 11 and later
^^^^^^^^^^^^^^^^^^
After downloading the ``LAMMPS-macOS-multiarch-GUI-<version>.dmg``
installer package, you need to double-click it and then, in the window
that opens, drag the app bundle as indicated into the "Applications"
folder. The follow the instructions in the "README.txt" file to
get access to the other included executables.
Linux on x86\_64
^^^^^^^^^^^^^^^^
For Linux with x86\_64 CPU there are currently two variants. The first
is compiled on Ubuntu 20.04LTS, is using some wrapper scripts, and
should be compatible with more recent Linux distributions. After
downloading and unpacking the
``LAMMPS-Linux-x86_64-GUI-<version>.tar.gz`` package. You can switch
into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly.
The second variant uses `flatpak <https://www.flatpak.org>`_ and
requires the flatpak management and runtime software to be installed.
After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``
flatpak bundle, you can install it with ``flatpak install --user
LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``. After installation,
LAMMPS-GUI should be integrated into your desktop environment under
"Applications > Science" but also can be launched from the console with
``flatpak run org.lammps.lammps-gui``. The flatpak bundle also includes
the console LAMMPS executable ``lmp`` which can be launched to run
simulations with, for example: ``flatpak run --command=lmp
org.lammps.lammps-gui -in in.melt``.
Compiling from Source
^^^^^^^^^^^^^^^^^^^^^
There also are instructions for :ref:`compiling LAMMPS-GUI from source
code <lammps_gui_compilation>` available elsewhere in the manual.
Compilation from source *requires* using CMake.
-----
Starting LAMMPS-GUI
-------------------
@ -71,9 +144,13 @@ When LAMMPS-GUI starts, it shows the main window, labeled *Editor*, with
either an empty buffer or the contents of the file used as argument. In
the latter case it may look like the following:
.. image:: JPG/lammps-gui-main.png
:align: center
:scale: 50%
.. |gui-main1| image:: JPG/lammps-gui-main.png
:width: 48%
.. |gui-main2| image:: JPG/lammps-gui-dark.png
:width: 48%
|gui-main1| |gui-main2|
There is the typical menu bar at the top, then the main editor buffer,
and a status bar at the bottom. The input file contents are shown
@ -88,23 +165,30 @@ window is stored when exiting and restored when starting again.
Opening Files
^^^^^^^^^^^^^
The LAMMPS-GUI application tries to open the first command line argument
as a LAMMPS input script, further arguments are ignored. When no
argument is given, LAMMPS-GUI starts with an empty buffer. Files can
also be opened via the ``File`` menu or by drag-and-drop of a file from
a graphical file manager into the editor window. Only one file can be
edited at a time, so opening a new file with a filled buffer closes that
buffer. If the buffer has unsaved modifications, you are asked to
either cancel the operation, discard the changes, or save them. A
buffer with modifications can be saved any time from the "File" menu, by
the keyboard shortcut `Ctrl-S` (`Command-S` on macOS), or by clicking on
the "Save" button at the very left in the status bar.
The LAMMPS-GUI application can be launched without command line arguments
and then starts with an empty buffer in the *Editor* window. If arguments
are given LAMMPS will use first command line argument as the file name for
the *Editor* buffer and reads its contents into the buffer, if the file
exists. All further arguments are ignored. Files can also be opened via
the *File* menu, the `Ctrl-O` (`Command-O` on macOS) keyboard shortcut
or by drag-and-drop of a file from a graphical file manager into the editor
window. If a file extension (e.g. ``.lmp``) has been registered with the
graphical environment to launch LAMMPS-GUI, an existing input file can
be launched with LAMMPS-GUI through double clicking.
Only one file can be edited at a time, so opening a new file with a
filled buffer closes that buffer. If the buffer has unsaved
modifications, you are asked to either cancel the operation, discard the
changes, or save them. A buffer with modifications can be saved any
time from the "File" menu, by the keyboard shortcut `Ctrl-S`
(`Command-S` on macOS), or by clicking on the "Save" button at the very
left in the status bar.
Running LAMMPS
^^^^^^^^^^^^^^
From within the LAMMPS-GUI main window LAMMPS can be started either from
the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by
the *Run* menu using the *Run LAMMPS from Editor Buffer* entry, by
the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by
clicking on the green "Run" button in the status bar. All of these
operations causes LAMMPS to process the entire input script in the
@ -119,7 +203,7 @@ using the contents of the input buffer for the run (via the
interface), and **not** the original file it was read from. Thus, if
there are unsaved changes in the buffer, they *will* be used. As an
alternative, it is also possible to run LAMMPS by reading the contents
of a file from the ``Run LAMMPS from File`` menu entry or with
of a file from the *Run LAMMPS from File* menu entry or with
`Ctrl-Shift-Enter`. This option may be required in some rare cases
where the input uses some functionality that is not compatible with
running LAMMPS from a string buffer. For consistency, any unsaved
@ -133,7 +217,7 @@ before LAMMPS can be run from a file.
While LAMMPS is running, the contents of the status bar change. On
the left side there is a text indicating that LAMMPS is running, which
also indicates the number of active threads, when thread-parallel
acceleration was selected in the ``Preferences`` dialog. On the right
acceleration was selected in the *Preferences* dialog. On the right
side, a progress bar is shown that displays the estimated progress for
the current :doc:`run <run>` or :doc:`minimize <minimize>` command.
@ -160,8 +244,8 @@ Up to three additional windows may open during a run:
More information on those windows and how to adjust their behavior and
contents is given below.
An active LAMMPS run can be stopped cleanly by using either the ``Stop
LAMMPS`` entry in the ``Run`` menu, the keyboard shortcut `Ctrl-/`
An active LAMMPS run can be stopped cleanly by using either the *Stop
LAMMPS* entry in the *Run* menu, the keyboard shortcut `Ctrl-/`
(`Command-/` on macOS), or by clicking on the red button in the status
bar. This will cause the running LAMMPS process to complete the current
timestep (or iteration for energy minimization) and then complete the
@ -191,7 +275,7 @@ The runs are counted and the run number for the current run is displayed
in the window title. It is possible to change the behavior of
LAMMPS-GUI in the preferences dialog to create a *new* *Output* window
for every run or to not show the current *Output* window. It is also
possible to show or hide the *current* *Output* window from the ``View``
possible to show or hide the *current* *Output* window from the *View*
menu.
The text in the *Output* window is read-only and cannot be modified, but
@ -206,8 +290,6 @@ right mouse button into the *Output* window text area.
:align: center
:scale: 50%
.. versionadded:: 1.6
Should the *Output* window contain embedded YAML format text (see above for a
demonstration), for example from using :doc:`thermo_style yaml
<thermo_style>` or :doc:`thermo_modify line yaml <thermo_modify>`, the
@ -228,27 +310,51 @@ plot of thermodynamic output of the LAMMPS calculation as shown below.
The drop down menu on the top right allows selection of different
properties that are computed and written to thermo output. Only one
property can be shown at a time. The plots are updated with new data as
the run progresses, so they can be used to visually monitor the
evolution of available properties. The window title shows the current
run number that this chart window corresponds to. Same as for the
*Output* window, the chart window is replaced on each new run, but the
behavior can be changed in the preferences dialog.
property can be shown at a time. The plots are updated regularly with
new data as the run progresses, so they can be used to visually monitor
the evolution of available properties. The update interval can be set
in the *Preferences* dialog. By default, the raw data for the selected
property is plotted as a blue graph. As soon as there are a sufficient
number of data points, there will be a second graph shown in red with a
smoothed version of the data. From the drop down menu on the top left,
you can select whether to plot only the raw data, only the smoothed
data or both. The smoothing uses a `Savitzky-Golay convolution filter
<https://en.wikipedia.org/wiki/Savitzky%E2%80%93Golay_filter>`_ The
window width (left) and order (right) parameters can be set in the boxes
next to the drop down menu. Default settings are 10 and 4 which means
that the smoothing window includes 10 points each to the left and the
