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This commit is contained in:
Chris Knight
2024-10-02 15:27:17 +00:00
parent 663aa8aa80 ec2fece8db
commit 715a0c3d18
1906 changed files with 233027 additions and 77910 deletions
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25
.github/CODEOWNERS vendored
View File

@ -38,6 +38,7 @@ src/ML-HDNNP/* @singraber
src/ML-IAP/* @athomps
src/ML-PACE/* @yury-lysogorskiy
src/ML-POD/* @exapde
src/ML-UF3/* @monk-04
src/MOFFF/* @hheenen
src/MOLFILE/* @akohlmey
src/NETCDF/* @pastewka
@ -49,6 +50,7 @@ src/PTM/* @pmla
src/QMMM/* @akohlmey
src/REACTION/* @jrgissing
src/REAXFF/* @hasanmetin @stanmoore1
src/RHEO/* @jtclemm
src/SCAFACOS/* @rhalver
src/SNAP/* @athomps
src/SPIN/* @julient31
@ -58,11 +60,15 @@ src/VTK/* @rbberger
# individual files in packages
src/GPU/pair_vashishta_gpu.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane
src/KOKKOS/pair_vashishta_kokkos.* @andeplane @stanmoore1
src/KOSSOS/pair_pod_kokkos.* @exapde @stanmoore1
src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMMAND/geturl.* @akohlmey
src/EXTRA-COMMAND/group_ndx.* @akohlmey
src/EXTRA-COMMAND/ndx_group.* @akohlmey
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
@ -72,6 +78,8 @@ src/MC/fix_sgcmc.* @athomps
src/REAXFF/compute_reaxff_atom.* @rbberger
src/KOKKOS/compute_reaxff_atom_kokkos.* @rbberger
src/REPLICA/fix_pimd_langevin.* @Yi-FanLi
src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
# core LAMMPS classes
src/lammps.* @sjplimp
@ -91,9 +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
@ -101,12 +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 update
sudo apt-get install -y ccache \
libeigen3-dev \
libcurl4-openssl-dev \
mold \
mpi-default-bin \
mpi-default-dev \
ninja-build \
python3-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-vla-ccache-${{ github.sha }}
restore-keys: linux-vla-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -S cmake -B build \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER=g++ \
-D CMAKE_C_COMPILER=gcc \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D CMAKE_BUILD_TYPE=Debug \
-D CMAKE_CXX_FLAGS_DEBUG="-Og -g -Werror=vla" \
-D DOWNLOAD_POTENTIALS=off \
-D BUILD_MPI=on \
-D BUILD_SHARED_LIBS=off \
-D BUILD_TOOLS=off \
-D ENABLE_TESTING=off \
-D MLIAP_ENABLE_ACE=on \
-D MLIAP_ENABLE_PYTHON=off \
-D PKG_AWPMD=on \
-D PKG_GPU=on \
-D GPU_API=opencl \
-D PKG_LATBOLTZ=on \
-D PKG_MDI=on \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=off \
-D PKG_MOLFILE=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s

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

109
.github/workflows/full-regression.yml vendored Normal file
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@ -0,0 +1,109 @@
# GitHub action to build LAMMPS on Linux and run regression tests
name: "Full Regression Test"
on:
push:
branches:
- develop
workflow_dispatch:
jobs:
build:
name: Build LAMMPS
# restrict to official LAMMPS repository
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 8
matrix:
idx: [ 0, 1, 2, 3, 4, 5, 6, 7 ]
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 2
show-progress: false
- name: Install extra packages
run: |
sudo apt-get update
sudo apt-get install -y ccache ninja-build libeigen3-dev \
libcurl4-openssl-dev python3-dev \
mpi-default-bin mpi-default-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-full-ccache-${{ github.sha }}
restore-keys: linux-full-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install numpy pyyaml junit_xml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=off \
-D DOWNLOAD_POTENTIALS=off \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Full Regression Tests
shell: bash
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_serial.yaml \
--examples-top-level=examples --analyze --num-workers=8
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_serial.yaml \
--list-input=input-list-${{ matrix.idx }}.txt \
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log
tar -cvf full-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
- name: Upload artifacts
uses: actions/upload-artifact@v4
with:
name: full-regression-test-artifact-${{ matrix.idx }}
path: full-regression-test-${{ matrix.idx }}.tar
merge:
runs-on: ubuntu-latest
needs: build
steps:
- name: Merge Artifacts
uses: actions/upload-artifact/merge@v4
with:
name: merged-full-regresssion-artifact
pattern: full-regression-test-artifact-*

118
.github/workflows/quick-regression.yml vendored Normal file
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@ -0,0 +1,118 @@
# GitHub action to build LAMMPS on Linux and run selected regression tests
name: "Quick Regression Test"
on:
pull_request:
branches:
- develop
workflow_dispatch:
concurrency:
group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: ${{github.event_name == 'pull_request'}}
jobs:
build:
name: Build LAMMPS
# restrict to official LAMMPS repository
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
env:
CCACHE_DIR: ${{ github.workspace }}/.ccache
strategy:
max-parallel: 4
matrix:
idx: [ 0, 1, 2, 3 ]
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 0
show-progress: false
- name: Install extra packages
run: |
sudo apt-get update
sudo apt-get install -y ccache ninja-build libeigen3-dev \
libcurl4-openssl-dev python3-dev \
mpi-default-bin mpi-default-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-quick-ccache-${{ github.sha }}
restore-keys: linux-quick-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install numpy pyyaml junit_xml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=off \
-D DOWNLOAD_POTENTIALS=off \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Regression Tests for Modified Styles
shell: bash
run: |
source linuxenv/bin/activate
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_quick.yaml \
--examples-top-level=examples \
--quick-reference=tools/regression-tests/reference.yaml \
--quick --quick-branch=origin/develop --quick-max=100 --num-workers=4
if [ -f input-list-${{ matrix.idx }}.txt ]
then \
python3 tools/regression-tests/run_tests.py \
--lmp-bin=build/lmp \
--config-file=tools/regression-tests/config_quick.yaml \
--list-input=input-list-${{ matrix.idx }}.txt \
--output-file=output-${{ matrix.idx }}.xml \
--progress-file=progress-${{ matrix.idx }}.yaml \
--log-file=run-${{ matrix.idx }}.log
fi
tar -cvf quick-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
- name: Upload artifacts
uses: actions/upload-artifact@v4
with:
name: quick-regression-test-artifact-${{ matrix.idx }}
path: quick-regression-test-${{ matrix.idx }}.tar
merge:
runs-on: ubuntu-latest
needs: build
steps:
- name: Merge Artifacts
uses: actions/upload-artifact/merge@v4
with:
name: merged-quick-regresssion-artifact
pattern: quick-regression-test-artifact-*

