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Merge branch 'develop' into small-patches

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This commit is contained in:
jtclemm
2024-09-27 15:30:31 -06:00
parent 10e5f4270f ec2fece8db
commit ba071fe55a
571 changed files with 25176 additions and 18802 deletions
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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

31
cmake/CMakeLists.txt
View File

@ -12,6 +12,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about requiring execute permission for find_program
# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
@ -469,13 +474,13 @@ if(BUILD_OMP)
if(CMAKE_VERSION VERSION_LESS 3.28)
get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
endif()
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
endif()
endif()
endif()
@ -492,7 +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)
@ -510,14 +515,6 @@ if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_T
endif()
endif()
find_package(CURL QUIET COMPONENTS HTTP HTTPS)
option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
if(WITH_CURL)
find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
target_link_libraries(lammps PRIVATE CURL::libcurl)
endif()
# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
set(JPEG_NAMES libjpeg libjpeg-62)
find_package(JPEG QUIET)
@ -575,7 +572,7 @@ else()
endif()
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
@ -968,6 +965,9 @@ message(STATUS "<<< Compilers and Flags: >>>
C++ Standard: ${CMAKE_CXX_STANDARD}
C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines: ${DEFINES}")
if(CMAKE_CXX_COMPILER_LAUNCHER)
message(STATUS " Launcher: ${CMAKE_CXX_COMPILER_LAUNCHER}")
endif()
get_target_property(OPTIONS lammps COMPILE_OPTIONS)
if(OPTIONS)
message(" Options: ${OPTIONS}")
@ -986,6 +986,9 @@ if(_index GREATER -1)
Type: ${CMAKE_C_COMPILER_ID}
Version: ${CMAKE_C_COMPILER_VERSION}
C Flags: ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
if(CMAKE_C_COMPILER_LAUNCHER)
message(STATUS " Launcher: ${CMAKE_C_COMPILER_LAUNCHER}")
endif()
endif()
message(STATUS "<<< Linker flags: >>>")
message(STATUS "Executable name: ${LAMMPS_BINARY}")

48
cmake/Modules/Documentation.cmake
View File

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

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)

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)

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

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

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

@ -1,2 +0,0 @@
find_package(GSL 2.6 REQUIRED)
target_link_libraries(lammps PRIVATE GSL::gsl)

BIN
cmake/packaging/LAMMPS_DMG_Background.xcf Normal file
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Binary file not shown.

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

1
cmake/presets/mingw-cross.cmake
View File

@ -67,6 +67,7 @@ set(WIN_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SHOCK
SMTBQ

1
cmake/presets/most.cmake
View File

@ -60,6 +60,7 @@ set(ALL_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SHOCK
SPH

1
cmake/presets/windows.cmake
View File

@ -60,6 +60,7 @@ set(WIN_PACKAGES
REACTION
REAXFF
REPLICA
RHEO
RIGID
SHOCK
SMTBQ

4
doc/lammps.1
View File

@ -1,7 +1,7 @@
.TH LAMMPS "1" "27 June 2024" "2024-06-27"
.TH LAMMPS "1" "29 August 2024" "2024-08-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 27 June 2024
\- Molecular Dynamics Simulator. Version 29 August 2024
.SH SYNOPSIS
.B lmp

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

65
doc/src/Build_development.rst
View File

@ -138,12 +138,27 @@ during development:
The status of this automated testing can be viewed on `https://ci.lammps.org
<https://ci.lammps.org>`_.
The scripts and inputs for integration, run, and regression testing
are maintained in a
`separate repository <https://github.com/lammps/lammps-testing>`_
of the LAMMPS project on GitHub. A few tests are also run as GitHub
Actions and their configuration files are in the ``.github/workflows/``
folder of the LAMMPS git tree.
The scripts and inputs for integration, run, and legacy regression
testing are maintained in a `separate repository
<https://github.com/lammps/lammps-testing>`_ of the LAMMPS project on
GitHub. A few tests are also run as GitHub Actions and their
configuration files are in the ``.github/workflows/`` folder of the
LAMMPS git tree.
Regression tests can also be performed locally with the :ref:`regression
tester tool <regression>`. The tool checks if a given LAMMPS binary run
with selected input examples produces thermo output that is consistent
with the provided log files. The script can be run in one pass over all
available input files, but it can also first create multiple lists of
inputs or folders that can then be run with multiple workers
concurrently to speed things up. Another mode allows to do a quick
check of inputs that contain commands that have changes in the current
checkout branch relative to a git branch. This works similar to the two
pass mode, but will select only shorter runs and no more than 100 inputs
that are chosen randomly. This ensures that this test runs
significantly faster compared to the full test run. These test runs can
also be performed with instrumented LAMMPS binaries (see previous
section).
The unit testing facility is integrated into the CMake build process of
the LAMMPS source code distribution itself. It can be enabled by
@ -630,11 +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.

87
doc/src/Build_extras.rst
View File

@ -7,6 +7,8 @@ in addition to
.. list-table::
:align: center
:header-rows: 1
:widths: 50 50
:width: 80%
* - CMake build
- Traditional make
@ -115,7 +117,7 @@ GPU package
To build with this package, you must choose options for precision and
which GPU hardware to build for. The GPU package currently supports
three different types of backends: OpenCL, CUDA and HIP.
three different types of back ends: OpenCL, CUDA and HIP.
CMake build
^^^^^^^^^^^
@ -205,7 +207,7 @@ necessary for ``hipcc`` and the linker to work correctly.
.. versionadded:: 3Aug2022
Using the CHIP-SPV implementation of HIP is supported. It allows one to
run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
run HIP code on Intel GPUs via the OpenCL or Level Zero back ends. To use
CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
the use of HIP for Intel GPUs is experimental. You should only use this
@ -751,14 +753,27 @@ This list was last updated for version 4.3.0 of the Kokkos library.
platform-appropriate vendor library: rocFFT on AMD GPUs or cuFFT on
NVIDIA GPUs.
To simplify compilation, five preset files are included in the
For Intel GPUs using SYCL, set these variables:
.. code-block:: bash
-D Kokkos_ARCH_HOSTARCH=yes # HOSTARCH = HOST from list above
-D Kokkos_ARCH_GPUARCH=yes # GPUARCH = GPU from list above
-D Kokkos_ENABLE_SYCL=yes
-D Kokkos_ENABLE_OPENMP=yes
-D FFT_KOKKOS=MKL_GPU
This will enable FFTs on the GPU using the oneMKL library.
To simplify compilation, six preset files are included in the
``cmake/presets`` folder, ``kokkos-serial.cmake``,
``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``. They will enable
the KOKKOS package and enable some hardware choices. For GPU
support those preset files must be customized to match the
hardware used. So to compile with CUDA device parallelization with
some common packages enabled, you can do the following:
``kokkos-hip.cmake``, ``kokkos-sycl-nvidia.cmake``, and
``kokkos-sycl-intel.cmake``. They will enable the KOKKOS
package and enable some hardware choices. For GPU support those
preset files must be customized to match the hardware used. So
to compile with CUDA device parallelization with some common
packages enabled, you can do the following:
.. code-block:: bash
@ -830,6 +845,18 @@ This list was last updated for version 4.3.0 of the Kokkos library.
FFT_INC = -DFFT_HIPFFT # enable use of hipFFT (optional)
FFT_LIB = -lhipfft # link to hipFFT library
For Intel GPUs using SYCL:
.. code-block:: make
KOKKOS_DEVICES = SYCL
KOKKOS_ARCH = HOSTARCH,GPUARCH # HOSTARCH = HOST from list above that is
# hosting the GPU
# GPUARCH = GPU from list above
FFT_INC = -DFFT_KOKKOS_MKL_GPU # enable use of oneMKL for Intel GPUs (optional)
# link to oneMKL FFT library
FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -mkl_core -ltbb
Advanced KOKKOS compilation settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -1517,6 +1544,11 @@ in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
Instead of including the ML-PACE package directly into LAMMPS, it
is also possible to skip this step and build the ML-PACE package as
a plugin using the CMake script files in the ``examples/PACKAGE/pace/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
@ -1701,6 +1733,11 @@ try a different one, switch to a different build system, consider a
global PLUMED installation or consider downloading PLUMED during the
LAMMPS build.
Instead of including the PLUMED package directly into LAMMPS, it
is also possible to skip this step and build the PLUMED package as
a plugin using the CMake script files in the ``examples/PACKAGE/plumed/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
@ -2214,28 +2251,38 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
RHEO package
------------
To build with this package you must have the `GNU Scientific Library
(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
are accessible in your environment. The GSL library should be at least
version 2.7.
This package depends on the BPM package.
.. tabs::
.. tab:: CMake build
If CMake cannot find the GSL library or include files, you can set:
.. code-block:: bash
-D GSL_ROOT_DIR=path # path to root of GSL installation
-D PKG_RHEO=yes # enable the package itself
-D PKG_BPM=yes # the RHEO package requires BPM
-D USE_INTERNAL_LINALG=value # prefer internal LAPACK if true
Some features in the RHEO package are dependent on code in the BPM
package so the latter one *must* be enabled as well.
The RHEO package also requires LAPACK (and BLAS) and CMake
can identify their locations and pass that info to the RHEO
build script. But on some systems this may cause problems when
linking or the dependency is not desired. By using the setting
``-D USE_INTERNAL_LINALG=yes`` when running the CMake
configuration, you will select compiling and linking the bundled
linear algebra library and work around the limitations.
.. tab:: Traditional make
LAMMPS will try to auto-detect the GSL compiler and linker flags
from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
you can edit the file ``lib/rheo/Makefile.lammps``
to specify the paths and library names where indicated by comments.
This must be done **before** the package is installed.
The RHEO package requires LAPACK (and BLAS) which can be either
a system provided library or the bundled "linalg" library. This
is a subset of LAPACK translated to C++. For that, one of the
provided ``Makefile.lammps.<config>`` files needs to be copied
to ``Makefile.lammps`` and edited as needed. The default file
uses the bundled "linalg" library, which can be built by
``make lib-linalg args='-m serial'`` in the ``src`` folder.
----------