right of the current data point and a fourth order polynomial is fit to
the data in the window.
From the ``File`` menu on the top left, it is possible to save an image
You can use the mouse to zoom into the graph (hold the left button and
drag to mark an area) or zoom out (right click) and you can reset the
view with a click to the "lens" button next to the data drop down menu.
The window title shows the current run number that this chart window
corresponds to. Same as for the *Output* window, the chart window is
replaced on each new run, but the behavior can be changed in the
*Preferences* dialog.
From the *File* menu on the top left, it is possible to save an image
of the currently displayed plot or export the data in either plain text
columns (for use by plotting tools like `gnuplot
<http://www.gnuplot.info/>`_ or `grace
<https://plasma-gate.weizmann.ac.il/Grace/>`_), or as CSV data which can
be imported for further processing with Microsoft Excel or `pandas
<https://pandas.pydata.org/>`_
<https://plasma-gate.weizmann.ac.il/Grace/>`_), as CSV data which can be
imported for further processing with Microsoft Excel `LibreOffice Calc
<https://www.libreoffice.org/>`_ or with Python via `pandas
<https://pandas.pydata.org/>`_, or as YAML which can be imported into
Python with `PyYAML <https://pyyaml.org/>`_ or pandas.
Thermo output data from successive run commands in the input script is
combined into a single data set unless the format, number, or names of
output columns are changed with a :doc:`thermo_style <thermo_style>` or
a :doc:`thermo_modify <thermo_modify>` command, or the current time step
is reset with :doc:`reset_timestep <reset_timestep>`, or if a
:doc:`clear <clear>` command is issued.
:doc:`clear <clear>` command is issued. This is where the YAML export
from the *Charts* window differs from that of the *Output* window:
here you get the compounded data set starting with the last change of
output fields or timestep setting, while the export from the log will
contain *all* YAML output but *segmented* into individual runs.
Image Slide Show
----------------
@ -269,8 +375,6 @@ zoom in or zoom out of the displayed images. The button on the very
left triggers an export of the slide show animation to a movie file,
provided the `FFmpeg program <https://ffmpeg.org/>`_ is installed.
.. versionadded:: 1.6
When clicking on the "garbage can" icon, all image files of the slide
show will be deleted. Since their number can be large for long
simulations, this option enables to safely and quickly clean up the
@ -282,20 +386,20 @@ Variable Info
During a run, it may be of interest to monitor the value of input script
variables, for example to monitor the progress of loops. This can be
done by enabling the "Variables Window" in the ``View`` menu or by using
done by enabling the "Variables Window" in the *View* menu or by using
the `Ctrl-Shift-W` keyboard shortcut. This shows info similar to the
:doc:`info variables <info>` command in a separate window as shown
below.
.. image:: JPG/lammps-gui-variable-info.png
:align: center
:scale: 75%
:scale: 50%
Like for the *Output* and *Charts* windows, its content is continuously
updated during a run. It will show "(none)" if there are no variables
defined. Note that it is also possible to *set* :doc:`index style
variables <variable>`, that would normally be set via command line
flags, via the "Set Variables..." dialog from the ``Run`` menu.
flags, via the "Set Variables..." dialog from the *Run* menu.
LAMMPS-GUI automatically defines the variable "gui_run" to the current
value of the run counter. That way it is possible to automatically
record a separate log for each run attempt by using the command
@ -307,10 +411,12 @@ record a separate log for each run attempt by using the command
at the beginning of an input file. That would record logs to files
``logfile-1.txt``, ``logfile-2.txt``, and so on for successive runs.
.. _snapshot_viewer:
Snapshot Image Viewer
---------------------
By selecting the ``Create Image`` entry in the ``Run`` menu, or by
By selecting the *Create Image* entry in the *Run* menu, or by
hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
clicking on the "palette" button in the status bar of the *Editor*
window, LAMMPS-GUI sends a custom :doc:`write_dump image <dump_image>`
@ -331,35 +437,41 @@ instance when using reduced (= 'lj') :doc:`units <units>`, then
LAMMPS-GUI will check the current pair style and if it is a
Lennard-Jones type potential, it will extract the *sigma* parameter
for each atom type and assign atom diameters from those numbers.
For cases where atom diameters are not auto-detected, the *Atom size* field
can be edited and a suitable value set manually. The default value
is inferred from the x-direction lattice spacing.
Otherwise the default sequence of colors of the :doc:`dump image
<dump_image>` command is assigned to the different atom types and the
diameters are all the same.
If elements cannot be detected the default sequence of colors of the
:doc:`dump image <dump_image>` command is assigned to the different atom
types.
.. image:: JPG/lammps-gui-image.png
:align: center
:scale: 50%
.. |gui-image1| image:: JPG/lammps-gui-image.png
:width: 48%
.. |gui-image2| image:: JPG/lammps-gui-funnel.png
:width: 48%
|gui-image1| |gui-image2|
The default image size, some default image quality settings, the view
style and some colors can be changed in the ``Preferences`` dialog
style and some colors can be changed in the *Preferences* dialog
window. From the image viewer window further adjustments can be made:
actual image size, high-quality (SSAO) rendering, anti-aliasing, view
style, display of box or axes, zoom factor. The view of the system can
be rotated horizontally and vertically. It is also possible to only
display the atoms within a group defined in the input script (default is
"all"). After each change, the image is rendered again and the display
updated. The small palette icon on the top left is colored while LAMMPS
is running to render the new image; it is grayed out when LAMMPS is
finished. When there are many atoms to render and high quality images
with anti-aliasing are requested, re-rendering may take several seconds.
From the ``File`` menu of the image window, the current image can be
saved to a file (keyboard shortcut `Ctrl-S`) or copied to the clipboard
(keyboard shortcut `Ctrl-C`) for pasting the image into another
application.
"all"). The image can also be re-centered on the center of mass of the
selected group. After each change, the image is rendered again and the
display updated. The small palette icon on the top left is colored
while LAMMPS is running to render the new image; it is grayed out when
LAMMPS is finished. When there are many atoms to render and high
quality images with anti-aliasing are requested, re-rendering may take
several seconds. From the *File* menu of the image window, the
current image can be saved to a file (keyboard shortcut `Ctrl-S`) or
copied to the clipboard (keyboard shortcut `Ctrl-C`) for pasting the
image into another application.
.. versionadded:: 1.6
From the ``File`` menu it is also possible to copy the current
From the *File* menu it is also possible to copy the current
:doc:`dump image <dump_image>` and :doc:`dump_modify <dump_image>`
commands to the clipboard so they can be pasted into a LAMMPS input file
so that the visualization settings of the snapshot image can be repeated
@ -377,6 +489,10 @@ Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
dialog will pop up asking whether to cancel the exit operation, or to
save or not save the buffer contents to a file.
The editor has an auto-save mode that can be enabled or disabled in the
*Preferences* dialog. In auto-save mode, the editor buffer is
automatically saved before running LAMMPS or before exiting LAMMPS-GUI.
Context Specific Word Completion
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -391,7 +507,7 @@ a word have been typed.
The word can then be completed through selecting an entry by scrolling
up and down with the cursor keys and selecting with the 'Enter' key or
by clicking on the entry with the mouse. The automatic completion
pop-up can be disabled in the ``Preferences`` dialog, but the completion
pop-up can be disabled in the *Preferences* dialog, but the completion
can still be requested manually by either hitting the 'Shift-TAB' key or
by right-clicking with the mouse and selecting the option from the
context menu. Most of the completion information is retrieved from the
@ -406,11 +522,12 @@ Line Reformatting
The editor supports reformatting lines according to the syntax in order
to have consistently aligned lines. This primarily means adding
whitespace padding to commands, type specifiers, IDs and names. This
reformatting is performed by default when hitting the 'Enter' key to
start a new line. This feature can be turned on or off in the
``Preferences`` dialog, but it can still be manually performed by