37
.github/workflows/style-check.yml vendored Normal file
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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 update
sudo apt-get install -y ccache \
libeigen3-dev \
libcurl4-openssl-dev \
mold \
ninja-build \
python3-dev
- name: Create Build Environment
run: mkdir build
- name: Set up ccache
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: linux-unit-ccache-${{ github.sha }}
restore-keys: linux-unit-ccache-
- name: Building LAMMPS via CMake
shell: bash
run: |
ccache -z
python3 -m venv linuxenv
source linuxenv/bin/activate
python3 -m pip install numpy
python3 -m pip install pyyaml
cmake -S cmake -B build \
-C cmake/presets/gcc.cmake \
-C cmake/presets/most.cmake \
-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-D CMAKE_C_COMPILER_LAUNCHER=ccache \
-D BUILD_SHARED_LIBS=on \
-D LAMMPS_SIZES=bigbig \
-D DOWNLOAD_POTENTIALS=off \
-D ENABLE_TESTING=on \
-D MLIAP_ENABLE_ACE=on \
-D MLIAP_ENABLE_PYTHON=off \
-D PKG_MANIFOLD=on \
-D PKG_ML-PACE=on \
-D PKG_ML-RANN=on \
-D PKG_RHEO=on \
-D PKG_PTM=on \
-D PKG_PYTHON=on \
-D PKG_QTB=on \
-D PKG_SMTBQ=on \
-G Ninja
cmake --build build
ccache -s
- name: Run Tests
working-directory: build
shell: bash
run: ctest -V

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

11
.gitignore vendored
View File

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

59
cmake/CMakeLists.txt
View File

@ -12,6 +12,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about requiring execute permission for find_program
# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
@ -23,6 +28,7 @@ project(lammps CXX)
set(SOVERSION 0)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
include(GNUInstallDirs)
get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
# collect all executables and shared libs in the top level build folder
@ -163,6 +169,22 @@ if(MSVC)
add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
endif()
# warn about potentially problematic GCC compiler versions
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
endif()
endif()
if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
"with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
endif()
endif()
endif()
# export all symbols when building a .dll file on windows
if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@ -197,18 +219,17 @@ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
option(BUILD_SHARED_LIBS "Build shared library" OFF)
option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
# Support using clang-tidy for C++ files with selected options
set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
if(ENABLE_CLANG_TIDY)
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
else()
unset(CMAKE_CXX_CLANG_TIDY CACHE)
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@ -256,6 +277,7 @@ set(STANDARD_PACKAGES
DRUDE
EFF
ELECTRODE
EXTRA-COMMAND
EXTRA-COMPUTE
EXTRA-DUMP
EXTRA-FIX
@ -281,10 +303,11 @@ set(STANDARD_PACKAGES
ML-HDNNP
ML-IAP
ML-PACE
ML-POD
ML-QUIP
ML-RANN
ML-SNAP
ML-POD
ML-UF3
MOFFF
MOLECULE
MOLFILE
@ -303,6 +326,7 @@ set(STANDARD_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SCAFACOS
SHOCK
@ -407,6 +431,7 @@ pkg_depends(CG-DNA ASPHERE)
pkg_depends(ELECTRODE KSPACE)
pkg_depends(EXTRA-MOLECULE MOLECULE)
pkg_depends(MESONT MOLECULE)
pkg_depends(RHEO BPM)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
@ -449,13 +474,13 @@ if(BUILD_OMP)
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${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()
@ -472,7 +497,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
PROPERTIES COMPILE_OPTIONS "-std=c++14")
endif()
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
enable_language(C)
if (NOT USE_INTERNAL_LINALG)
find_package(LAPACK)
@ -547,7 +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)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -689,7 +714,7 @@ endif()
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -867,7 +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
@ -937,8 +962,12 @@ message(STATUS "<<< Compilers and Flags: >>>
-- C++ Compiler: ${CMAKE_CXX_COMPILER}
Type: ${CMAKE_CXX_COMPILER_ID}
Version: ${CMAKE_CXX_COMPILER_VERSION}
C++ Standard: ${CMAKE_CXX_STANDARD}
C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines: ${DEFINES}")
if(CMAKE_CXX_COMPILER_LAUNCHER)
message(STATUS " Launcher: ${CMAKE_CXX_COMPILER_LAUNCHER}")
endif()
get_target_property(OPTIONS lammps COMPILE_OPTIONS)
if(OPTIONS)
message(" Options: ${OPTIONS}")
@ -957,6 +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}")
@ -1043,9 +1075,6 @@ endif()
if(BUILD_TOOLS)
message(STATUS "<<< Building Tools >>>")
endif()
if(BUILD_LAMMPS_SHELL)
message(STATUS "<<< Building LAMMPS Shell >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)

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)

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

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

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

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

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

@ -8,8 +8,24 @@ endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
option(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC "CUDA asynchronous malloc support" OFF)
mark_as_advanced(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
if(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
message(STATUS "KOKKOS: CUDA malloc async support enabled")
else()
message(STATUS "KOKKOS: CUDA malloc async support disabled")
endif()
endif()
if(Kokkos_ENABLE_HIP)
option(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS "Enable multiple kernel instantiations with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS)
option(Kokkos_ENABLE_ROCTHRUST "Use RoCThrust library" ON)
mark_as_advanced(Kokkos_ENABLE_ROCTHRUST)
if(Kokkos_ARCH_AMD_GFX942 OR Kokkos_ARCH_AMD_GFX940)
option(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY "Enable unified memory with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY)
endif()
endif()
# Adding OpenMP compiler flags without the checks done for
# BUILD_OMP can result in compile failures. Enforce consistency.
@ -18,6 +34,15 @@ if(Kokkos_ENABLE_OPENMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
endif()
endif()
if(Kokkos_ENABLE_SERIAL)
if(NOT (Kokkos_ENABLE_OPENMP OR Kokkos_ENABLE_THREADS OR
Kokkos_ENABLE_CUDA OR Kokkos_ENABLE_HIP OR Kokkos_ENABLE_SYCL
OR Kokkos_ENABLE_OPENMPTARGET))
option(Kokkos_ENABLE_ATOMICS_BYPASS "Disable atomics for Kokkos Serial Backend" ON)
mark_as_advanced(Kokkos_ENABLE_ATOMICS_BYPASS)
endif()
endif()
########################################################################
option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
@ -45,8 +70,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" CACHE STRING "MD5 checksum of KOKKOS tarball")
set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "de6ee80d00b6212b02bfb7f1e71a8392" CACHE STRING "MD5 checksum of KOKKOS tarball")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -71,7 +96,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.3.01 REQUIRED CONFIG)
find_package(Kokkos 4.4.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -127,7 +152,7 @@ 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 ${FFT_KOKKOS} FFT_KOKKOS)
@ -137,10 +162,8 @@ if(PKG_KSPACE)
message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
elseif(FFT_KOKKOS STREQUAL "KISS")
message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
elseif(FFT_KOKKOS STREQUAL "CUFFT")
find_package(CUDAToolkit REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
target_link_libraries(lammps PRIVATE CUDA::cufft)
endif()
elseif(Kokkos_ENABLE_HIP)
@ -152,10 +175,21 @@ if(PKG_KSPACE)
elseif(FFT_KOKKOS STREQUAL "HIPFFT")
include(DetectHIPInstallation)
find_package(hipfft REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
target_link_libraries(lammps PRIVATE hip::hipfft)
endif()
elseif(FFT_KOKKOS STREQUAL "MKL_GPU")
if(NOT Kokkos_ENABLE_SYCL)
message(FATAL_ERROR "Using MKL_GPU FFT currently requires the SYCL backend of Kokkos.")
endif()
find_package(MKL REQUIRED)
target_link_libraries(lammps PRIVATE mkl_sycl_dft mkl_intel_ilp64 mkl_tbb_thread mkl_core tbb)
elseif(FFT_KOKKOS STREQUAL "MKL")
find_package(MKL REQUIRED)
elseif(FFT_KOKKOS STREQUAL "NVPL")
find_package(nvpl_fft REQUIRED)
target_link_libraries(lammps PRIVATE nvpl::fftw)
endif()
target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_${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)