31
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@ -67,10 +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
@ -103,6 +103,8 @@ libraries and better pipelining for packing and communication.
-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::
@ -121,9 +123,10 @@ libraries and better pipelining for packing and communication.
.. code-block:: make
FFT_INC = -DFFT_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), or MKL
# FFTW (same as FFTW3), NVPL, or MKL
FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
# FFTW (same as FFTW3), MKL, CUFFT, or HIPFFT
# 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
@ -141,6 +144,9 @@ libraries and better pipelining for packing and communication.
# 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
@ -165,6 +171,10 @@ libraries and better pipelining for packing and communication.
# 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
files in its default search path. You must specify ``FFT_LIB``
@ -218,10 +228,15 @@ 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
@ -492,7 +507,7 @@ during a run.
Support for downloading files
-----------------------------
.. versionadded:: TBD
.. versionadded:: 29Aug2024
The :doc:`geturl command <geturl>` command uses the `the libcurl library
<https://curl.se/libcurl/>`_ to download files. This requires that

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

2
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@ -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

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

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

2
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@ -160,7 +160,7 @@ message and before the include guards for the class definition:
#endif
This block of between ``#ifdef PAIR_CLASS`` and ``#else`` will be
This block between ``#ifdef PAIR_CLASS`` and ``#else`` will be
included by the ``Force`` class in ``force.cpp`` to build a map of
"factory functions" that will create an instance of these classes and
return a pointer to it. The map connects the name of the pair style,