hitting the 'TAB' key. The amount of padding can be adjusted in the
``Preferences`` dialog for the *Editor*.
reformatting is performed manually by hitting the 'Tab' key. It is
also possible to have this done automatically when hitting the 'Enter'
key to start a new line. This feature can be turned on or off in the
*Preferences* dialog for *Editor Settings* with the
"Reformat with 'Enter'" checkbox. The amount of padding for multiple
categories can be adjusted in the same dialog.
Internally this functionality is achieved by splitting the line into
"words" and then putting it back together with padding added where the
@ -427,7 +544,7 @@ Context Specific Help
|gui-popup1| |gui-popup2|
A unique feature of the LAMMPS-GUI is the option to look up the
A unique feature of LAMMPS-GUI is the option to look up the LAMMPS
documentation for the command in the current line. This can be done by
either clicking the right mouse button or by using the `Ctrl-?` keyboard
shortcut. When using the mouse, there are additional entries in the
@ -437,55 +554,85 @@ keyboard, the first of those entries is chosen.
If the word under the cursor is a file, then additionally the context
menu has an entry to open the file in a read-only text viewer window.
This is a convenient way to view the contents of files that are
referenced in the input.
If the file is a LAMMPS restart file, instead the menu entry offers to
:ref:`inspect the restart <inspect_restart>`.
The text viewer is a convenient way to view the contents of files that
are referenced in the input. The file viewer also supports on-the-fly
decompression based on the file name suffix in a :ref:`similar fashion
as available with LAMMPS <gzip>`. If the necessary decompression
program is missing or the file cannot be decompressed, the viewer window
will contain a corresponding message.
.. _inspect_restart:
Inspecting a Restart file
^^^^^^^^^^^^^^^^^^^^^^^^^
When LAMMPS-GUI is asked to "Inspect a Restart", it will read the
restart file into a LAMMPS instance and then open three different
windows. The first window is a text viewer with the output of an
:doc:`info command <info>` with system information stored in the
restart. The second window is text viewer containing a data file
generated with a :doc:`write_data command <write_data>`. The third
window is a :ref:`Snapshot Image Viewer <snapshot_viewer>` containing a
visualization of the system in the restart.
If the restart file is larger than 250 MBytes, a dialog will ask
for confirmation before continuing, since large restart files
may require large amounts of RAM since the entire system must
be read into RAM. Thus restart file for large simulations that
have been run on an HPC cluster may overload a laptop or local
workstation. The *Show Details...* button will display a rough
estimate of the additional memory required.
Menu
----
The menu bar has entries ``File``, ``Edit``, ``Run``, ``View``, and
``About``. Instead of using the mouse to click on them, the individual
The menu bar has entries *File*, *Edit*, *Run*, *View*, and
*About*. Instead of using the mouse to click on them, the individual
menus can also be activated by hitting the `Alt` key together with the
corresponding underlined letter, that is `Alt-F` activates the
``File`` menu. For the corresponding activated sub-menus, the key
*File* menu. For the corresponding activated sub-menus, the key
corresponding the underlined letters can be used to select entries
instead of using the mouse.
File
^^^^
The ``File`` menu offers the usual options:
The *File* menu offers the usual options:
- ``New`` clears the current buffer and resets the file name to ``*unknown*``
- ``Open`` opens a dialog to select a new file for editing in the *Editor*
- ``View`` opens a dialog to select a file for viewing in a *separate* window (read-only)
- ``Save`` saves the current file; if the file name is ``*unknown*``
- *New* clears the current buffer and resets the file name to ``*unknown*``
- *Open* opens a dialog to select a new file for editing in the *Editor*
- *View* opens a dialog to select a file for viewing in a *separate* window (read-only) with support for on-the-fly decompression as explained above.
- *Inspect restart* opens a dialog to select a file. If that file is a :doc:`LAMMPS restart <write_restart>` three windows with :ref:`information about the file are opened <inspect_restart>`.
- *Save* saves the current file; if the file name is ``*unknown*``
a dialog will open to select a new file name
- ``Save As`` opens a dialog to select and new file name (and folder, if
- *Save As* opens a dialog to select and new file name (and folder, if
desired) and saves the buffer to it. Writing the buffer to a
different folder will also switch the current working directory to
that folder.
- ``Quit`` exits LAMMPS-GUI. If there are unsaved changes, a dialog will
- *Quit* exits LAMMPS-GUI. If there are unsaved changes, a dialog will
appear to either cancel the operation, or to save, or to not save the
modified buffer.
In addition, up to 5 recent file names will be listed after the ``Open``
In addition, up to 5 recent file names will be listed after the *Open*
entry that allows re-opening recently opened files. This list is stored
when quitting and recovered when starting again.
Edit
^^^^
The ``Edit`` menu offers the usual editor functions like ``Undo``,
``Redo``, ``Cut``, ``Copy``, ``Paste``. It can also open a
``Preferences`` dialog (keyboard shortcut `Ctrl-P`) and allows deletion
of all stored preferences and settings, so they are reset to their
default values.
The *Edit* menu offers the usual editor functions like *Undo*, *Redo*,
*Cut*, *Copy*, *Paste*, and a *Find and Replace* dialog (keyboard
shortcut `Ctrl-F`). It can also open a *Preferences* dialog (keyboard
shortcut `Ctrl-P`) and allows deleting all stored preferences and
settings, so they are reset to their default values.
Run
^^^
The ``Run`` menu has options to start and stop a LAMMPS process. Rather
The *Run* menu has options to start and stop a LAMMPS process. Rather
than calling the LAMMPS executable as a separate executable, the
LAMMPS-GUI is linked to the LAMMPS library and thus can run LAMMPS
internally through the :ref:`LAMMPS C-library interface <lammps_c_api>`
@ -505,69 +652,109 @@ from a string buffer.
The LAMMPS calculations are run in a concurrent thread so that the GUI
can stay responsive and be updated during the run. The GUI can retrieve
data from the running LAMMPS instance and tell it to stop at the next
timestep. The ``Stop LAMMPS`` entry will do this by calling the
timestep. The *Stop LAMMPS* entry will do this by calling the
:cpp:func:`lammps_force_timeout` library function, which is equivalent
to a :doc:`timer timeout 0 <timer>` command.
The ``Set Variables...`` entry opens a dialog box where
The *Set Variables...* entry opens a dialog box where
:doc:`index style variables <variable>` can be set. Those variables
are passed to the LAMMPS instance when it is created and are thus
set *before* a run is started.
.. image:: JPG/lammps-gui-variables.png
:align: center
:scale: 75%
:scale: 50%
The ``Set Variables`` dialog will be pre-populated with entries that
The *Set Variables* dialog will be pre-populated with entries that
are set as index variables in the input and any variables that are
used but not defined, if the built-in parser can detect them. New
rows for additional variables can be added through the ``Add Row``
button and existing rows can be deleted by clicking on the ``X`` icons
rows for additional variables can be added through the *Add Row*
button and existing rows can be deleted by clicking on the *X* icons
on the right.
The ``Create Image`` entry will send a :doc:`dump image <dump_image>`
The *Create Image* entry will send a :doc:`dump image <dump_image>`
command to the LAMMPS instance, read the resulting file, and show it
in an ``Image Viewer`` window.
in an *Image Viewer* window.
The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
The *View in OVITO* entry will launch `OVITO <https://ovito.org>`_
with a :doc:`data file <write_data>` containing the current state of
the system. This option is only available if the LAMMPS-GUI can find
the system. This option is only available if LAMMPS-GUI can find
the OVITO executable in the system path.
The ``View in VMD`` entry will launch VMD with a :doc:`data file
The *View in VMD* entry will launch VMD with a :doc:`data file
<write_data>` containing the current state of the system. This option
is only available if the LAMMPS-GUI can find the VMD executable in the
is only available if LAMMPS-GUI can find the VMD executable in the
system path.
View
^^^^
The ``View`` menu offers to show or hide additional windows with log
The *View* menu offers to show or hide additional windows with log
output, charts, slide show, variables, or snapshot images. The
default settings for their visibility can be changed in the
``Preferences dialog``.
*Preferences* dialog.
About