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

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

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

@ -1,5 +1,14 @@
# Plumed2 support for PLUMED package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
@ -21,9 +30,11 @@ else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
# Note: must also adjust check for supported API versions in
# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-src-2.9.2.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)
@ -75,6 +86,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
DEPENDS plumed_build
COMMENT "Copying Plumed files"
)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
endif()
else()
@ -149,21 +163,26 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
endif()
endif()
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

4
cmake/Modules/Testing.cmake
View File

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

31
cmake/Modules/Tools.cmake
View File

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

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

Binary file not shown.

7
cmake/packaging/build_linux_tgz.sh
View File

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

9
cmake/packaging/build_macos_dmg.sh
View File

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

5
cmake/packaging/build_windows_cross_zip.sh
View File

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

14
cmake/packaging/linux_wrapper.sh
View File

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

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

File diff suppressed because it is too large Load Diff

5
cmake/presets/all_off.cmake
View File

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

5
cmake/presets/all_on.cmake
View File

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

4
cmake/presets/clang.cmake
View File

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

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

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

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

3
cmake/presets/most.cmake
View File

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

5
cmake/presets/windows.cmake
View File

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

18
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "17 April 2024" "2024-04-17"
.TH LAMMPS "1" "29 August 2024" "2024-08-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 17 April 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).
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94
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).
@ -488,9 +498,10 @@ using CMake or Make.
.. code-block:: bash
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt
-D BUILD_LAMMPS_SHELL=value # yes or no (default). Build lammps-shell
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build lammps-gui
-D BUILD_TOOLS=value # yes or no (default). Build binary2txt,
# chain.x, micelle2d.x, msi2lmp, phana,
# stl_bin2txt
-D BUILD_LAMMPS_GUI=value # yes or no (default). Build LAMMPS-GUI
The generated binaries will also become part of the LAMMPS installation
(see below).
@ -505,8 +516,9 @@ using CMake or Make.
make chain # build only chain tool
make micelle2d # build only micelle2d tool
cd lammps/tools/lammps-shell
make # build LAMMPS shell
.. note::
Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
----------

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

177
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@ -88,8 +88,8 @@ on recording all commands required to do the compilation.
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------
Address, Leak, Undefined Behavior, and Thread Sanitizer Support (CMake only)
----------------------------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in the code
@ -110,6 +110,7 @@ compilation and linking stages. This is done through setting the
-D ENABLE_SANITIZER=none # no sanitizer active (default)
-D ENABLE_SANITIZER=address # enable address sanitizer / memory leak checker
-D ENABLE_SANITIZER=hwaddress # enable hardware assisted address sanitizer / memory leak checker
-D ENABLE_SANITIZER=leak # enable memory leak checker (only)
-D ENABLE_SANITIZER=undefined # enable undefined behavior sanitizer
-D ENABLE_SANITIZER=thread # enable thread sanitizer
@ -137,12 +138,27 @@ during development:
The status of this automated testing can be viewed on `https://ci.lammps.org
<https://ci.lammps.org>`_.
The scripts and inputs for integration, run, and regression testing
are maintained in a
`separate repository <https://github.com/lammps/lammps-testing>`_
of the LAMMPS project on GitHub. A few tests are also run as GitHub
Actions and their configuration files are in the ``.github/workflows/``
folder of the LAMMPS git tree.
The scripts and inputs for integration, run, and legacy regression
testing are maintained in a `separate repository
<https://github.com/lammps/lammps-testing>`_ of the LAMMPS project on
GitHub. A few tests are also run as GitHub Actions and their
configuration files are in the ``.github/workflows/`` folder of the
LAMMPS git tree.
Regression tests can also be performed locally with the :ref:`regression
tester tool <regression>`. The tool checks if a given LAMMPS binary run
with selected input examples produces thermo output that is consistent
with the provided log files. The script can be run in one pass over all
available input files, but it can also first create multiple lists of
inputs or folders that can then be run with multiple workers
concurrently to speed things up. Another mode allows to do a quick
check of inputs that contain commands that have changes in the current
checkout branch relative to a git branch. This works similar to the two
pass mode, but will select only shorter runs and no more than 100 inputs
that are chosen randomly. This ensures that this test runs
significantly faster compared to the full test run. These test runs can
also be performed with instrumented LAMMPS binaries (see previous
section).
The unit testing facility is integrated into the CMake build process of
the LAMMPS source code distribution itself. It can be enabled by
@ -152,7 +168,12 @@ development headers to compile (if those are not found locally a recent
version of that library will be downloaded and compiled along with
LAMMPS and the test programs) and will download and compile a specific
version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
test framework that is used to implement the tests.
test framework that is used to implement the tests. Those unit tests
may be combined with memory access and leak checking with valgrind
(see below for how to enable it). In that case, running so-called
death tests will create a lot of false positives and thus they can be
disabled by configuring compilation with the additional setting
``-D SKIP_DEATH_TESTS=on``.
.. admonition:: Software version and LAMMPS configuration requirements
:class: note
@ -175,24 +196,24 @@ The output of this command will be looking something like this:
$ ctest
Test project /home/akohlmey/compile/lammps/build-testing
Start 1: RunLammps
1/563 Test #1: RunLammps .......................................... Passed 0.28 sec
1/563 Test #1: RunLammps .................................. Passed 0.28 sec
Start 2: HelpMessage
2/563 Test #2: HelpMessage ........................................ Passed 0.06 sec
2/563 Test #2: HelpMessage ................................ Passed 0.06 sec
Start 3: InvalidFlag
3/563 Test #3: InvalidFlag ........................................ Passed 0.06 sec
3/563 Test #3: InvalidFlag ................................ Passed 0.06 sec
Start 4: Tokenizer
4/563 Test #4: Tokenizer .......................................... Passed 0.05 sec
4/563 Test #4: Tokenizer .................................. Passed 0.05 sec
Start 5: MemPool
5/563 Test #5: MemPool ............................................ Passed 0.05 sec
5/563 Test #5: MemPool .................................... Passed 0.05 sec
Start 6: ArgUtils
6/563 Test #6: ArgUtils ........................................... Passed 0.05 sec
6/563 Test #6: ArgUtils ................................... Passed 0.05 sec
[...]
Start 561: ImproperStyle:zero
561/563 Test #561: ImproperStyle:zero ................................. Passed 0.07 sec
561/563 Test #561: ImproperStyle:zero ......................... Passed 0.07 sec
Start 562: TestMliapPyUnified
562/563 Test #562: TestMliapPyUnified ................................. Passed 0.16 sec
562/563 Test #562: TestMliapPyUnified ......................... Passed 0.16 sec
Start 563: TestPairList
563/563 Test #563: TestPairList ....................................... Passed 0.06 sec
563/563 Test #563: TestPairList ............................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 563
@ -207,24 +228,25 @@ The output of this command will be looking something like this:
The ``ctest`` command has many options, the most important ones are:
.. list-table::
:widths: 20 80
* - Option
- Function
* - -V
* - ``-V``
- verbose output: display output of individual test runs
* - -j <num>
* - ``-j <num>``
- parallel run: run <num> tests in parallel
* - -R <regex>
* - ``-R <regex>``
- run subset of tests matching the regular expression <regex>
* - -E <regex>
* - ``-E <regex>``
- exclude subset of tests matching the regular expression <regex>
* - -L <regex>
* - ``-L <regex>``
- run subset of tests with a label matching the regular expression <regex>
* - -LE <regex>
* - ``-LE <regex>``
- exclude subset of tests with a label matching the regular expression <regex>
* - -N
* - ``-N``
- dry-run: display list of tests without running them
* - -T memcheck
* - ``-T memcheck``
- run tests with valgrind memory checker (if available)
In its full implementation, the unit test framework will consist of multiple
@ -330,16 +352,17 @@ paths in the individual source files.
The force style test programs have a common set of options:
.. list-table::
:widths: 25 75
* - Option
- Function
* - -g <newfile>
* - ``-g <newfile>``
- regenerate reference data in new YAML file
* - -u
* - ``-u``
- update reference data in the original YAML file
* - -s
* - ``-s``
- print error statistics for each group of comparisons
* - -v
* - ``-v``
- verbose output: also print the executed LAMMPS commands
The ``ctest`` tool has no mechanism to directly pass flags to the individual
@ -353,10 +376,10 @@ set in an environment variable ``TEST_ARGS``. Example:
To add a test for a style that is not yet covered, it is usually best
to copy a YAML file for a similar style to a new file, edit the details
of the style (how to call it, how to set its coefficients) and then
run test command with either the *-g* and the replace the initial
test file with the regenerated one or the *-u* option. The *-u* option
run test command with either the ``-g`` and the replace the initial
test file with the regenerated one or the ``-u`` option. The ``-u`` option
will destroy the original file, if the generation run does not complete,
so using *-g* is recommended unless the YAML file is fully tested
so using ``-g`` is recommended unless the YAML file is fully tested
and working.
Some of the force style tests are rather slow to run and some are very
@ -506,27 +529,51 @@ After post-processing with ``gen_coverage_html`` the results are in
a folder ``coverage_html`` and can be viewed with a web browser.
The images below illustrate how the data is presented.
.. list-table::
.. only:: not latex
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
.. list-table::
Top of the overview page
* - .. figure:: JPG/coverage-overview-top.png
:scale: 25%
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
Top of the overview page
Styles with good coverage
- .. figure:: JPG/coverage-overview-manybody.png
:scale: 25%
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
Styles with good coverage
Top of individual source page
- .. figure:: JPG/coverage-file-top.png
:scale: 25%
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Top of individual source page
Source page with branches
- .. figure:: JPG/coverage-file-branches.png
:scale: 25%
Source page with branches
.. only:: latex
.. figure:: JPG/coverage-overview-top.png
:width: 60%
Top of the overview page
.. figure:: JPG/coverage-overview-manybody.png
:width: 60%
Styles with good coverage
.. figure:: JPG/coverage-file-top.png
:width: 60%
Top of individual source page
.. figure:: JPG/coverage-file-branches.png
:width: 60%
Source page with branches
Coding style utilities
----------------------
@ -598,11 +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.