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

189
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@ -19,9 +19,9 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
(Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
Sur or later), and Windows (version 10 or later) :ref:`are available
<lammps_gui_install>` for download. None-MPI LAMMPS executables for
running LAMMPS from the command line and :doc:`some LAMMPS tools <Tools>`
are also included.
<lammps_gui_install>` for download. Non-MPI LAMMPS executables (as
``lmp``) for running LAMMPS from the command line and :doc:`some
LAMMPS tools <Tools>` compiled executables are also included.
The source code for LAMMPS-GUI is included in the LAMMPS source code
distribution and can be found in the ``tools/lammps-gui`` folder. It
@ -29,40 +29,50 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
<Build_cmake>`.
LAMMPS-GUI tries to provide an experience similar to what people
traditionally would have running LAMMPS using a command line window
and the console LAMMPS executable but just rolled into a single executable:
traditionally would have running LAMMPS using a command line window and
the console LAMMPS executable but just rolled into a single executable:
- writing & editing LAMMPS input files with a text editor
- run LAMMPS on those input file with selected command line flags
- use or extract data from the created files and visualize it with
either a molecular visualization program or a plotting program
- extract data from the created files and visualize it with and
external software
That procedure is quite effective for people proficient in using the
command line, as that allows them to use tools for the individual steps
that they are most comfortable with. It is often *required* to adopt
this workflow when running LAMMPS simulations on high-performance
that they are most comfortable with. In fact, it is often *required* to
adopt this workflow when running LAMMPS simulations on high-performance
computing facilities.
The main benefit of using LAMMPS-GUI is that many basic tasks can be
done directly from the GUI without switching to a text console window or
using external programs, let alone writing scripts to extract data from
the generated output. It also integrates well with graphical desktop
environments where the `.lmp` filename extension can be registered with
LAMMPS-GUI as the executable to launch when double clicking on such
files. Also, LAMMPS-GUI has support for drag-n-drop, i.e. an input
file can be selected and then moved and dropped on the LAMMPS-GUI
executable, and LAMMPS-GUI will launch and read the file into its
buffer.
done directly from the GUI **without** switching to a text console
window or using external programs, let alone writing scripts to extract
data from the generated output. It also integrates well with graphical
desktop environments where the `.lmp` filename extension can be
registered with LAMMPS-GUI as the executable to launch when double
clicking on such files. Also, LAMMPS-GUI has support for drag-n-drop,
i.e. an input file can be selected and then moved and dropped on the
LAMMPS-GUI executable, and LAMMPS-GUI will launch and read the file into
its buffer. In many cases LAMMPS-GUI will be integrated into the
graphical desktop environment and can be launched like other
applications.
LAMMPS-GUI thus makes it easier for beginners to get started running
simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
since you only need to learn how to use a single program for most tasks
and thus time can be saved and people can focus on learning LAMMPS.
The tutorials at https://lammpstutorials.github.io/ were specifically
The tutorials at https://lammpstutorials.github.io/ are specifically
updated for use with LAMMPS-GUI.
Another design goal is to keep the barrier low when replacing part of
the functionality of LAMMPS-GUI with external tools.
the functionality of LAMMPS-GUI with external tools. That said, LAMMPS-GUI
has some unique functionality that is not found elsewhere:
- auto-adapting to features available in the integrated LAMMPS library
- interactive visualization using the :doc:`dump image <dump_image>`
command with the option to copy-paste the resulting settings
- automatic slide show generation from dump image out at runtime
- automatic plotting of thermodynamics data at runtime
- inspection of binary restart files
The following text provides a detailed tour of the features and
functionality of LAMMPS-GUI. Suggestions for new features and
@ -134,9 +144,13 @@ When LAMMPS-GUI starts, it shows the main window, labeled *Editor*, with
either an empty buffer or the contents of the file used as argument. In
the latter case it may look like the following:
.. image:: JPG/lammps-gui-main.png
:align: center
:scale: 50%
.. |gui-main1| image:: JPG/lammps-gui-main.png
:width: 48%
.. |gui-main2| image:: JPG/lammps-gui-dark.png
:width: 48%
|gui-main1| |gui-main2|
There is the typical menu bar at the top, then the main editor buffer,
and a status bar at the bottom. The input file contents are shown
@ -276,8 +290,6 @@ right mouse button into the *Output* window text area.
:align: center
:scale: 50%
.. versionadded:: 1.6
Should the *Output* window contain embedded YAML format text (see above for a
demonstration), for example from using :doc:`thermo_style yaml
<thermo_style>` or :doc:`thermo_modify line yaml <thermo_modify>`, the
@ -289,10 +301,6 @@ text area.
Charts Window
-------------
.. versionadded:: 1.6
Plot smoothing support
By default, when starting a run, a *Charts* window opens that displays a
plot of thermodynamic output of the LAMMPS calculation as shown below.
@ -327,10 +335,6 @@ corresponds to. Same as for the *Output* window, the chart window is
replaced on each new run, but the behavior can be changed in the
*Preferences* dialog.
.. versionadded:: 1.6
Support for YAML export added
From the *File* menu on the top left, it is possible to save an image
of the currently displayed plot or export the data in either plain text
columns (for use by plotting tools like `gnuplot
@ -371,8 +375,6 @@ zoom in or zoom out of the displayed images. The button on the very
left triggers an export of the slide show animation to a movie file,
provided the `FFmpeg program <https://ffmpeg.org/>`_ is installed.
.. versionadded:: 1.6
When clicking on the "garbage can" icon, all image files of the slide
show will be deleted. Since their number can be large for long
simulations, this option enables to safely and quickly clean up the
@ -391,7 +393,7 @@ below.
.. image:: JPG/lammps-gui-variable-info.png
:align: center
:scale: 75%
:scale: 50%
Like for the *Output* and *Charts* windows, its content is continuously
updated during a run. It will show "(none)" if there are no variables
@ -435,20 +437,21 @@ instance when using reduced (= 'lj') :doc:`units <units>`, then
LAMMPS-GUI will check the current pair style and if it is a
Lennard-Jones type potential, it will extract the *sigma* parameter
for each atom type and assign atom diameters from those numbers.
For cases where atom diameters are not auto-detected, the *Atom size* field
can be edited and a suitable value set manually. The default value
is inferred from the x-direction lattice spacing.
Otherwise the default sequence of colors of the :doc:`dump image
<dump_image>` command is assigned to the different atom types and the
diameters are all the same.
If elements cannot be detected the default sequence of colors of the
:doc:`dump image <dump_image>` command is assigned to the different atom
types.
.. figure:: JPG/lammps-gui-image.png
:align: center
:scale: 50%
.. |gui-image1| image:: JPG/lammps-gui-image.png
:width: 48%
Visualization of LAMMPS "peptide" example
.. |gui-image2| image:: JPG/lammps-gui-funnel.png
:width: 48%
.. versionchanged:: 1.6
Buttons for toggling shininess and re-centering were added.
|gui-image1| |gui-image2|
The default image size, some default image quality settings, the view
style and some colors can be changed in the *Preferences* dialog
@ -468,8 +471,6 @@ current image can be saved to a file (keyboard shortcut `Ctrl-S`) or
copied to the clipboard (keyboard shortcut `Ctrl-C`) for pasting the
image into another application.
.. versionadded:: 1.6
From the *File* menu it is also possible to copy the current
:doc:`dump image <dump_image>` and :doc:`dump_modify <dump_image>`
commands to the clipboard so they can be pasted into a LAMMPS input file
@ -488,8 +489,6 @@ Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
dialog will pop up asking whether to cancel the exit operation, or to
save or not save the buffer contents to a file.
.. versionadded:: 1.6
The editor has an auto-save mode that can be enabled or disabled in the
*Preferences* dialog. In auto-save mode, the editor buffer is
automatically saved before running LAMMPS or before exiting LAMMPS-GUI.
@ -553,8 +552,6 @@ context menu that open the corresponding documentation page in the
online LAMMPS documentation in a web browser window. When using the
keyboard, the first of those entries is chosen.
.. versionadded:: 1.6
If the word under the cursor is a file, then additionally the context
menu has an entry to open the file in a read-only text viewer window.
If the file is a LAMMPS restart file, instead the menu entry offers to
@ -572,8 +569,6 @@ will contain a corresponding message.
Inspecting a Restart file
^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionadded:: 1.6
When LAMMPS-GUI is asked to "Inspect a Restart", it will read the
restart file into a LAMMPS instance and then open three different
windows. The first window is a text viewer with the output of an
@ -629,9 +624,10 @@ Edit
^^^^
The *Edit* menu offers the usual editor functions like *Undo*, *Redo*,
*Cut*, *Copy*, *Paste*. It can also open a *Preferences* dialog
(keyboard shortcut `Ctrl-P`) and allows deleting all stored preferences
and settings, so they are reset to their default values.
*Cut*, *Copy*, *Paste*, and a *Find and Replace* dialog (keyboard
shortcut `Ctrl-F`). It can also open a *Preferences* dialog (keyboard
shortcut `Ctrl-P`) and allows deleting all stored preferences and
settings, so they are reset to their default values.
Run
^^^
@ -667,7 +663,7 @@ set *before* a run is started.
.. image:: JPG/lammps-gui-variables.png
:align: center
:scale: 75%
:scale: 50%
The *Set Variables* dialog will be pre-populated with entries that
are set as index variables in the input and any variables that are
@ -716,6 +712,43 @@ https://lammpstutorials.github.io/ in a web browser window.
-----
Find and Replace
----------------
.. image:: JPG/lammps-gui-find.png
:align: center
:scale: 33%
The *Find and Replace* dialog allows searching for and replacing
text in the *Editor* window.
The dialog can be opened either from the *Edit* menu or with the
keyboard shortcut `Ctrl-F`. You can enter the text to search for.
Through three check-boxes the search behavior can be adjusted:
- If checked, "Match case" does a case sensitive search; otherwise
the search is case insensitive.
- If checked, "Wrap around" starts searching from the start of the
document, if there is no match found from the current cursor position
until the end of the document; otherwise the search will stop.
- If checked, the "Whole word" setting only finds full word matches
(white space and special characters are word boundaries).
Clicking on the *Next* button will search for the next occurrence of the
search text and select / highlight it. Clicking on the *Replace* button
will replace an already highlighted search text and find the next one.
If no text is selected, or the selected text does not match the
selection string, then the first click on the *Replace* button will
only search and highlight the next occurrence of the search string.
Clicking on the *Replace All* button will replace all occurrences from
the cursor position to the end of the file; if the *Wrap around* box is
checked, then it will replace **all** occurrences in the **entire**
document. Clicking on the *Done* button will dismiss the dialog.
------
Preferences
-----------
@ -848,7 +881,7 @@ available (On macOS use the Command key instead of Ctrl/Control).
.. list-table::
:header-rows: 1
:widths: auto
:widths: 16 19 13 16 13 22
* - Shortcut
- Function
@ -890,32 +923,32 @@ available (On macOS use the Command key instead of Ctrl/Control).
- Quit Application
- Ctrl+A
- Select All
- Ctrl+P
- Preferences
- Ctrl+F
- Find and Replace
* - Ctrl+W
- Close Window
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS-GUI Howto
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+?
- Context Help
- Ctrl+Shift+W
- Show Variables
* - Ctrl+Shift+M
- LAMMPS Manual
- TAB
- Reformat line
- Shift+TAB
- Show Completions
* - Ctrl+Shift+T
- LAMMPS Tutorial
- Ctrl+Shift+Enter
* - Ctrl+Shift+Enter
- Run File
-
-
- Ctrl+Shift+W
- Show Variables
- Ctrl+P
- Preferences
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS-GUI Howto
* - Ctrl+Shift+M
- LAMMPS Manual
- Ctrl+?
- Context Help
- Ctrl+Shift+T
- LAMMPS Tutorial
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In

4
doc/src/Howto_pylammps.rst
View File

@ -39,16 +39,18 @@ lammps.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 :py:class:`ctypes based interface <lammps.lammps>`
* 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
-----------