^^^^^
The ``About`` menu finally offers a couple of dialog windows and an
The *About* menu finally offers a couple of dialog windows and an
option to launch the LAMMPS online documentation in a web browser. The
``About LAMMPS-GUI`` entry displays a dialog with a summary of the
*About LAMMPS-GUI* entry displays a dialog with a summary of the
configuration settings of the LAMMPS library in use and the version
number of LAMMPS-GUI itself. The ``Quick Help`` displays a dialog with
a minimal description of LAMMPS-GUI. The ``LAMMPS-GUI Howto`` entry
number of LAMMPS-GUI itself. The *Quick Help* displays a dialog with
a minimal description of LAMMPS-GUI. The *LAMMPS-GUI Howto* entry
will open this documentation page from the online documentation in a web
browser window. The ``LAMMPS Manual`` entry will open the main page of
browser window. The *LAMMPS Manual* entry will open the main page of
the LAMMPS online documentation in a web browser window.
The *LAMMPS Tutorial* entry will open the main page of the set of
LAMMPS tutorials authored and maintained by Simon Gravelle at
https://lammpstutorials.github.io/ in a web browser window.
-----
Find and Replace
----------------
.. image:: JPG/lammps-gui-find.png
:align: center
:scale: 33%
The *Find and Replace* dialog allows searching for and replacing
text in the *Editor* window.
The dialog can be opened either from the *Edit* menu or with the
keyboard shortcut `Ctrl-F`. You can enter the text to search for.
Through three check-boxes the search behavior can be adjusted:
- If checked, "Match case" does a case sensitive search; otherwise
the search is case insensitive.
- If checked, "Wrap around" starts searching from the start of the
document, if there is no match found from the current cursor position
until the end of the document; otherwise the search will stop.
- If checked, the "Whole word" setting only finds full word matches
(white space and special characters are word boundaries).
Clicking on the *Next* button will search for the next occurrence of the
search text and select / highlight it. Clicking on the *Replace* button
will replace an already highlighted search text and find the next one.
If no text is selected, or the selected text does not match the
selection string, then the first click on the *Replace* button will
only search and highlight the next occurrence of the search string.
Clicking on the *Replace All* button will replace all occurrences from
the cursor position to the end of the file; if the *Wrap around* box is
checked, then it will replace **all** occurrences in the **entire**
document. Clicking on the *Done* button will dismiss the dialog.
------
Preferences
-----------
The ``Preferences`` dialog allows customization of the behavior and
look of the LAMMPS-GUI application. The settings are grouped and each
group is displayed within a tab.
The *Preferences* dialog allows customization of the behavior and
look of LAMMPS-GUI. The settings are grouped and each group is
displayed within a tab.
.. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
:width: 24%
@ -612,7 +799,7 @@ General Settings:
otherwise each command will create a new image window.
- *Path to LAMMPS Shared Library File:* this option is only visible
when LAMMPS-GUI was compiled to load the LAMMPS library at run time
instead of being linked to it directly. With the ``Browse..`` button
instead of being linked to it directly. With the *Browse..* button
or by changing the text, a different shared library file with a
different compilation of LAMMPS with different settings or from a
different version can be loaded. After this setting was changed,
@ -622,14 +809,19 @@ General Settings:
log) of the application can be set.
- *Select Text Font:* Opens a font selection dialog where the type and
size for the text editor and log font of the application can be set.
- *GUI update interval:* Allows to set the time interval between GUI
and data updates during a LAMMPS run in milliseconds. The default is
to update the GUI every 10 milliseconds. This is good for most cases.
For LAMMPS runs that run *very* fast, however, data may be missed and
through lowering this interval, this can be corrected. However, this
will make the GUI use more resources, which may be a problem on some
computers with slower CPUs and a small number of CPU cores. This
- *Data update interval:* Allows to set the time interval between data
updates during a LAMMPS run in milliseconds. The default is to update
the data (for charts and output window) every 10 milliseconds. This
is good for many cases. Set this to 100 milliseconds or more if
LAMMPS-GUI consumes too many resources during a run. For LAMMPS runs
that run *very* fast (for example in tutorial examples), however, data
may be missed and through lowering this interval, this can be
corrected. However, this will make the GUI use more resources. This
setting may be changed to a value between 1 and 1000 milliseconds.
- *Charts update interval:* Allows to set the time interval between redrawing
the plots in the *Charts* window in milliseconds. The default is to
redraw the plots every 500 milliseconds. This is just for the drawing,
data collection is managed with the previous setting.
Accelerators:
^^^^^^^^^^^^^
@ -645,18 +837,23 @@ Snapshot Image:
^^^^^^^^^^^^^^^
This tab allows setting defaults for the snapshot images displayed in
the ``Image Viewer`` window, such as its dimensions and the zoom
factor applied. The *Antialias* switch will render images with twice
the number of pixels for width and height and then smoothly scale the
image back to the requested size. This produces higher quality images
with smoother edges at the expense of requiring more CPU time to
render the image. The *HQ Image mode* option turns on screen space
ambient occlusion (SSAO) mode when rendering images. This is also
more time consuming, but produces a more 'spatial' representation of
the system shading of atoms by their depth. The *VDW Style* checkbox
selects whether atoms are represented by space filling spheres when
checked or by smaller spheres and sticks. Finally there are a couple
of drop down lists to select the background and box colors.
the *Image Viewer* window, such as its dimensions and the zoom factor
applied. The *Antialias* switch will render images with twice the
number of pixels for width and height and then smoothly scale the image
back to the requested size. This produces higher quality images with
smoother edges at the expense of requiring more CPU time to render the
image. The *HQ Image mode* option turns on screen space ambient
occlusion (SSAO) mode when rendering images. This is also more time
consuming, but produces a more 'spatial' representation of the system
shading of atoms by their depth. The *Shiny Image mode* option will
render objects with a shiny surface when enabled. Otherwise the
surfaces will be matted. The *Show Box* option selects whether the
system box is drawn as a colored set of sticks. Similarly, the *Show
Axes* option selects whether a representation of the three system axes
will be drawn as colored sticks. The *VDW Style* checkbox selects
whether atoms are represented by space filling spheres when checked or
by smaller spheres and sticks. Finally there are a couple of drop down
lists to select the background and box colors.
Editor Settings:
^^^^^^^^^^^^^^^^
@ -667,9 +864,11 @@ ranges, IDs (e.g. for fixes), and names (e.g. for groups). The value
set is the minimum width for the text element and it can be chosen in
the range between 1 and 32.
The two settings which follow enable or disable the automatic
reformatting when hitting the 'Enter' key and the automatic display of
the completion pop-up window.
The three settings which follow enable or disable the automatic
reformatting when hitting the 'Enter' key, the automatic display of
the completion pop-up window, and whether auto-save mode is enabled.
In auto-save mode the editor buffer is saved before a run or before
exiting LAMMPS-GUI.
-----------
@ -682,7 +881,7 @@ available (On macOS use the Command key instead of Ctrl/Control).
.. list-table::
:header-rows: 1
:widths: auto
:widths: 16 19 13 16 13 22
* - Shortcut
- Function
@ -724,32 +923,32 @@ available (On macOS use the Command key instead of Ctrl/Control).
- Quit Application
- Ctrl+A
- Select All
- Ctrl+P
- Preferences
- Ctrl+F
- Find and Replace
* - Ctrl+W
- Close Window
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS-GUI Howto
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+?
- Context Help
- Ctrl+Shift+W
- Show Variables
* - Ctrl+Shift+M
- LAMMPS Manual
- TAB
- Reformat line
- Shift+TAB
- Show Completions
* - Ctrl+Shift+Enter
- Run File
-
-
-
-
- Ctrl+Shift+W
- Show Variables
- Ctrl+P
- Preferences
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS-GUI Howto
* - Ctrl+Shift+M
- LAMMPS Manual
- Ctrl+?
- Context Help
- Ctrl+Shift+T
- LAMMPS Tutorial
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In