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

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

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

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@ -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
doc/src/Commands_all.rst
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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>`

57
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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
@ -23,11 +9,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <bond_none>`
* :doc:`zero <bond_zero>`
* :doc:`hybrid <bond_hybrid>`
* :doc:`hybrid (k) <bond_hybrid>`
*
*
*
*
*
@ -54,13 +42,14 @@ OPT.
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`rheo/shell <bond_rheo_shell>`
* :doc:`special <bond_special>`
* :doc:`table (o) <bond_table>`
.. _angle:
Angle_style potentials
======================
Angle styles
============
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -68,11 +57,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <angle_none>`
* :doc:`zero <angle_zero>`
* :doc:`hybrid <angle_hybrid>`
* :doc:`hybrid (k) <angle_hybrid>`
*
*
*
*
*
@ -100,13 +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
@ -114,11 +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>`
*
*
*
*
*
@ -143,8 +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
@ -152,11 +145,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 5
* :doc:`none <improper_none>`
* :doc:`zero <improper_zero>`
* :doc:`hybrid <improper_hybrid>`
* :doc:`hybrid (k) <improper_hybrid>`
*
*
*
*
*

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

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

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

26
doc/src/Commands_fix.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Fix commands
============
Fix styles
==========
An alphabetic list of all LAMMPS :doc:`fix <fix>` commands. Some styles
have accelerated versions. This is indicated by additional letters in
@ -21,13 +7,14 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 5
:columns: 4
* :doc:`accelerate/cos <fix_accelerate_cos>`
* :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
* :doc:`adapt <fix_adapt>`
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`add/heat <fix_add_heat>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`alchemy <fix_alchemy>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
@ -204,6 +191,11 @@ OPT.
* :doc:`reaxff/species (k) <fix_reaxff_species>`
* :doc:`recenter <fix_recenter>`
* :doc:`restrain <fix_restrain>`
* :doc:`rheo <fix_rheo>`
* :doc:`rheo/oxidation <fix_rheo_oxidation>`
* :doc:`rheo/pressure <fix_rheo_pressure>`
* :doc:`rheo/thermal <fix_rheo_thermal>`
* :doc:`rheo/viscosity <fix_rheo_viscosity>`
* :doc:`rhok <fix_rhok>`
* :doc:`rigid (o) <fix_rigid>`
* :doc:`rigid/meso <fix_rigid_meso>`