4
doc/src/Intro_authors.rst
View File

@ -56,7 +56,7 @@ lammps.org". General questions about LAMMPS should be posted in the
- SNL
- jmgoff at sandia.gov
- machine learned potentials, QEq solvers, Python
* - Megan McCarthy
* - Meg McCarthy
- SNL
- megmcca at sandia.gov
- alloys, micro-structure, machine learned potentials
@ -67,7 +67,7 @@ lammps.org". General questions about LAMMPS should be posted in the
* - `Trung Nguyen <tn_>`_
- U Chicago
- ndactrung at gmail.com
- soft matter, GPU package
- soft matter, GPU package, DIELECTRIC package, regression testing
.. _rb: https://rbberger.github.io/
.. _gc: https://enthalpiste.fr/

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6
doc/src/Library_atoms.rst
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@ -4,6 +4,7 @@ Per-atom properties
This section documents the following functions:
- :cpp:func:`lammps_extract_atom_datatype`
- :cpp:func:`lammps_extract_atom_size`
- :cpp:func:`lammps_extract_atom`
-----------------------
@ -13,6 +14,11 @@ This section documents the following functions:
-----------------------
.. doxygenfunction:: lammps_extract_atom_size
:project: progguide
-----------------------
.. doxygenfunction:: lammps_extract_atom
:project: progguide

9
doc/src/Packages_details.rst
View File

@ -1823,7 +1823,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
**Install:**
This package has :ref:`specific installation instructions <ml-pace>` on the
:doc:`Build extras <Build_extras>` page.
:doc:`Build extras <Build_extras>` page. This package may also be compiled
as a plugin to avoid licensing conflicts when distributing binaries.
**Supporting info:**
@ -2344,7 +2345,9 @@ and Gareth Tribello.
**Install:**
This package has :ref:`specific installation instructions <plumed>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <plumed>` on the
:doc:`Build extras <Build_extras>` page. This package may also be compiled
as a plugin to avoid licensing conflicts when distributing binaries.
**Supporting info:**
@ -2642,7 +2645,7 @@ This package has :ref:`specific installation instructions <rheo>` on the :doc:`B
**Authors:** Joel T. Clemmer (Sandia National Labs),
Thomas C. O'Connor (Carnegie Mellon University)
.. versionadded:: TBD
.. versionadded:: 29Aug2024
**Supporting info:**

2
doc/src/Run_options.rst
View File

@ -508,7 +508,7 @@ e.g. the *nfile* and *fileper* keywords. See the
**-restart2info restartfile keyword ...**
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Write out some info about the restart file and and immediately exit.
This is the same operation as if the following 2-line input script were

32
doc/src/Tools.rst
View File

@ -590,20 +590,31 @@ and the LAMMPS library, via ``-D LAMMPS_SOURCE_DIR=/path/to/lammps/src``.
CMake will try to guess a build folder with the LAMMPS library from that
path, but it can also be set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
Plugin version
""""""""""""""
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader that will load
the LAMMPS library dynamically at runtime during the start of the GUI
from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
possible to compile the GUI with a plugin loader that will load the
LAMMPS library dynamically at runtime during the start of the GUI from a
shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
``liblammps.dll`` (depending on the operating system). This has the
advantage that the LAMMPS library can be built from updated or modified
LAMMPS source without having to recompile the GUI. The ABI of the
LAMMPS C-library interface is very stable and generally backward
compatible. This feature is enabled by setting
``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
compatible. This feature is enabled by setting ``-D
LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
distribution.
When compiling LAMMPS-GUI with plugin support, there is an additional
command line flag (``-p <path>`` or ``--pluginpath <path>``) which
allows to override the path to LAMMPS shared library used by the GUI.
This is usually auto-detected on the first run and can be changed in the
LAMMPS-GUI *Preferences* dialog. The command line flag allows to reset
this path to a valid value in case the original setting has become
invalid. An empty path ("") as argument restores the default setting.
Platform notes
^^^^^^^^^^^^^^
@ -671,6 +682,15 @@ folder> --target tgz`` or ``make tgz`` to build a
``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
support libraries.
It is also possible to build a `flatpak bundle
<https://docs.flatpak.org/en/latest/single-file-bundles.html>`_ which is
a way to distribute applications in a way that is compatible with most
Linux distributions. Use the "flatpak" target to trigger a compile
(``cmake --build <build folder> --target flatpak`` or ``make flatpak``).
Please note that this will not build from the local sources but from the
repository and branch listed in the ``org.lammps.lammps-gui.yml``
LAMMPS-GUI source folder.
----------
.. _arc:
@ -1002,7 +1022,7 @@ regression tests with a given LAMMPS binary. The tool launches the
LAMMPS binary with any given input script under one of the `examples`
subdirectories, and compares the thermo output in the generated log file
with those in the provided log file with the same number of processors
ub the same subdirectory. If the differences between the actual and
in the same subdirectory. If the differences between the actual and
reference values are within specified tolerances, the test is considered
passed. For each test batch, that is, a set of example input scripts,
the mpirun command, the LAMMPS command line arguments, and the

2
doc/src/bond_rheo_shell.rst
View File

@ -38,7 +38,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
The *rheo/shell* bond style is designed to work with
:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate

2
doc/src/compute_rheo_property_atom.rst
View File

@ -55,7 +55,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Define a computation that stores atom attributes specific to the RHEO
package for each atom in the group. This is useful so that the values

2
doc/src/compute_temp.rst
View File

@ -59,7 +59,7 @@ factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
:doc:`compute_modify <compute_modify>` command if this is not the case.

78
doc/src/fix_adapt.rst
View File

@ -319,25 +319,32 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
:math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *bond* does not support bond_style hybrid nor bond_style
hybrid/overlay as bond styles. The bond styles that currently work
with fix_adapt are
If :doc:`bond_style hybrid <bond_hybrid>` is used, *bstyle* should be a
sub-style name. The bond styles that currently work with fix adapt are:
+------------------------------------+------------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+------------------------------------+------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+------------------------------------+------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+------------------------------------+------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+------------------------------------+------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+------------------------------------+------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+------------------------------------+------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+------------------------------------+------------+------------+
+---------------------------------------------------+---------------------------+------------+
| :doc:`class2 <bond_class2>` | r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`fene <bond_fene>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`fene/expand <bond_fene_expand>` | k,r0,epsilon,sigma,shift | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`fene/nm <bond_fene>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`gromos <bond_gromos>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`harmonic <bond_harmonic>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/shift <bond_harmonic_shift>` | k,r0,r1 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`harmonic/restrain <bond_harmonic_restrain>` | k | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`mm3 <bond_mm3>` | k,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`morse <bond_morse>` | r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
| :doc:`nonlinear <bond_nonlinear>` | epsilon,r0 | type bonds |
+---------------------------------------------------+---------------------------+------------+
----------
@ -357,15 +364,34 @@ all types from 1 to :math:`N`. A leading asterisk means all types from
:math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
Currently *angle* does not support angle_style hybrid nor angle_style
hybrid/overlay as angle styles. The angle styles that currently work
with fix_adapt are
If :doc:`angle_style hybrid <angle_hybrid>` is used, *astyle* should be a
sub-style name. The angle styles that currently work with fix adapt are:
+------------------------------------+----------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+------------------------------------+----------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+------------------------------------+----------+-------------+
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`harmonic <angle_harmonic>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`charmm <angle_charmm>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`class2 <angle_class2>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine <angle_cosine>` | k | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/periodic <angle_cosine_periodic>` | k,b,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`dipole <angle_dipole>` | k,gamma0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier <angle_fourier>` | k,c0,c1,c2 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`fourier/simple <angle_fourier_simple>` | k,c,n | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`mm3 <angle_mm3>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`quartic <angle_quartic>` | k2,k3,k4,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
| :doc:`spica <angle_spica>` | k,theta0 | type angles |
+--------------------------------------------------------------------+-----------------+-------------+
Note that internally, theta0 is stored in radians, so the variable
this fix uses to reset theta0 needs to generate values in radians.