3
doc/src/Howto_moltemplate.rst
View File

@ -367,5 +367,4 @@ And execute the simulation with the following:
.. _OPLSAA96:
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc,
118(45), 11225-11236 (1996).
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).

10
doc/src/Howto_multiple.rst
View File

@ -44,7 +44,7 @@ For large numbers of independent simulations, you can use
:doc:`variables <variable>` and the :doc:`next <next>` and
:doc:`jump <jump>` commands to loop over the same input script
multiple times with different settings. For example, this
script, named in.polymer
script, named ``in.polymer``
.. code-block:: LAMMPS
@ -57,7 +57,7 @@ script, named in.polymer
next d
jump in.polymer
would run 8 simulations in different directories, using a data.polymer
would run 8 simulations in different directories, using a ``data.polymer``
file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable
and storing the output in different log and dump files, for example
@ -83,10 +83,10 @@ partition of processors. LAMMPS can be run on multiple partitions via
the :doc:`-partition command-line switch <Run_options>`.
In the last 2 examples, if LAMMPS were run on 3 partitions, the same
scripts could be used if the "index" and "loop" variables were
scripts could be used if the ``index`` and ``loop`` variables were
replaced with *universe*\ -style variables, as described in the
:doc:`variable <variable>` command. Also, the "next t" and "next a"
commands would need to be replaced with a single "next a t" command.
:doc:`variable <variable>` command. Also, the :lammps:`next t` and :lammps:`next a`
commands would need to be replaced with a single :lammps:`next a t` command.
With these modifications, the 8 simulations of each script would run
on the 3 partitions one after the other until all were finished.
Initially, 3 simulations would be started simultaneously, one on each

58
doc/src/Howto_pylammps.rst
View File

@ -6,19 +6,22 @@ PyLammps Tutorial
Overview
--------
``PyLammps`` is a Python wrapper class for LAMMPS which can be created
on its own or use an existing lammps Python object. It creates a simpler,
:py:class:`PyLammps <lammps.PyLammps>` is a Python wrapper class for
LAMMPS which can be created on its own or use an existing
:py:class:`lammps Python <lammps.lammps>` object. It creates a simpler,
more "pythonic" interface to common LAMMPS functionality, in contrast to
the ``lammps`` wrapper for the C-style LAMMPS library interface which
is written using `Python ctypes <ctypes_>`_. The ``lammps`` wrapper
is discussed on the :doc:`Python_head` doc page.
the :py:class:`lammps <lammps.lammps>` wrapper for the LAMMPS :ref:`C
language library interface API <lammps_c_api>` which is written using
`Python ctypes <ctypes_>`_. The :py:class:`lammps <lammps.lammps>`
wrapper is discussed on the :doc:`Python_head` doc page.
Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable
API. It no longer requires knowledge of the underlying C++ code
implementation. Finally, the ``IPyLammps`` wrapper builds on top of
``PyLammps`` and adds some additional features for
`IPython integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_,
e.g. for embedded visualization output from :doc:`dump style image <dump_image>`.
Unlike the flat `ctypes <ctypes_>`_ interface, PyLammps exposes a
discoverable API. It no longer requires knowledge of the underlying C++
code implementation. Finally, the :py:class:`IPyLammps
<lammps.IPyLammps>` wrapper builds on top of :py:class:`PyLammps
<lammps.PyLammps>` and adds some additional features for `IPython
integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for
embedded visualization output from :doc:`dump style image <dump_image>`.
.. _ctypes: https://docs.python.org/3/library/ctypes.html
.. _ipython: https://ipython.org/
@ -30,19 +33,24 @@ Comparison of lammps and PyLammps interfaces
lammps.lammps
"""""""""""""
* uses ``ctypes``
* direct memory access to native C++ data
* uses `ctypes <ctypes_>`_
* direct memory access to native C++ data with optional support for NumPy arrays
* provides functions to send and receive data to LAMMPS
* interface modeled after the LAMMPS :ref:`C language library interface API <lammps_c_api>`
* requires knowledge of how LAMMPS internally works (C pointers, etc)
* full support for running Python with MPI using `mpi4py <https://mpi4py.readthedocs.io>`_
* no overhead from creating a more Python-like interface
lammps.PyLammps
"""""""""""""""
* higher-level abstraction built on top of original ctypes interface
* higher-level abstraction built on *top* of the original :py:class:`ctypes based interface <lammps.lammps>`
* manipulation of Python objects
* communication with LAMMPS is hidden from API user
* shorter, more concise Python
* better IPython integration, designed for quick prototyping
* designed for serial execution
* additional overhead from capturing and parsing the LAMMPS screen output
Quick Start
-----------
@ -506,14 +514,26 @@ inside of the IPython notebook.
Using PyLammps and mpi4py (Experimental)
----------------------------------------
PyLammps can be run in parallel using mpi4py. This python package can be installed using
PyLammps can be run in parallel using `mpi4py
<https://mpi4py.readthedocs.io>`_. This python package can be installed
using
.. code-block:: bash
pip install mpi4py
The following is a short example which reads in an existing LAMMPS input file and
executes it in parallel. You can find in.melt in the examples/melt folder.
.. warning::
Usually, any :py:class:`PyLammps <lammps.PyLammps>` command must be
executed by *all* MPI processes. However, evaluations and querying
the system state is only available on MPI rank 0. Using these
functions from other MPI ranks will raise an exception.
The following is a short example which reads in an existing LAMMPS input
file and executes it in parallel. You can find in.melt in the
examples/melt folder. Please take note that the
:py:meth:`PyLammps.eval() <lammps.PyLammps.eval>` is called only from
MPI rank 0.
.. code-block:: python
@ -535,10 +555,6 @@ following mpirun command:
mpirun -np 4 python melt.py
.. warning::
Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
Feedback and Contributing
-------------------------