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>`

40
doc/src/Commands_pair.rst
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@ -1,19 +1,5 @@
.. table_from_list::
:columns: 3
* :doc:`General commands <Commands_all>`
* :doc:`Fix styles <Commands_fix>`
* :doc:`Compute styles <Commands_compute>`
* :doc:`Pair styles <Commands_pair>`
* :ref:`Bond styles <bond>`
* :ref:`Angle styles <angle>`
* :ref:`Dihedral styles <dihedral>`
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
* :doc:`Dump styles <Commands_dump>`
Pair_style potentials
======================
Pair styles
===========
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
@ -21,20 +7,20 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
OPT.
.. table_from_list::
:columns: 4
:columns: 3
* :doc:`none <pair_none>`
* :doc:`zero <pair_zero>`
* :doc:`hybrid (k) <pair_hybrid>`
* :doc:`hybrid/overlay (k) <pair_hybrid>`
* :doc:`hybrid/scaled <pair_hybrid>`
* :doc:`hybrid (ko) <pair_hybrid>`
* :doc:`hybrid/molecular (o) <pair_hybrid>`
* :doc:`hybrid/overlay (ko) <pair_hybrid>`
* :doc:`hybrid/scaled (o) <pair_hybrid>`
* :doc:`kim <pair_kim>`
* :doc:`list <pair_list>`
* :doc:`tracker <pair_tracker>`
*
*
*
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@ -94,9 +80,10 @@ OPT.
* :doc:`coul/wolf (ko) <pair_coul>`
* :doc:`coul/wolf/cs <pair_cs>`
* :doc:`dpd (giko) <pair_dpd>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
* :doc:`dpd/ext (ko) <pair_dpd_ext>`
* :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
* :doc:`dpd/fdt <pair_dpd_fdt>`
* :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
* :doc:`dpd/tstat (gko) <pair_dpd>`
* :doc:`dsmc <pair_dsmc>`
@ -190,7 +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>`
@ -246,7 +233,7 @@ OPT.
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pedone (o) <pair_pedone>`
* :doc:`pod <pair_pod>`
* :doc:`pod (k) <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
@ -259,6 +246,8 @@ OPT.
* :doc:`rebo (io) <pair_airebo>`
* :doc:`rebomos (o) <pair_rebomos>`
* :doc:`resquared (go) <pair_resquared>`
* :doc:`rheo <pair_rheo>`
* :doc:`rheo/solid <pair_rheo_solid>`
* :doc:`saip/metal (t) <pair_saip_metal>`
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smatb <pair_smatb>`
@ -269,7 +258,7 @@ OPT.
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (ik) <pair_snap>`
* :doc:`soft (go) <pair_soft>`
* :doc:`soft (gko) <pair_soft>`
* :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
* :doc:`sph/idealgas <pair_sph_idealgas>`
* :doc:`sph/lj (g) <pair_sph_lj>`
@ -303,6 +292,7 @@ OPT.
* :doc:`tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`tri/lj <pair_tri_lj>`
* :doc:`ufm (got) <pair_ufm>`
* :doc:`uf3 (k) <pair_uf3>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`

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

35
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@ -8,6 +8,18 @@ stop LAMMPS and print a suitable error message in most cases, when a
style/command is used that has been removed or will replace the command
with the direct alternative (if available) and print a warning.
restart2data tool
-----------------
.. versionchanged:: 23Nov2013
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`
Fix ave/spatial and fix ave/spatial/sphere
------------------------------------------
@ -148,12 +160,19 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
and the :ref:`GPU package <PKG-GPU>` are maintained
and allow running LAMMPS with GPU acceleration.
restart2data tool
-----------------
i-PI tool
---------
.. versionchanged:: 27Jun2024
The i-PI tool has been removed from the LAMMPS distribution. Instead,
instructions to install i-PI from PyPI via pip are provided.
LAMMPS shell
------------
.. versionchanged:: 29Aug2024
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
The functionality of the restart2data tool has been folded into the
LAMMPS executable directly instead of having a separate tool. A
combination of the commands :doc:`read_restart <read_restart>` and
:doc:`write_data <write_data>` can be used to the same effect. For
added convenience this conversion can also be triggered by
:doc:`command line flags <Run_options>`

8
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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
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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
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@ -69,7 +69,7 @@ The basic LAMMPS class hierarchy which is created by the LAMMPS class
constructor is shown in :ref:`class-topology`. When input commands
are processed, additional class instances are created, or deleted, or
replaced. Likewise, specific member functions of specific classes are
called to trigger actions such creating atoms, computing forces,
called to trigger actions such as creating atoms, computing forces,
computing properties, time-propagating the system, or writing output.
Compositing and Inheritance
@ -110,9 +110,10 @@ As mentioned above, there can be multiple instances of classes derived
from the ``Fix`` or ``Compute`` base classes. They represent a
different facet of LAMMPS' flexibility, as they provide methods which
can be called at different points within a timestep, as explained in
`Developer_flow`. This allows the input script to tailor how a specific
simulation is run, what diagnostic computations are performed, and how
the output of those computations is further processed or output.
the :doc:`How a timestep works <Developer_flow>` doc page. This allows
the input script to tailor how a specific simulation is run, what
diagnostic computations are performed, and how the output of those
computations is further processed or output.
Additional code sharing is possible by creating derived classes from the
derived classes (e.g., to implement an accelerated version of a pair

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

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

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

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
doc/src/Developer_par_long.rst
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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
doc/src/Developer_par_openmp.rst
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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
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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
doc/src/Developer_updating.rst
View File

@ -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.

5
doc/src/Developer_utils.rst
View File

@ -211,6 +211,9 @@ Argument processing
.. doxygenfunction:: bounds
:project: progguide
.. doxygenfunction:: bounds_typelabel
:project: progguide
.. doxygenfunction:: expand_args
:project: progguide
@ -619,7 +622,7 @@ classes:
of a dense, symmetric, real matrix.
#. The "PEigenDense" class only calculates the principal eigenvalue
(ie. the largest or smallest eigenvalue), and its corresponding
(i.e. the largest or smallest eigenvalue), and its corresponding
eigenvector. However it is much more efficient than "Jacobi" when
applied to large matrices (larger than 13x13). PEigenDense also can
understand complex-valued Hermitian matrices.