2
doc/src/fix_meso_move.rst
View File

@ -247,7 +247,7 @@ defined by the :doc:`atom_style sph <atom_style>` command.
All particles in the group must be mesoscopic SPH/SDPD particles.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_mvv_dpd.rst
View File

@ -97,7 +97,7 @@ These fixes are part of the DPD-MESO package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_rheo.rst
View File

@ -43,7 +43,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Perform time integration for RHEO particles, updating positions, velocities,
and densities. For an overview of other features available in the RHEO package,

2
doc/src/fix_rheo_oxidation.rst
View File

@ -27,7 +27,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix dynamically creates bonds on the surface of fluids to
represent physical processes such as oxidation. It is intended

2
doc/src/fix_rheo_pressure.rst
View File

@ -33,7 +33,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix defines a pressure equation of state for RHEO particles. One can
define different equations of state for different atom types. An equation

2
doc/src/fix_rheo_thermal.rst
View File

@ -48,7 +48,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix performs time integration of temperature for atom style rheo/thermal.
In addition, it defines multiple thermal properties of particles and handles

2
doc/src/fix_rheo_viscosity.rst
View File

@ -38,7 +38,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix defines a viscosity for RHEO particles. One can define different
viscosities for different atom types, but a viscosity must be specified for

2
doc/src/fix_rigid_meso.rst
View File

@ -353,7 +353,7 @@ defined by the :doc:`atom_style sph <atom_style>` command.
All particles in the group must be mesoscopic SPH/SDPD particles.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_shake.rst
View File

@ -137,7 +137,7 @@ constrained (within a fudge factor of MASSDELTA specified in
both bonds in the angle are constrained then the angle will also be
constrained if its type is in the list.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
The types may be given as type labels *only* if there is no atom, bond,
or angle type label named *b*, *a*, *t*, or *m* defined in the

2
doc/src/fix_smd_integrate_tlsph.rst
View File

@ -53,7 +53,7 @@ Restrictions
This fix is part of the MACHDYN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_smd_integrate_ulsph.rst
View File

@ -61,7 +61,7 @@ Restrictions
This fix is part of the MACHDYN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/geturl.rst
View File

@ -32,7 +32,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Download a file from an URL to the local disk. This is implemented with
the `libcurl library <https:://curl.se/libcurl/>`_ which supports a

2
doc/src/group2ndx.rst
View File

@ -51,7 +51,7 @@ index file. When specifying group IDs, only those groups will be
written to the index file. In order to follow the Gromacs conventions,
the group *all* will be renamed to *System* in the index file.
The *ndx2group* command will create of update group definitions from
The *ndx2group* command will create or update group definitions from
those stored in an index file. Without specifying any group IDs, all
groups except *System* will be read from the index file and the
corresponding groups recreated. If a group of the same name already

2
doc/src/neigh_modify.rst
View File

@ -159,7 +159,7 @@ sample scenarios where this is useful:
* When one or more rigid bodies are specified, interactions within each
body can be turned off to save needless computation. See the :doc:`fix rigid <fix_rigid>` command for more details.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
Support for type labels was added.

21
doc/src/pair_hbond_dreiding.rst
View File

@ -18,28 +18,27 @@ Syntax
.. code-block:: LAMMPS
pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutoff
* style = *hbond/dreiding/lj* or *hbond/dreiding/morse*
* n = cosine angle periodicity
* N = power of cosine of angle theta (integer)
* inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units)
* outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
* angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
* interactions (degrees)
* angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor interactions (degrees)
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90.0
pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90.0
pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9.0 11.0 90.0
labelmap atom 1 C 2 O 3 H
pair_coeff C O hbond/dreiding/morse H i 3.88 1.7241379 2.9 2 9 11 90
pair_coeff C O hbond/dreiding/morse H i 3.88 1.7241379 2.9 2 9.0 11.0 90.0
Description
"""""""""""
@ -65,7 +64,8 @@ force field, given by:
where :math:`r_{\rm in}` is the inner spline distance cutoff,
:math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is
the angle cutoff, and *n* is the cosine periodicity.
the angle cutoff, and :math:`n` is the power of the cosine of the angle
:math:`\theta`.
Here, *r* is the radial distance between the donor (D) and acceptor
(A) atoms and :math:`\theta` is the bond angle between the acceptor, the
@ -217,7 +217,8 @@ These pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.
These pair styles do not write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need to be
These pair styles do not write their information to :doc:`binary restart
files <restart>`, so pair_style and pair_coeff commands need to be
re-specified in an input script that reads a restart file.
These pair styles can only be used via the *pair* keyword of the

2
doc/src/pair_rheo.rst
View File

@ -31,7 +31,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Pair style *rheo* computes pressure and viscous forces between particles
in the :doc:`rheo package <Howto_rheo>`. If thermal evolution is turned

2
doc/src/pair_rheo_solid.rst
View File

@ -21,7 +21,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Style *rheo/solid* is effectively a copy of pair style
:doc:`bpm/spring <pair_bpm_spring>` except it only applies forces

14
doc/src/region.rst
View File

@ -18,13 +18,13 @@ Syntax
*delete* = no args
*block* args = xlo xhi ylo yhi zlo zhi
xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all dimensions (distance units)
xlo,xhi,ylo,yhi,zlo,zhi can be a variable
xlo,xhi,ylo,yhi,zlo,zhi can be a variable (see below)
*cone* args = dim c1 c2 radlo radhi lo hi
dim = *x* or *y* or *z* = axis of cone
c1,c2 = coords of cone axis in other 2 dimensions (distance units)
radlo,radhi = cone radii at lo and hi end (distance units)
lo,hi = bounds of cone in dim (distance units)
c1,c2,radlo,radhi,lo,hi can be a variable (see below)
c1,c2,radlo,radhi,lo,hi can be a variable (see below)
*cylinder* args = dim c1 c2 radius lo hi
dim = *x* or *y* or *z* = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
@ -38,6 +38,7 @@ Syntax
*plane* args = px py pz nx ny nz
px,py,pz = point on the plane (distance units)
nx,ny,nz = direction normal to plane (distance units)
px,py,pz can be a variable (see below)
*prism* args = xlo xhi ylo yhi zlo zhi xy xz yz
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
xy = distance to tilt y in x direction (distance units)
@ -166,7 +167,7 @@ extending in the y-direction from -5.0 to the upper box boundary.
.. versionadded:: 4May2022
For style *ellipsoid*, an axis-aligned ellipsoid is defined. The
For style *ellipsoid*, an axis-aligned ellipsoid is defined. The
ellipsoid has its center at (x,y,z) and is defined by 3 axis-aligned
vectors given by A = (a,0,0); B = (0,b,0); C = (0,0,c). Note that
although the ellipsoid is specified as axis-aligned it can be rotated
@ -206,9 +207,10 @@ parameters a,b,c for style *ellipsoid*, can each be specified as an
equal-style :doc:`variable <variable>`. Likewise, for style *sphere*
and *ellipsoid* the x-, y-, and z- coordinates of the center of the
sphere/ellipsoid can be specified as an equal-style variable. And for
style *cylinder* the two center positions c1 and c2 for the location
of the cylinder axes can be specified as a equal-style variable. For style *cone*
all properties can be defined via equal-style variables.
style *cylinder* the two center positions c1 and c2 for the location of
the cylinder axes can be specified as a equal-style variable. For style
*cone* all properties can be defined via equal-style variables. For
style *plane* the point can be defined via equal-style variables.
If the value is a variable, it should be specified as v_name, where
name is the variable name. In this case, the variable will be