18
doc/src/Howto_restart.rst
View File

@ -26,8 +26,8 @@ scripts are based on. If that script had the line
restart 50 tmp.restart
added to it, it would produce 2 binary restart files (tmp.restart.50
and tmp.restart.100) as it ran.
added to it, it would produce two binary restart files (``tmp.restart.50``
and ``tmp.restart.100``) as it ran.
This script could be used to read the first restart file and re-run the
last 50 timesteps:
@ -47,21 +47,21 @@ last 50 timesteps:
run 50
Note that the following commands do not need to be repeated because
their settings are included in the restart file: *units, atom_style,
special_bonds, pair_style, bond_style*. However, these commands do
their settings are included in the restart file: :lammps:`units`, :lammps:`atom_style`,
:lammps:`special_bonds`, :lammps:`pair_style`, :lammps:`bond_style`. However, these commands do
need to be used, since their settings are not in the restart file:
*neighbor, fix, timestep*\ .
:lammps:`neighbor`, :lammps:`fix`, :lammps:`timestep`.
If you actually use this script to perform a restarted run, you will
notice that the thermodynamic data match at step 50 (if you also put a
"thermo 50" command in the original script), but do not match at step
:lammps:`thermo 50` command in the original script), but do not match at step
100. This is because the :doc:`fix langevin <fix_langevin>` command
uses random numbers in a way that does not allow for perfect restarts.
As an alternate approach, the restart file could be converted to a data
file as follows:
.. code-block:: LAMMPS
.. code-block:: bash
lmp_g++ -r tmp.restart.50 tmp.restart.data
@ -89,8 +89,8 @@ Then, this script could be used to re-run the last 50 steps:
reset_timestep 50
run 50
Note that nearly all the settings specified in the original *in.chain*
script must be repeated, except the *pair_coeff* and *bond_coeff*
Note that nearly all the settings specified in the original ``in.chain``
script must be repeated, except the :lammps:`pair_coeff` and :lammps:`bond_coeff`
commands, since the new data file lists the force field coefficients.
Also, the :doc:`reset_timestep <reset_timestep>` command is used to tell
LAMMPS the current timestep. This value is stored in restart files, but

8
doc/src/Howto_rheo.rst
View File

@ -15,8 +15,8 @@ details of the system, or develop new capabilities. For instance, the numerics
associated with calculating gradients, reproducing kernels, etc. are separated
into distinct classes to simplify the development of new integration schemes
which can call these calculations. Additional numerical details can be found in
:ref:`(Palermo) <howto_rheo_palermo>` and
:ref:`(Clemmer) <howto_rheo_clemmer>`.
:ref:`(Clemmer) <howto_rheo_clemmer>`. Example movies illustrating some of these
capabilities are found at https://www.lammps.org/movies.html#rheopackage.
Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
<PKG-SPH>` package is likely better suited for your application. It has fewer advanced
@ -107,10 +107,6 @@ criteria for creating/deleting a bond or altering force calculations).
----------
.. _howto_rheo_palermo:
**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.
.. _howto_rheo_clemmer:
**(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

6
doc/src/Howto_spc.rst
View File

@ -2,7 +2,7 @@ SPC water model
===============
The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
charges and Lennard-Jones parameters assigned to each of the three atoms.
In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
*harmonic* and an angle style of *harmonic* or *charmm* should also be
@ -33,7 +33,7 @@ the partial charge assignments change:
| O charge = -0.8476
| H charge = 0.4238
See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
See the :ref:`(Berendsen2) <howto-Berendsen>` reference for more details on both
the SPC and SPC/E models.
Below is the code for a LAMMPS input file and a molecule file
@ -149,4 +149,4 @@ Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wik
.. _howto-Berendsen:
**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
**(Berendsen2)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).

10
doc/src/Howto_structured_data.rst
View File

@ -341,7 +341,12 @@ data files and obtain a list of dictionaries.
.. code-block::
[{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003}, {'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798}, {'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103}, {'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545}, {'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694}, {'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
[{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003},
{'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798},
{'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103},
{'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545},
{'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694},
{'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
Line Delimited JSON (LD-JSON)
-----------------------------
@ -352,7 +357,8 @@ Each line represents one JSON object.
.. code-block:: LAMMPS
fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" title "" file output.json screen no
fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" &
title "" file output.json screen no
.. code-block:: json
:caption: output.json

6
doc/src/Howto_tip3p.rst
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@ -3,7 +3,7 @@ TIP3P water model
The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
<howto-tip3p>` specifies a 3-site rigid water molecule with charges and
Lennard-Jones parameters assigned to each of the 3 atoms.
Lennard-Jones parameters assigned to each of the three atoms.
A suitable pair style with cutoff Coulomb would be:
@ -32,9 +32,9 @@ optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
model (without fix shake) is desired, for rigid bonds/angles they are
ignored.
.. list-table::
.. list-table::
:header-rows: 1
:widths: auto
:widths: 38 22 20 20
* - Parameter
- TIP3P-CHARMM

6
doc/src/Howto_tip4p.rst
View File

@ -25,7 +25,7 @@ There are two ways to implement TIP4P water in LAMMPS:
This can be done with the following pair styles for Coulomb with a cutoff:
* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
* :doc:`pair_style tip4p/cut <pair_coul>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
or these commands for a long-range Coulomb treatment:
@ -70,9 +70,9 @@ parameters adjusted for use with a long-range Coulombic solver
OM distance is specified in the :doc:`pair_style <pair_style>` command,
not as part of the pair coefficients.
.. list-table::
.. list-table::
:header-rows: 1
:widths: auto
:widths: 36 19 13 15 17
* - Parameter
- TIP4P (original)

4
doc/src/Howto_tip5p.rst
View File

@ -32,9 +32,9 @@ The table below lists the force field parameters (in real :doc:`units
<Mahoney>` and the TIP5P-E model :ref:`(Rick) <Rick>` for use with a
long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
.. list-table::
.. list-table::
:header-rows: 1
:widths: auto
:widths: 50 25 25
* - Parameter
- TIP5P

24
doc/src/Howto_viscosity.rst
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@ -1,22 +1,24 @@
Calculate viscosity
===================
The shear viscosity eta of a fluid can be measured in at least 6 ways
using various options in LAMMPS. See the examples/VISCOSITY directory
The shear viscosity :math:`\eta` of a fluid can be measured in at least 6 ways
using various options in LAMMPS. See the ``examples/VISCOSITY`` directory
for scripts that implement the 5 methods discussed here for a simple
Lennard-Jones fluid model and 1 method for SPC/E water model.
Also, see the :doc:`page on calculating thermal conductivity <Howto_kappa>`
for an analogous discussion for thermal conductivity.
Eta is a measure of the propensity of a fluid to transmit momentum in
:math:`\eta` is a measure of the propensity of a fluid to transmit momentum in
a direction perpendicular to the direction of velocity or momentum
flow. Alternatively it is the resistance the fluid has to being
sheared. It is given by
J = -eta grad(Vstream)
.. math::
where J is the momentum flux in units of momentum per area per time.
and grad(Vstream) is the spatial gradient of the velocity of the fluid
J = -\eta \cdot \text{grad}(V_{\text{stream}})
where :math:`J` is the momentum flux in units of momentum per area per time.
and :math:`\text{grad}(V_{\text{stream}})` is the spatial gradient of the velocity of the fluid
moving in another direction, normal to the area through which the
momentum flows. Viscosity thus has units of pressure-time.
@ -38,11 +40,11 @@ velocity to prevent the fluid from heating up.
In both cases, the velocity profile setup in the fluid by this
procedure can be monitored by the :doc:`fix ave/chunk <fix_ave_chunk>`
command, which determines grad(Vstream) in the equation above.
E.g. the derivative in the y-direction of the Vx component of fluid
motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of
command, which determines :math:`\text{grad}(V_{\text{stream}})` in the equation above.
E.g. the derivative in the y-direction of the :math:`V_x` component of fluid
motion or :math:`\text{grad}(V_{\text{stream}}) = \frac{\text{d} V_x}{\text{d} y}`. The :math:`P_{xy}` off-diagonal component of
the pressure or stress tensor, as calculated by the :doc:`compute pressure <compute_pressure>` command, can also be monitored, which
is the J term in the equation above. See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations.
is the :math:`J` term in the equation above. See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations.
The third method is to perform a reverse non-equilibrium MD simulation
using the :doc:`fix viscosity <fix_viscosity>` command which implements
@ -55,7 +57,7 @@ See the :doc:`fix viscosity <fix_viscosity>` command for details.
The fourth method is based on the Green-Kubo (GK) formula which
relates the ensemble average of the auto-correlation of the
stress/pressure tensor to eta. This can be done in a fully
stress/pressure tensor to :math:`\eta`. This can be done in a fully
equilibrated simulation which is in contrast to the two preceding
non-equilibrium methods, where momentum flows continuously through the
simulation box.