1
doc/src/Developer_write.rst
View File

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

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

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

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

59
doc/src/Developer_write_pair.rst
View File

@ -50,6 +50,30 @@ We are looking at the following cases:
- `Case 3: a potential requiring communication`_
- `Case 4: potentials without a compute() function`_
Package and build system considerations
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In general, new pair styles should be added to the :ref:`EXTRA-PAIR
package <PKG-EXTRA-PAIR>` unless they are an accelerated pair style and
then they should be added to the corresponding accelerator package
(:ref:`GPU <PKG-GPU>`, :ref:`INTEL <PKG-INTEL>`, :ref:`KOKKOS
<PKG-KOKKOS>`, :ref:`OPENMP <PKG-OPENMP>`, :ref:`OPT <PKG-OPT>`). If
you feel that your contribution should be added to a different package,
please consult with the LAMMPS developers first.
The contributed code needs to support the :doc:`traditional GNU make
build process <Build_make>` **and** the :doc:`CMake build process
<Build_cmake>`. For the GNU make process and if the package has an
``Install.sh`` file, most likely that file needs to be updated to
correctly copy the sources when installing the package and properly
delete them when uninstalling. This is particularly important when
added a new pair style that is a derived class from an existing pair
style in a package, so that its installation depends on the the
installation status of the package of the derived class. For the CMake
process, it is sometimes necessary to make changes to the package
specific CMake scripting in ``cmake/Modules/Packages``.
----
Case 1: a pairwise additive model
@ -136,7 +160,7 @@ message and before the include guards for the class definition:
#endif
This block of between ``#ifdef PAIR_CLASS`` and ``#else`` will be
This block between ``#ifdef PAIR_CLASS`` and ``#else`` will be
included by the ``Force`` class in ``force.cpp`` to build a map of
"factory functions" that will create an instance of these classes and
return a pointer to it. The map connects the name of the pair style,
@ -347,9 +371,9 @@ but moving this to a separate function allows users to change global
settings like the default cutoff without having to reissue all
pair_coeff commands or re-read the ``Pair Coeffs`` sections from the
data file. In the ``settings()`` function, also the arrays for storing
parameters, to define cutoffs, track with pairs of parameters have been
explicitly set are allocated and, if needed, initialized. In this case,
the memory allocation and initialization is moved to a function
parameters, to define cutoffs, track which pairs of parameters have been
explicitly set and allocated and, if needed, initialized. In this case,
the memory allocation and initialization are moved to a function
``allocate()``.
.. code-block:: c++
@ -564,17 +588,20 @@ loop atoms are also initialized.
jnum = numneigh[i];
The inner loop (index *j*) processes the neighbor lists. The neighbor
list code encodes in the upper 2 bits whether a pair is a regular pair
of neighbor (= 0) or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3)
:doc:`"special" neighbor <special_bonds>`. The ``sbmask()`` inline
function extracts those bits and converts them into a number. This
number is used to look up the corresponding scaling factor for the
non-bonded interaction from the ``force->special_lj`` array and stores
it in the `factor_lj` variable. Due to the additional bits, the value
of *j* would be out of range when accessing data from per-atom arrays,
so we apply the NEIGHMASK constant with a bit-wise and operation to mask
them out. This step *must* be done, even if a pair style does not use
special bond scaling of forces and energies to avoid segmentation faults.
list code encodes extra information using the upper 3 bits. The 2
highest bits encode whether a pair is a regular pair of neighbor (= 0)
or a pair of 1-2 (= 1), 1-3 (= 2), or 1-4 (= 3) :doc:`"special" neighbor
<special_bonds>`. The next highest bit encodes whether the pair stores
data in a ``fix neigh/history`` instance (an undocumented internal fix
style). The ``sbmask()`` inline function extracts those bits and
converts them into a number. This number is used to look up the
corresponding scaling factor for the non-bonded interaction from the
``force->special_lj`` array and stores it in the `factor_lj` variable.
Due to the additional bits, the value of *j* would be out of range when
accessing data from per-atom arrays, so we apply the NEIGHMASK constant
with a bit-wise and operation to mask them out. This step *must* be
done, even if a pair style does not use special bond scaling of forces
and energies to avoid segmentation faults.
With the corrected *j* index, it is now possible to compute the distance
of the pair. For efficiency reasons, the square root is only taken
@ -867,7 +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
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@ -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
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@ -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

2
doc/src/Examples.rst
View File

@ -134,6 +134,8 @@ Lowercase directories
+-------------+------------------------------------------------------------------+
| rerun | use of rerun and read_dump commands |
+-------------+------------------------------------------------------------------+
| rheo | RHEO simulations of fluid flows and phase transitions |
+-------------+------------------------------------------------------------------+
| rigid | rigid bodies modeled as independent or coupled |
+-------------+------------------------------------------------------------------+
| shear | sideways shear applied to 2d solid, with and without a void |

8
doc/src/Fortran.rst
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@ -305,6 +305,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype extract_setting: function
:f extract_global: :f:func:`extract_global`
:ftype extract_global: function
:f map_atom: :f:func:`map_atom`
:ftype map_atom: function
:f extract_atom: :f:func:`extract_atom`
:ftype extract_atom: function
:f extract_compute: :f:func:`extract_compute`
@ -1075,7 +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
@ -1165,7 +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
@ -2325,7 +2327,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
retrieved via :f:func:`get_last_error_message`. This allows to
restart a calculation or delete and recreate the LAMMPS instance when
a C++ exception occurs. One application of using exceptions this way
is the :ref:`lammps_shell`.
is the :ref:`lammps_gui`.
:to: :cpp:func:`lammps_config_has_exceptions`
:r has_exceptions:

1
doc/src/Howto.rst
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@ -89,6 +89,7 @@ Packages howto
Howto_drude2
Howto_peri
Howto_manifold
Howto_rheo
Howto_spins
Tutorials howto