2
doc/src/variable.rst
View File

@ -1042,7 +1042,7 @@ label2type(), but returns 1 if the type label has been assigned,
otherwise it returns 0. This function can be used to check if a
particular type label already exists in the simulation.
.. versionadded:: TBD
.. versionadded:: 29Aug2024
The is_timeout() function returns 1 when the :doc:`timer timeout
<timer>` has expired otherwise it returns 0. This function can be used

7
doc/utils/sphinx-config/false_positives.txt
View File

@ -141,6 +141,7 @@ arg
arge
args
argv
Armv
arrhenius
Arun
arXiv
@ -215,7 +216,6 @@ ba
Babadi
Babaei
backcolor
backends
Baczewski
Bagchi
Bagi
@ -1539,6 +1539,7 @@ idx
ie
ielement
ieni
ifdef
ifdefs
iff
ifort
@ -2725,6 +2726,7 @@ OMP
oneAPI
onebody
onelevel
oneMKL
oneway
onlysalt
ons
@ -4130,6 +4132,7 @@ Xiaowang
Xie
xk
xlat
xlattice
xlo
xmax
Xmax
@ -4181,6 +4184,7 @@ yflag
yhi
yi
ylat
ylattice
ylo
ylz
ymax
@ -4229,6 +4233,7 @@ Ziegenhain
zincblende
zj
Zj
zlattice
zlim
zlo
Zm

5
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -41,7 +41,6 @@
#include <stdlib.h>
liblammpsplugin_t *liblammpsplugin_load(const char *lib)
{
liblammpsplugin_t *lmp;
@ -106,6 +105,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(map_atom);
ADDSYM(extract_atom_datatype);
ADDSYM(extract_atom_size);
ADDSYM(extract_atom);
ADDSYM(extract_compute);
@ -191,6 +191,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(is_running);
ADDSYM(force_timeout);
// symbol not present
if (!lmp->config_has_exceptions) return NULL;
lmp->has_exceptions = lmp->config_has_exceptions();
if (lmp->has_exceptions) {
ADDSYM(has_error);

1
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -151,6 +151,7 @@ struct _liblammpsplugin {
int (*map_atom)(void *, const void *);
int (*extract_atom_datatype)(void *, const char *);
int (*extract_atom_size)(void *, const char *, int);
void *(*extract_atom)(void *, const char *);
void *(*extract_compute)(void *, const char *, int, int);

8
examples/PACKAGES/pace/plugin/CMakeLists.txt
View File

@ -5,7 +5,7 @@
cmake_minimum_required(VERSION 3.16)
project(paceplugin VERSION 1.0 LANGUAGES CXX)
project(paceplugin VERSION 1.1 LANGUAGES CXX)
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
include(CheckIncludeFileCXX)
@ -15,7 +15,11 @@ include(ML-PACE)
##########################
# building the plugins
add_library(paceplugin MODULE paceplugin.cpp ${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp)
add_library(paceplugin MODULE paceplugin.cpp
${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace.cpp
${LAMMPS_SOURCE_DIR}/ML-PACE/pair_pace_extrapolation.cpp
${LAMMPS_SOURCE_DIR}/ML-PACE/compute_pace.cpp)
target_link_libraries(paceplugin PRIVATE pace)
target_link_libraries(paceplugin PRIVATE lammps)
target_include_directories(paceplugin PRIVATE ${LAMMPS_SOURCE_DIR}/ML-PACE)

32
examples/PACKAGES/pace/plugin/paceplugin.cpp
View File

@ -3,6 +3,8 @@
#include "version.h"
#include "pair_pace.h"
#include "pair_pace_extrapolation.h"
#include "compute_pace.h"
using namespace LAMMPS_NS;
@ -11,6 +13,16 @@ static Pair *pair_pace_creator(LAMMPS *lmp)
return new PairPACE(lmp);
}
static Pair *pair_pace_extrapolation_creator(LAMMPS *lmp)
{
return new PairPACEExtrapolation(lmp);
}
static Compute *compute_pace_creator(LAMMPS *lmp, int argc, char **argv)
{
return new ComputePACE(lmp, argc, argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
@ -25,4 +37,24 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_creator;
plugin.handle = handle;
(*register_plugin)(&plugin, lmp);
// register pace/extrapolation pair style
plugin.version = LAMMPS_VERSION;
plugin.style = "pair";
plugin.name = "pace/extrapolation";
plugin.info = "PACE plugin extrapolation pair style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &pair_pace_extrapolation_creator;
plugin.handle = handle;
(*register_plugin)(&plugin, lmp);
// register pace compute style
plugin.version = LAMMPS_VERSION;
plugin.style = "compute";
plugin.name = "pace";
plugin.info = "PACE plugin compute style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v2 = (lammpsplugin_factory2 *) &compute_pace_creator;
plugin.handle = handle;
(*register_plugin)(&plugin, lmp);
}

2
examples/PACKAGES/pace/plugin/paceplugin.nsis
View File

@ -39,7 +39,7 @@ InstallDir "$LOCALAPPDATA\${PACEPLUGIN}"
ShowInstDetails show
ShowUninstDetails show
SetCompressor lzma
SetCompressor zlib
!define MUI_ABORTWARNING

59
examples/PACKAGES/plumed/plugin/CMakeLists.txt Normal file
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@ -0,0 +1,59 @@
# -*- CMake -*- build system for plugin examples.
# The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package.
##########################################
cmake_minimum_required(VERSION 3.16)
project(plumedplugin VERSION 1.0 LANGUAGES CXX)
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfacePlugin)
include(PLUMED)
##########################
# building the plugins
add_library(plumedplugin MODULE plumedplugin.cpp ${LAMMPS_SOURCE_DIR}/PLUMED/fix_plumed.cpp)
target_link_libraries(plumedplugin PRIVATE LAMMPS::PLUMED)
target_link_libraries(plumedplugin PRIVATE lammps)
target_include_directories(plumedplugin PRIVATE ${LAMMPS_SOURCE_DIR}/PLUMED)
set_target_properties(plumedplugin PROPERTIES PREFIX "" SUFFIX ".so")
# MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
set_target_properties(plumedplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
if(CMAKE_CROSSCOMPILING)
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
find_program(MAKENSIS_PATH makensis)
if(MAKENSIS_PATH)
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/plumedplugin.nsis
${CMAKE_BINARY_DIR})
if(BUILD_MPI)
if(USE_MSMPI)
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI plumedplugin.nsis
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MSMPI.exe)
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI plumedplugin.nsis
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MPI.exe)
endif()
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} plumedplugin.nsis
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}.exe)
endif()
endif()
else()
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-rdynamic")
endif()

1
examples/PACKAGES/plumed/plugin/LAMMPSInterfacePlugin.cmake Symbolic link
View File

@ -0,0 +1 @@
../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake

1
examples/PACKAGES/plumed/plugin/PLUMED.cmake Symbolic link
View File

@ -0,0 +1 @@
../../../../cmake/Modules/Packages/PLUMED.cmake

2
examples/PACKAGES/plumed/plugin/README.txt Normal file
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@ -0,0 +1,2 @@
This folder contains a loader and support files to build the PLUMED package as plugin.
For more information please see: https://docs.lammps.org/Developer_plugins.html

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28
examples/PACKAGES/plumed/plugin/plumedplugin.cpp Normal file
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@ -0,0 +1,28 @@
#include "lammpsplugin.h"
#include "version.h"
#include "fix_plumed.h"
using namespace LAMMPS_NS;
static Fix *fix_plumed_creator(LAMMPS *lmp, int argc, char **argv)
{
return new FixPlumed(lmp, argc, argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
// register plumed fix style
plugin.version = LAMMPS_VERSION;
plugin.style = "fix";
plugin.name = "plumed";
plugin.info = "Plumed2 plugin fix style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &fix_plumed_creator;
plugin.handle = handle;
(*register_plugin)(&plugin, lmp);
}