10
doc/src/Howto_viz.rst
View File

@ -6,7 +6,7 @@ analyzed in a variety of ways.
LAMMPS snapshots are created by the :doc:`dump <dump>` command, which
can create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized by
text file (see :lammps:`dump atom` or :lammps:`dump custom`) which can be visualized by
`several visualization tools <https://www.lammps.org/viz.html>`_ for MD
simulation trajectories. `OVITO <https://www.ovito.org>`_ and `VMD
<https://www.ks.uiuc.edu/Research/vmd>`_ seem to be the most popular
@ -14,7 +14,13 @@ choices among them.
The :doc:`dump image <dump_image>` and :doc:`dump movie <dump_image>`
styles can output internally rendered images or convert them to a movie
during the MD run.
during the MD run. It is also possible to create visualizations from
LAMMPS inputs or restart file with the :doc:`LAMMPS-GUI
<Howto_lammps_gui>`, which uses the :doc:`dump image <dump_image>`
command internally. The ``Snapshot Image Viewer`` can be used to
adjust the visualization of the system interactively and then export
the corresponding LAMMPS commands to the clipboard to be inserted
into input files.
Programs included with LAMMPS as auxiliary tools can convert
between LAMMPS format files and other formats. See the :doc:`Tools

58
doc/src/Install.rst
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@ -35,35 +35,35 @@ you **must** build LAMMPS from the source code.
These are the files and subdirectories in the LAMMPS distribution:
+------------+---------------------------------------------+
| README | Short description of the LAMMPS package |
+------------+---------------------------------------------+
| LICENSE | GNU General Public License (GPL) |
+------------+---------------------------------------------+
| SECURITY.md| Security policy for the LAMMPS package |
+------------+---------------------------------------------+
| bench | benchmark inputs |
+------------+---------------------------------------------+
| cmake | CMake build files |
+------------+---------------------------------------------+
| doc | documentation and tools to build the manual |
+------------+---------------------------------------------+
| examples | example input files |
+------------+---------------------------------------------+
| fortran | Fortran module for LAMMPS library interface |
+------------+---------------------------------------------+
| lib | additional provided or external libraries |
+------------+---------------------------------------------+
| potentials | selected interatomic potential files |
+------------+---------------------------------------------+
| python | Python module for LAMMPS library interface |
+------------+---------------------------------------------+
| src | LAMMPS source files |
+------------+---------------------------------------------+
| tools | pre- and post-processing tools |
+------------+---------------------------------------------+
| unittest | source code and inputs for testing LAMMPS |
+------------+---------------------------------------------+
+-----------------+---------------------------------------------+
| ``README`` | Short description of the LAMMPS package |
+-----------------+---------------------------------------------+
| ``LICENSE`` | GNU General Public License (GPL) |
+-----------------+---------------------------------------------+
| ``SECURITY.md`` | Security policy for the LAMMPS package |
+-----------------+---------------------------------------------+
| ``bench`` | benchmark inputs |
+-----------------+---------------------------------------------+
| ``cmake`` | CMake build files |
+-----------------+---------------------------------------------+
| ``doc`` | documentation and tools to build the manual |
+-----------------+---------------------------------------------+
| ``examples`` | example input files |
+-----------------+---------------------------------------------+
| ``fortran`` | Fortran module for LAMMPS library interface |
+-----------------+---------------------------------------------+
| ``lib`` | additional provided or external libraries |
+-----------------+---------------------------------------------+
| ``potentials`` | selected interatomic potential files |
+-----------------+---------------------------------------------+
| ``python`` | Python module for LAMMPS library interface |
+-----------------+---------------------------------------------+
| ``src`` | LAMMPS source files |
+-----------------+---------------------------------------------+
| ``tools`` | pre- and post-processing tools |
+-----------------+---------------------------------------------+
| ``unittest`` | source code and inputs for testing LAMMPS |
+-----------------+---------------------------------------------+
You will have all of these if you downloaded the LAMMPS source code.
You will have only some of them if you downloaded executables, as

4
doc/src/Install_git.rst
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@ -60,7 +60,7 @@ between them at any time using "git checkout <branch name>".)
files (mostly by accident). If you do not need access to the entire
commit history (most people don't), you can speed up the "cloning"
process and reduce local disk space requirements by using the
*--depth* git command line flag. That will create a "shallow clone"
``--depth`` git command line flag. That will create a "shallow clone"
of the repository, which contains only a subset of the git history.
Using a depth of 1000 is usually sufficient to include the head
commits of the *develop*, the *release*, and the *maintenance*
@ -122,7 +122,7 @@ changed. How to do this depends on the build system you are using.
.. code-block:: bash
cmake . --build
cmake --build .
CMake should auto-detect whether it needs to re-run the CMake
configuration step and otherwise redo the build for all files

2
doc/src/Install_tarball.rst
View File

@ -31,7 +31,7 @@ command:
tar -xzvf lammps*.tar.gz
This will create a LAMMPS directory with the version date in its name,
e.g. lammps-28Mar23.
e.g. ``lammps-28Mar23``.
----------

2
doc/src/Install_windows.rst
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@ -34,7 +34,7 @@ When you download the installer package, you run it on your Windows
machine. It will then prompt you with a dialog, where you can choose
the installation directory, unpack and copy several executables,
potential files, documentation PDFs, selected example files, etc. It
will then update a few system settings (e.g. PATH, LAMMPS_POTENTIALS)
will then update a few system settings (e.g. ``PATH``, ``LAMMPS_POTENTIALS``)
and add an entry into the Start Menu (with references to the
documentation, LAMMPS homepage and more). From that menu, there is
also a link to an uninstaller that removes the files and undoes the