198
doc/src/Howto_bioFF.rst
View File

@ -1,6 +1,10 @@
CHARMM, AMBER, COMPASS, and DREIDING force fields
=================================================
A compact summary of the concepts, definitions, and properties of
force fields with explicit bonded interactions (like the ones discussed
in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
formulas implemented in LAMMPS that correspond to formulas commonly used
@ -11,12 +15,42 @@ commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
<bond_coeff>` and so on. See the :doc:`Tools <Tools>` doc page for
additional tools that can use CHARMM, AMBER, or Materials Studio
generated files to assign force field coefficients and convert their
output into LAMMPS input.
output into LAMMPS input. LAMMPS input scripts can also be generated by
`charmm-gui.org <https://charmm-gui.org/>`_.
See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
force field. See :ref:`(Cornell) <howto-Cornell>` for a description of
the AMBER force field. See :ref:`(Sun) <howto-Sun>` for a description
of the COMPASS force field.
CHARMM and AMBER
----------------
The `CHARMM force field
<https://mackerell.umaryland.edu/charmm_ff.shtml>`_ :ref:`(MacKerell)
<howto-MacKerell>` and `AMBER force field
<https://ambermd.org/AmberModels.php>`_ :ref:`(Cornell) <howto-Cornell>`
have potential energy function of the form
.. math::
V & = \sum_{bonds} E_b + \sum_{angles} \!E_a + \!\overbrace{\sum_{dihedral} \!\!E_d}^{\substack{
\text{charmm} \\
\text{charmmfsw}
}} +\!\!\! \sum_{impropers} \!\!\!E_i \\[.6em]
& \quad + \!\!\!\!\!\!\!\!\!\!\underbrace{~\sum_{pairs} \left(E_{LJ}+E_{coul}\right)}_{\substack{
\text{lj/charmm/coul/charmm} \\
\text{lj/charmm/coul/charmm/implicit} \\
\text{lj/charmm/coul/long} \\
\text{lj/charmm/coul/msm} \\
\text{lj/charmmfsw/coul/charmmfsh} \\
\text{lj/charmmfsw/coul/long}
}} \!\!\!\!\!\!\!\!+ \!\!\sum_{special}\! E_s + \!\!\!\!\sum_{residues} \!\!\!{\scriptstyle\mathrm{CMAP}(\phi,\psi)}
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
details) corrects for pairs of dihedral angles ("Correction MAP") to
significantly improve the structural and dynamic properties of proteins
in crystalline and solution environments :ref:`(Brooks)
<howto-Brooks>`. The AMBER force field does not include the CMAP term.
The interaction styles listed below compute force field formulas that
are consistent with common options in CHARMM or AMBER. See each
@ -31,10 +65,81 @@ command's documentation for the formula it computes.
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/charmm/implicit
* :doc:`pair_style <pair_charmm>` lj/charmm/coul/long
* :doc:`special_bonds <special_bonds>` charmm
* :doc:`special_bonds <special_bonds>` amber
The pair styles compute Lennard Jones (LJ) and Coulombic interactions
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) :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
in some cases can result in complications in energy minimization and
detectable artifacts in MD simulations.
.. grid:: 1 1 2 2
.. grid-item::
.. math::
LJ(r) &= 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]\\[.6em]
C(r) &= \frac{C q_i q_j}{ \epsilon r}\\[.6em]
S(r) &= \frac{ \left(b^2 - r^2\right)^2 \left(b^2 + 2r^2 - 3{a^2}\right)}
{ \left(b^2 - a^2\right)^3 }\\[.6em]
E_{LJ}(r) &= \begin{cases}
LJ(r), & r \leq a \\
LJ(r) S(r), & a < r \leq b \\
0, &r > b
\end{cases} \\[.6em]
E_{coul}(r) &= \begin{cases}
C(r), & r \leq a \\
C(r) S(r), & a < r \leq b \\
0, & r > b
\end{cases}
.. grid-item::
.. image:: img/howto_charmm_ELJ.png
:align: center
The newer styles with *charmmfsw* or *charmmfsh* in their name replace
energy switching with force switching (fsw) for LJ interactions and
force shifting (fsh) functions for Coulombic interactions
:ref:`(Steinbach) <howto-Steinbach>`
.. grid:: 1 1 2 2
.. grid-item::
.. math::
E_{LJ}(r) = & \begin{cases}
4 \epsilon \sigma^6 \left(\frac{\displaystyle\sigma
^6-r^6}{\displaystyle r^{12}}-\frac{\displaystyle\sigma ^6}{\displaystyle a^6
b^6}+\frac{\displaystyle 1}{\displaystyle a^3 b^3}\right) & r\leq a \\
\frac{\displaystyle 4 \epsilon \sigma^6 \left(\sigma ^6
\left(b^6-r^6\right)^2-b^3 r^6 \left(a^3+b^3\right)
\left(b^3-r^3\right)^2\right)}{\displaystyle b^6 r^{12}
\left(b^6-a^6\right)} & a<r \leq b\\
0, & r>b
\end{cases}\\[.6em]
E_{coul}(r) & = \begin{cases}
C(r) \frac{\displaystyle (b-r)^2}{\displaystyle r b^2}, & r \leq b \\
0, & r > b
\end{cases}
.. grid-item::
.. image:: img/howto_charmmfsw_ELJ.png
:align: center
These styles are used by LAMMPS input scripts generated by
https://charmm-gui.org/ :ref:`(Brooks) <howto-Brooks>`.
.. note::
For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
@ -43,17 +148,33 @@ command's documentation for the formula it computes.
<pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
pages.
.. note::
The TIP3P water model is strongly recommended for use with the CHARMM
force field. In fact, `"using the SPC model with CHARMM parameters is
a bad idea"
<https://matsci.org/t/using-spc-water-with-charmm-ff/24715>`_ and `"to
enable TIP4P style water in CHARMM, you would have to write a new pair
style"
<https://matsci.org/t/hybrid-pair-styles-for-charmm-and-tip4p-ew/32609>`_
. LAMMPS input scripts generated by Solution Builder on https://charmm-gui.org
use TIP3P molecules for solvation. Any other water model can and
probably will lead to false conclusions.
COMPASS
-------
COMPASS is a general force field for atomistic simulation of common
organic molecules, inorganic small molecules, and polymers which was
developed using ab initio and empirical parameterization techniques.
See the :doc:`Tools <Tools>` page for the msi2lmp tool for creating
LAMMPS template input and data files from BIOVIA's Materials Studio
files. Please note that the msi2lmp tool is very old and largely
unmaintained, so it does not support all features of Materials Studio
provided force field files, especially additions during the last decade.
You should watch the output carefully and compare results, where
possible. See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS force
field.
developed using ab initio and empirical parameterization techniques
:ref:`(Sun) <howto-Sun>`. See the :doc:`Tools <Tools>` page for the
msi2lmp tool for creating LAMMPS template input and data files from
BIOVIA's Materials Studio files. Please note that the msi2lmp tool is
very old and largely unmaintained, so it does not support all features
of Materials Studio provided force field files, especially additions
during the last decade. You should watch the output carefully and
compare results, where possible. See :ref:`(Sun) <howto-Sun>` for a
description of the COMPASS force field.
These interaction styles listed below compute force field formulas that
are consistent with the COMPASS force field. See each command's
@ -70,14 +191,21 @@ documentation for the formula it computes.
* :doc:`special_bonds <special_bonds>` lj/coul 0 0 1
DREIDING is a generic force field developed by the `Goddard group <http://www.wag.caltech.edu>`_ at Caltech and is useful for
predicting structures and dynamics of organic, biological and main-group
inorganic molecules. The philosophy in DREIDING is to use general force
constants and geometry parameters based on simple hybridization
considerations, rather than individual force constants and geometric
parameters that depend on the particular combinations of atoms involved
in the bond, angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond term <pair_hbond_dreiding>` to describe interactions involving a
hydrogen atom on very electronegative atoms (N, O, F).
DREIDING
--------
DREIDING is a generic force field developed by the `Goddard group
<http://www.wag.caltech.edu>`_ at Caltech and is useful for predicting
structures and dynamics of organic, biological and main-group inorganic
molecules. The philosophy in DREIDING is to use general force constants
and geometry parameters based on simple hybridization considerations,
rather than individual force constants and geometric parameters that
depend on the particular combinations of atoms involved in the bond,
angle, or torsion terms. DREIDING has an :doc:`explicit hydrogen bond
term <pair_hbond_dreiding>` to describe interactions involving a
hydrogen atom on very electronegative atoms (N, O, F). Unlike CHARMM
or AMBER, the DREIDING force field has not been parameterized for
considering solvents (like water).
See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
@ -110,21 +238,31 @@ documentation for the formula it computes.
----------
.. _Typelabel2:
**(Gissinger)** 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).
.. _howto-MacKerell:
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998). J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f
.. _howto-Cornell:
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
**(Cornell)** Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman (1995). JACS 117, 5179-5197. https://doi.org/10.1021/ja00124a002
.. _howto-Steinbach:
**(Steinbach)** Steinbach, Brooks (1994). J Comput Chem, 15, 667. https://doi.org/10.1002/jcc.540150702
.. _howto-Brooks:
**(Brooks)** Brooks, et al (2009). J Comput Chem, 30, 1545. https://onlinelibrary.wiley.com/doi/10.1002/jcc.21287
.. _howto-Sun:
**(Sun)** Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
**(Sun)** Sun (1998). J. Phys. Chem. B, 102, 7338-7364. https://doi.org/10.1021/jp980939v
.. _howto-Mayo:
**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
**(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010