172
examples/PACKAGES/plumed/plugin/plumedplugin.nsis Normal file
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@ -0,0 +1,172 @@
#!Nsis Installer Command Script
#
# The following external defines are recognized:
# ${VERSION} = YYYYMMDD
!include "MUI2.nsh"
!include "FileFunc.nsh"
!define MUI_ICON "lammps.ico"
!define MUI_UNICON "lammps.ico"
!define MUI_HEADERIMAGE
!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp"
!define MUI_HEADERIMAGE_RIGHT
Unicode true
XPStyle on
!include "LogicLib.nsh"
!addplugindir "envvar/Plugins/x86-unicode"
!include "x64.nsh"
RequestExecutionLevel user
!macro VerifyUserIsAdmin
UserInfo::GetAccountType
pop $0
${If} $0 != "admin"
messageBox mb_iconstop "Administrator rights required!"
setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED
quit
${EndIf}
!macroend
!define PLUMEDPLUGIN "LAMMPS PLUMED Plugin ${VERSION}"
OutFile "LAMMPS-PLUMED-plugin-${VERSION}.exe"
Name "${PLUMEDPLUGIN}"
InstallDir "$LOCALAPPDATA\${PLUMEDPLUGIN}"
ShowInstDetails show
ShowUninstDetails show
SetCompressor zlib
!define MUI_ABORTWARNING
!insertmacro MUI_PAGE_DIRECTORY
!insertmacro MUI_PAGE_INSTFILES
!insertmacro MUI_UNPAGE_CONFIRM
!insertmacro MUI_UNPAGE_INSTFILES
!insertmacro MUI_LANGUAGE "English"
function .onInit
# Determine if LAMMPS was already installed and check whether it was in 32-bit
# or 64-bit. Then look up path to uninstaller and offer to uninstall or quit
SetRegView 32
ReadRegDWORD $0 HKCU "Software\LAMMPS-PLUMED" "Bits"
SetRegView LastUsed
${If} $0 == "32"
SetRegView 32
${ElseIf} $0 == "64"
SetRegView 64
${Else}
SetRegView 64
${EndIf}
ClearErrors
ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" "UninstallString"
SetRegView LastUsed
${If} ${Errors}
DetailPrint "LAMMPS PLUMED plugin not (yet) installed"
${Else}
MessageBox MB_YESNO "LAMMPS PLUMED plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit
Pop $R1
StrCmp $R1 2 Quit +1
Exec $R0
Quit:
Quit
${EndIf}
setShellVarContext all
functionEnd
Section "${PLUMEDPLUGIN}" SecPlumedplugin
SectionIn RO
# Write LAMMPS installation bitness marker. Always use 32-bit registry view
SetRegView 32
IntFmt $0 "0x%08X" 64
WriteRegDWORD HKCU "Software\LAMMPS-PLUMED" "Bits" $0
# Switch to "native" registry view
SetRegView 64
SetShellVarContext current
SetOutPath "$INSTDIR"
CreateDirectory "$INSTDIR\patches"
CreateDirectory "$INSTDIR\bin"
File lammps.ico
File plumedplugin.so
SetOutPath "$INSTDIR\bin"
File plumed.exe
# Register Application and its uninstaller
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayName" "${PLUMEDPLUGIN}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"Publisher" "The LAMMPS and PLUMED Developers"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"URLInfoAbout" "lammps.org"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayIcon" "$INSTDIR\lammps.ico"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayVersion" "${VERSION}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"InstallLocation" "$INSTDIR"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"UninstallString" "$\"$INSTDIR\uninstall.exe$\""
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S"
${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2
IntFmt $0 "0x%08X" $0
WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"EstimatedSize" "$0"
# update path variables
EnVar::SetHKCU
# add plumed executable path
EnVar::AddValue "PATH" "$INSTDIR\bin"
# add to LAMMPS plugin search path
EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
# add plumed2 patch files
EnVar::AddValue "PLUMED_ROOT" "$INSTDIR"
WriteUninstaller "$INSTDIR\Uninstall.exe"
SectionEnd
function un.onInit
SetShellVarContext current
functionEnd
Section "Uninstall"
# remove LAMMPS bitness/installation indicator always in 32-bit registry view
SetRegView 32
DeleteRegKey HKCU "Software\LAMMPS-PLUMED"
# unregister extension, and uninstall info
SetRegView 64
SetShellVarContext current
# unregister installation
DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED"
# update path variables
EnVar::SetHKCU
# remove plumed executable path
EnVar::DeleteValue "PATH" "$INSTDIR\bin"
# remove entry from LAMMPS plugin search path
EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
# remove plumed patch environment
EnVar::Delete "PLUMED_ROOT"
RMDir /r /REBOOTOK "$INSTDIR\patches"
RMDir /r /REBOOTOK "$INSTDIR\bin"
Delete /REBOOTOK "$INSTDIR\plumedplugin.so"
Delete /REBOOTOK "$INSTDIR\Uninstall.exe"
Delete /REBOOTOK "$INSTDIR\lammps.ico"
RMDir /REBOOTOK "$INSTDIR"
SectionEnd
# Local Variables:
# mode: sh
# End:

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40
fortran/lammps.f90
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@ -542,6 +542,14 @@ MODULE LIBLAMMPS
INTEGER(c_int) :: lammps_extract_atom_datatype
END FUNCTION lammps_extract_atom_datatype
FUNCTION lammps_extract_atom_size(handle, name, dtype) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: handle, name
INTEGER(c_int), INTENT(IN), VALUE :: dtype
INTEGER(c_int) :: lammps_extract_atom_size
END FUNCTION lammps_extract_atom_size
FUNCTION lammps_extract_atom(handle, name) BIND(C)
IMPORT :: c_ptr
IMPLICIT NONE
@ -1435,7 +1443,7 @@ CONTAINS
IF (SIZE_TAGINT == 8) THEN
Cptr = C_LOC(id)
ELSE
id32 = id
id32 = INT(id, c_int)
Cptr = C_LOC(id32)
END IF
lmp_map_atom_big = lammps_map_atom(self%handle, Cptr) + 1
@ -1461,43 +1469,35 @@ CONTAINS
ntypes = lmp_extract_setting(self, 'ntypes')
Cname = f2c_string(name)
datatype = lammps_extract_atom_datatype(self%handle, Cname)
nrows = lammps_extract_atom_size(self%handle, Cname, LMP_SIZE_ROWS)
ncols = lammps_extract_atom_size(self%handle, Cname, LMP_SIZE_COLS)
Cptr = lammps_extract_atom(self%handle, Cname)
CALL lammps_free(Cname)
SELECT CASE (name)
CASE ('mass')
ncols = ntypes + 1
nrows = 1
CASE ('x','v','f','mu','omega','torque','angmom')
ncols = nmax
nrows = 3
CASE DEFAULT
ncols = nmax
nrows = 1
END SELECT
peratom_data%lammps_instance => self
SELECT CASE (datatype)
CASE (LAMMPS_INT)
peratom_data%datatype = DATA_INT_1D
CALL C_F_POINTER(Cptr, peratom_data%i32_vec, [ncols])
CALL C_F_POINTER(Cptr, peratom_data%i32_vec, [nrows])
CASE (LAMMPS_INT64)
peratom_data%datatype = DATA_INT64_1D
CALL C_F_POINTER(Cptr, peratom_data%i64_vec, [ncols])
CALL C_F_POINTER(Cptr, peratom_data%i64_vec, [nrows])
CASE (LAMMPS_DOUBLE)
peratom_data%datatype = DATA_DOUBLE_1D
! The mass array is allocated from 0, but only used from 1. We also want to use it from 1.
IF (name == 'mass') THEN
CALL C_F_POINTER(Cptr, dummy, [ncols])
CALL C_F_POINTER(Cptr, dummy, [nrows])
peratom_data%r64_vec(0:) => dummy
ELSE
CALL C_F_POINTER(Cptr, peratom_data%r64_vec, [ncols])
CALL C_F_POINTER(Cptr, peratom_data%r64_vec, [nrows])
END IF
CASE (LAMMPS_DOUBLE_2D)
peratom_data%datatype = DATA_DOUBLE_2D
! First, we dereference the void** pointer to point to the void*
CALL C_F_POINTER(Cptr, Catomptr, [ncols])
CALL C_F_POINTER(Cptr, Catomptr, [nrows])
! Catomptr(1) now points to the first element of the array
CALL C_F_POINTER(Catomptr(1), peratom_data%r64_mat, [nrows,ncols])
! rows and columns are swapped in Fortran
CALL C_F_POINTER(Catomptr(1), peratom_data%r64_mat, [ncols,nrows])
CASE (-1)
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'per-atom property ' // name // ' not found in extract_setting')
@ -2604,6 +2604,8 @@ CONTAINS
TYPE(c_ptr) :: Cid, Ctype, Cx, Cv, Cimage
INTEGER(c_int) :: tagint_size, atoms_created
Ctype = c_null_ptr
Cx = c_null_ptr
! type is actually NOT optional, but we can't make id optional without it,
! so we check at run-time
IF (.NOT. PRESENT(type)) THEN