85
doc/src/Intro_authors.rst
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@ -1,19 +1,88 @@
Authors of LAMMPS
-----------------
The primary LAMMPS developers are at Sandia National Labs and Temple
University:
The current core LAMMPS developers are listed here (grouped by seniority
and sorted alphabetically by last name). You can email an individual
developer with code related questions for their area of expertise, or
send an email to all of them at this address: "developers at
lammps.org". General questions about LAMMPS should be posted in the
`LAMMPS forum on MatSci <https://matsci.org/lammps/>`_.
* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
* Aidan Thompson, athomps at sandia.gov
* Stan Moore, stamoor at sandia.gov
* `Axel Kohlmeyer <https://sites.google.com/site/akohlmey/>`_, akohlmey at gmail.com
* Richard Berger, richard.berger at outlook.com
.. raw:: latex
\small
.. list-table::
:widths: 17 15 25 43
:header-rows: 1
* - Name
- Affiliation
- Email
- Areas of expertise
* - `Axel Kohlmeyer <ak_>`_
- Temple U
- akohlmey at gmail.com
- OpenMP, library interfaces, LAMMPS-GUI, GitHub, MatSci forum, code maintenance, testing, releases
* - `Steve Plimpton <sjp_>`_
- SNL (retired)
- sjplimp at gmail.com
- MD kernels, parallel algorithms & scalability, code structure and design
* - `Aidan Thompson <at_>`_
- SNL
- athomps at sandia.gov
- manybody potentials, machine learned potentials, materials science, statistical mechanics
* -
-
-
-
* - `Richard Berger <rb_>`_
- LANL
- richard.berger at outlook.com
- Python, HPC, DevOps
* - `Germain Clavier <gc_>`_
- U Caen
- germain.clavier at unicaen.fr
- organic molecules, polymers, mechanical properties, surfaces, integrators, coarse-graining
* - Joel Clemmer
- SNL
- jtclemm at sandia.gov
- granular systems fluid/solid mechanics
* - `Jacob R. Gissinger <jg_>`_
- Stevens Institute of Technology
- jgissing at stevens.edu
- reactive molecular dynamics, macro-molecular systems, type labels
* - James Goff
- SNL
- jmgoff at sandia.gov
- machine learned potentials, QEq solvers, Python
* - Meg McCarthy
- SNL
- megmcca at sandia.gov
- alloys, micro-structure, machine learned potentials
* - Stan Moore
- SNL
- stamoor at sandia.gov
- Kokkos, KSpace solvers, ReaxFF
* - `Trung Nguyen <tn_>`_
- U Chicago
- ndactrung at gmail.com
- soft matter, GPU package, DIELECTRIC package, regression testing
.. _rb: https://rbberger.github.io/
.. _gc: https://enthalpiste.fr/
.. _jg: https://www.nanocipher.org/
.. _ak: https://sites.google.com/site/akohlmey/
.. _tn: https://sites.google.com/site/ndtrung8/
.. _at: https://www2.sandia.gov/~athomps/
.. _sjp: https://sjplimp.github.io
.. _lws: https://www.lammps.org
Past developers include Paul Crozier and Mark Stevens, both at Sandia,
.. raw:: latex
\normalsize
Past developers include Paul Crozier and Mark Stevens, both at SNL,
and Ray Shan, now at Materials Design.
----------

39
doc/src/Intro_nonfeatures.rst
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@ -25,9 +25,13 @@ Here are suggestions on how to perform these tasks:
wraps the library interface is provided. Thus, GUI interfaces can be
written in Python or C/C++ that run LAMMPS and visualize or plot its
output. Examples of this are provided in the python directory and
described on the :doc:`Python <Python_head>` doc page. As of version
2 August 2023 :ref:`a GUI tool <lammps_gui>` is included in LAMMPS.
Also, there are several external wrappers or GUI front ends.
described on the :doc:`Python <Python_head>` doc page.
Since version 2 August 2023 :ref:`a LAMMPS-GUI tool <lammps_gui>` is
included in LAMMPS. Also, there are several external wrappers or GUI
front ends that are mentioned on the `Pre-/post-processing tools page
<https://www.lammps.org/prepost.html>`_ of the LAMMPS homepage.
* **Builder:** Several pre-processing tools are packaged with LAMMPS.
Some of them convert input files in formats produced by other MD codes
such as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of
@ -35,12 +39,13 @@ Here are suggestions on how to perform these tasks:
such as linear bead-spring polymer chains. The moltemplate program is
a true molecular builder that will generate complex molecular models.
See the :doc:`Tools <Tools>` page for details on tools packaged with
LAMMPS. The `Pre-/post-processing page
LAMMPS. The `Pre-/post-processing tools page
<https://www.lammps.org/prepost.html>`_ of the LAMMPS homepage
describes a variety of third party tools for this task. Furthermore,
some internal LAMMPS commands allow reconstructing, or selectively adding
topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems.
* **Force-field assignment:** The conversion tools described in the previous
bullet for CHARMM, AMBER, and Insight will also assign force field
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
@ -49,6 +54,7 @@ Here are suggestions on how to perform these tasks:
`InterMol <https://github.com/shirtsgroup/InterMol>`_ are particularly
powerful and flexible in converting force field and topology data
between various MD simulation programs.
* **Simulation analysis:** If you want to perform analysis on-the-fly as
your simulation runs, see the :doc:`compute <compute>` and :doc:`fix
<fix>` doc pages, which list commands that can be used in a LAMMPS
@ -66,19 +72,38 @@ Here are suggestions on how to perform these tasks:
extract and massage data in dump files to make it easier to import
into other programs. See the :doc:`Tools <Tools>` page for details on
these various options.
The `Pre-/post-processing page <https://www.lammps.org/prepost.html>`_
on the LAMMPS homepage lists some external packages for analysis of MD
simulation data, including data produced by LAMMPS.
* **Visualization:** LAMMPS can produce NETPBM, JPG, or PNG format
snapshot images on-the-fly via its :doc:`dump image <dump_image>`
command and pass them to an external program, `FFmpeg <https://ffmpeg.org/>`_,
to generate movies from them. For high-quality, interactive visualization,
there are many excellent and free tools available. See the `Visualization Tools
command and pass them to an external program, `FFmpeg
<https://ffmpeg.org/>`_, to generate movies from them. The
:ref:`LAMMPS-GUI tool <lammps_gui>` has an *Snapshot Image Viewer*
which uses :doc:`dump image <dump_image>` and allows to modify the
visualization settings interactively. It also has a *Slide Show*
feature where images created by :doc:`dump image <dump_image>` are
collected during a simulation and can be animated interactively or
exported to a movie with FFmpeg.
For high-quality, interactive visualization, there are many excellent
and free tools available. See the `Visualization Tools
<https://www.lammps.org/viz.html>`_ page of the LAMMPS website for
visualization packages that can process LAMMPS output data.
* **Plotting:** See the next bullet about Pizza.py as well as the
:doc:`Python <Python_head>` page for examples of plotting LAMMPS
output. Scripts provided with the *python* tool in the ``tools``
directory will extract and process data in log and dump files to make
it easier to analyze and plot. See the :doc:`Tools <Tools>` doc page
for more discussion of the various tools.
The :ref:`LAMMPS-GUI tool <lammps_gui>` has an *Chart Viewer* where
:doc:`thermodynamic data <thermo_style>` computed by LAMMPS is
collected during the simulation and plotted immediately.
* **Pizza.py:** Our group has also written a separate toolkit called
`Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS

18
doc/src/Intro_opensource.rst
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@ -34,18 +34,20 @@ choose, including for commercial purposes.
(2) If you **distribute** a modified version of LAMMPS, it must remain
open-source, meaning you are required to distribute **all** of it under
the terms of the GPL. You should clearly annotate such a modified code
as a derivative version of LAMMPS.
the terms of the GPLv2. You should **clearly** annotate such a modified
code as a derivative version of LAMMPS. This is best done by changing
the name (example: LIGGGHTS is such a modified and extended version of
LAMMPS).
(3) If you release any code that includes or uses LAMMPS source code,
then it must also be open-sourced, meaning you distribute it under
the terms of the GPL. You may write code that interfaces LAMMPS to
a differently licensed library. In that case the code that provides
the interface must be licensed GPL, but not necessarily that library
then it must also be open-sourced, meaning you distribute it under the
terms of the GPLv2. You may write code that interfaces LAMMPS to a
differently licensed library. In that case the code that provides the
interface must be licensed GPLv2, but not necessarily that library
unless you are distributing binaries that require the library to run.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
(4) If you give LAMMPS files to someone else, the GPLv2 LICENSE file and
source file headers (including the copyright and GPLv2 notices) should
remain part of the code.

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