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

18
doc/src/Howto_chunk.rst
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@ -1,7 +1,7 @@
Use chunks to calculate system properties
=========================================
In LAMMS, "chunks" are collections of atoms, as defined by the
In LAMMPS, "chunks" are collections of atoms, as defined by the
:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns
each atom to a chunk ID (or to no chunk at all). The number of chunks
and the assignment of chunk IDs to atoms can be static or change over
@ -148,14 +148,14 @@ Example calculations with chunks
Here are examples using chunk commands to calculate various
properties:
(1) Average velocity in each of 1000 2d spatial bins:
1. Average velocity in each of 1000 2d spatial bins:
.. code-block:: LAMMPS
compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
(2) Temperature in each spatial bin, after subtracting a flow
2. Temperature in each spatial bin, after subtracting a flow
velocity:
.. code-block:: LAMMPS
@ -164,7 +164,7 @@ velocity:
compute vbias all temp/profile 1 0 0 y 10
fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out
(3) Center of mass of each molecule:
3. Center of mass of each molecule:
.. code-block:: LAMMPS
@ -172,7 +172,7 @@ velocity:
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
(4) Total force on each molecule and ave/max across all molecules:
4. Total force on each molecule and ave/max across all molecules:
.. code-block:: LAMMPS
@ -183,7 +183,7 @@ velocity:
thermo 1000
thermo_style custom step temp v_xave v_xmax
(5) Histogram of cluster sizes:
5. Histogram of cluster sizes:
.. code-block:: LAMMPS
@ -192,16 +192,16 @@ velocity:
compute size all property/chunk cc1 count
fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
(6) An example for using a per-chunk value to apply per-atom forces to
6. An example for using a per-chunk value to apply per-atom forces to
compress individual polymer chains (molecules) in a mixture, is
explained on the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command doc page.
(7) An example for using one set of per-chunk values for molecule
7. An example for using one set of per-chunk values for molecule
chunks, to create a second set of micelle-scale chunks (clustered
molecules, due to hydrophobicity), is explained on the
:doc:`compute reduce/chunk <compute_reduce_chunk>` command doc page.
(8) An example for using one set of per-chunk values (dipole moment
8. An example for using one set of per-chunk values (dipole moment
vectors) for molecule chunks, spreading the values to each atom in
each chunk, then defining a second set of chunks as spatial bins, and
using the :doc:`fix ave/chunk <fix_ave_chunk>` command to calculate an

4
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@ -339,8 +339,6 @@ Some common LAMMPS specific variables
- build LAMMPS with OpenMP support (default: ``on`` if compiler supports OpenMP fully, else ``off``)
* - ``BUILD_TOOLS``
- compile some additional executables from the ``tools`` folder (default: ``off``)
* - ``BUILD_LAMMPS_SHELL``
- compile the LAMMPS shell from the ``tools/lammps-shell`` folder (default: ``off``)
* - ``BUILD_DOC``
- include building the HTML format documentation for packaging/installing (default: ``off``)
* - ``CMAKE_TUNE_FLAGS``
@ -350,7 +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

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3
doc/src/Howto_moltemplate.rst
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@ -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
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@ -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
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@ -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
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@ -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

112
doc/src/Howto_rheo.rst Normal file
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@ -0,0 +1,112 @@
Reproducing hydrodynamics and elastic objects (RHEO)
====================================================
The RHEO package is a hybrid implementation of smoothed particle
hydrodynamics (SPH) for fluid flow, which can couple to the :doc:`BPM package
<Howto_bpm>` to model solid elements. RHEO combines these methods to enable
mesh-free modeling of multi-phase material systems. Its SPH solver supports
many advanced options including reproducing kernels, particle shifting, free
surface identification, and solid surface reconstruction. To model fluid-solid
systems, the status of particles can dynamically change between a fluid and
solid state, e.g. during melting/solidification, which determines how they
interact and their physical behavior. The package is designed with modularity
in mind, so one can easily turn various features on/off, adjust physical
details of the system, or develop new capabilities. For instance, the numerics
associated with calculating gradients, reproducing kernels, etc. are separated
into distinct classes to simplify the development of new integration schemes
which can call these calculations. Additional numerical details can be found in
:ref:`(Clemmer) <howto_rheo_clemmer>`. Example movies illustrating some of these
capabilities are found at https://www.lammps.org/movies.html#rheopackage.
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
features and therefore benefits from improved performance. The :ref:`MACHDYN
<PKG-MACHDYN>` package for solids may also be relevant for fluid-solid problems.
----------
At the core of the package is :doc:`fix rheo <fix_rheo>` which integrates
particle trajectories and controls many optional features (e.g. the use
of reproducing kernels). In conjunction to fix rheo, one must specify an
instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
of state and viscosity model, respectively. Optionally, one can model
a heat equation with :doc:`fix rheo/thermal <fix_rheo_thermal>`, which also
allows the user to specify equations for a particle's thermal conductivity,
specific heat, latent heat, and melting temperature. The ordering of these
fixes in an an input script matters. Fix rheo must be defined prior to all
other RHEO fixes.
Typically, RHEO requires atom style rheo. In addition to typical atom
properties like positions and forces, particles store a local density,
viscosity, pressure, and status. If thermal evolution is modeled, one must
use atom style rheo/thermal which also includes a local energy, temperature, and
conductivity. Note that the temperature is always derived from the energy.
This implies the *temperature* attribute of :doc:`the set command <set>` does not
affect particles. Instead, one should use the *sph/e* attribute.
The status variable uses bit-masking to track various properties of a particle
such as its current state of matter (fluid or solid) and its location relative
to a surface. Some of these properties (and others) can be accessed using
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
attribute in :doc:`the set command <set>` only allows control over the first bit
which sets the state of matter, 0 is fluid and 1 is solid.
Fluid interactions, including pressure forces, viscous forces, and heat exchange,
are calculated using :doc:`pair rheo <pair_rheo>`. Unlike typical pair styles,
pair rheo ignores the :doc:`special bond <special_bonds>` settings. Instead,
it determines whether to calculate forces based on the status of particles: e.g.,
hydrodynamic forces are only calculated if a fluid particle is involved.
----------
To model elastic objects, there are currently two mechanisms in RHEO, one designed
for bulk solid bodies and the other for thin shells. Both mechanisms rely on
introducing bonded forces between particles and therefore require a hybrid of atom
style bond and rheo (or rheo/thermal).
To create an elastic solid body, one has to (a) change the status of constituent
particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
pair rheo/solid considers a particles fluid/solid phase to determine whether to
apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
settings such that contact forces do not have to be calculated between two bonded
solid particles in the same elastic body.
In systems with thermal evolution, fix rheo/thermal can optionally set a
melting/solidification temperature allowing particles to dynamically swap their
state between fluid and solid when the temperature exceeds or drops below the
critical temperature, respectively. Using the *react* option, one can specify a maximum
bond length and a bond type. Then, when solidifying, particles will search their
local neighbors and automatically create bonds with any neighboring solid particles
in range. For BPM bond styles, bonds will then use the immediate position of the two
particles to calculate a reference state. When melting, particles will delete any
bonds of the specified type when reverting to a fluid state. Special bonds are updated
as bonds are created/broken.
The other option for elastic objects is an elastic shell that is nominally much
thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
on the surface of a fluid. Currently, this is implemented using
:doc:`fix rheo/oxidation <fix_rheo_oxidation>` and bond style
:doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidation creates candidate
bonds of a specified type between surface fluid particles within a specified distance.
a newly created rheo/shell bond will then start a timer. While the timer is counting
down, the bond will delete itself if particles move too far apart or move away from the
surface. However, if the timer reaches a user-defined threshold, then the bond will
activate and apply additional forces to the fluid particles. Bond style rheo/shell
then operates very similarly to a BPM bond style, storing a reference length and
breaking if stretched too far. Unlike the above method, this option does not remove
the underlying fluid interactions (although particle shifting is turned off) and does
not modify special bond settings of particles.
While these two options are not expected to be appropriate for every system,
either framework can be modified to create more suitable models (e.g. by changing the
criteria for creating/deleting a bond or altering force calculations).
----------
.. _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
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@ -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).

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