31
lib/gpu/Makefile.aurora Normal file
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@ -0,0 +1,31 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for OpenCL
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.opencl
# OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi
# OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler
# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress
OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
OCL_INC = -I/opt/intel/oneapi/compiler/latest/linux/include/sycl/ # Path to CL directory
OCL_CPP = mpicxx -cxx=icpx -DCUDA_PROXY $(DEFAULT_DEVICE) -xHost -O2 -ffp-model=fast -qoverride-limits -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC) -DGERYON_NO_PROF
OCL_LINK = -L/opt/intel/oneapi/compiler/latest/linux/lib/ -lOpenCL
OCL_PREC = -D_SINGLE_DOUBLE
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
include Opencl.makefile

21
lib/gpu/lal_neighbor.cpp
View File

@ -586,8 +586,25 @@ void Neighbor::build_nbor_list(double **x, const int inum, const int host_inum,
const int b2y=_block_cell_2d;
const int g2x=static_cast<int>(ceil(static_cast<double>(_maxspecial)/b2x));
const int g2y=static_cast<int>(ceil(static_cast<double>(nt)/b2y));
_shared->k_transpose.set_size(g2x,g2y,b2x,b2y);
_shared->k_transpose.run(&dev_special,&dev_special_t,&_maxspecial,&nt);
// the maximum number of blocks on the device is typically 65535
// in principle we can use a lower number to have more resource per block 32768
const int max_num_blocks = 65535;
int shift = 0;
if (g2y < max_num_blocks) {
_shared->k_transpose.set_size(g2x,g2y,b2x,b2y);
_shared->k_transpose.run(&dev_special,&dev_special_t,&_maxspecial,&nt,&shift);
} else {
// using a fixed number of blocks
int g2y_m = max_num_blocks;
_shared->k_transpose.set_size(g2x,g2y_m,b2x,b2y);
// number of chunks needed for the whole transpose
const int num_chunks = ceil(static_cast<double>(g2y) / g2y_m);
for (int i = 0; i < num_chunks; i++) {
_shared->k_transpose.run(&dev_special,&dev_special_t,&_maxspecial,&nt,&shift);
shift += g2y_m*b2y;
}
}
time_transpose.stop();
}

10
lib/gpu/lal_neighbor_gpu.cu
View File

@ -147,7 +147,7 @@ __kernel void kernel_calc_cell_counts(const unsigned *restrict cell_id,
__kernel void transpose(__global tagint *restrict out,
const __global tagint *restrict in,
int columns_in, int rows_in)
int columns_in, int rows_in, int shift)
{
__local tagint block[BLOCK_CELL_2D][BLOCK_CELL_2D+1];
@ -158,15 +158,15 @@ __kernel void transpose(__global tagint *restrict out,
unsigned i=bi*BLOCK_CELL_2D+ti;
unsigned j=bj*BLOCK_CELL_2D+tj;
if ((i<columns_in) && (j<rows_in))
block[tj][ti]=in[j*columns_in+i];
if ((i<columns_in) && (j+shift<rows_in))
block[tj][ti]=in[(j+shift)*columns_in+i];
__syncthreads();
i=bj*BLOCK_CELL_2D+ti;
j=bi*BLOCK_CELL_2D+tj;
if ((i<rows_in) && (j<columns_in))
out[j*rows_in+i] = block[ti][tj];
if ((i+shift<rows_in) && (j<columns_in))
out[j*rows_in+i+shift] = block[ti][tj];
}
#ifndef LAL_USE_OLD_NEIGHBOR

93
lib/kokkos/CHANGELOG.md
View File

@ -1,12 +1,103 @@
# CHANGELOG
## [4.4.01](https://github.com/kokkos/kokkos/tree/4.4.01)
[Full Changelog](https://github.com/kokkos/kokkos/compare/4.0.00...4.4.01)
### Features:
* Introduce new SequentialHostInit view allocation property [\#7229](https://github.com/kokkos/kokkos/pull/7229)
### Backend and Architecture Enhancements:
#### CUDA:
* Experimental support for unified memory mode (intended for Grace-Hopper etc.) [\#6823](https://github.com/kokkos/kokkos/pull/6823)
### Bug Fixes
* OpenMP: Fix issue related to the visibility of an internal symbol with shared libraries that affected `ScatterView` in particular [\#7284](https://github.com/kokkos/kokkos/pull/7284)
* Fix implicit copy assignment operators in few AVX2 masks being deleted [#7296](https://github.com/kokkos/kokkos/pull/7296)
## [4.4.00](https://github.com/kokkos/kokkos/tree/4.4.00)
[Full Changelog](https://github.com/kokkos/kokkos/compare/4.3.01...4.4.00)
### Features:
* Add `Kokkos::View` conversions from and to [`std::mdspan`](https://en.cppreference.com/w/cpp/container/mdspan) [\#6830](https://github.com/kokkos/kokkos/pull/6830) [\#7069](https://github.com/kokkos/kokkos/pull/7069)
### Backend and Architecture Enhancements:
#### CUDA:
* `nvcc_wrapper`: Adding ability to process `--disable-warnings` flag [\#6936](https://github.com/kokkos/kokkos/issues/6936)
* Use recommended/max team size functions in Cuda ParallelFor and Reduce constructors [\#6891](https://github.com/kokkos/kokkos/issues/6891)
* Improve compile-times when building with `Kokkos_ENABLE_DEBUG_BOUNDS_CHECK` in Cuda [\#7013](https://github.com/kokkos/kokkos/pull/7013)
#### HIP:
* Use HIP builtin atomics [\#6882](https://github.com/kokkos/kokkos/pull/6882) [\#7000](https://github.com/kokkos/kokkos/pull/7000)
* Enable user-specified compiler and linker flags for AMD GPUs [\#7127](https://github.com/kokkos/kokkos/pull/7127)
#### SYCL:
* Add support for Graphs [\#6912](https://github.com/kokkos/kokkos/pull/6912)
* Fix multi-GPU support [\#6887](https://github.com/kokkos/kokkos/pull/6887)
* Improve performance of reduction and scan operations [\#6562](https://github.com/kokkos/kokkos/pull/6562), [\#6750](https://github.com/kokkos/kokkos/pull/6750)
* Fix lock for guarding scratch space in `TeamPolicy` `parallel_reduce` [\#6988](https://github.com/kokkos/kokkos/pull/6988)
* Include submission command queue property information into `SYCL::print_configuration()` [\#7004](https://github.com/kokkos/kokkos/pull/7004)
#### OpenACC:
* Make `TeamPolicy` `parallel_for` execute on the correct async queue [\#7012](https://github.com/kokkos/kokkos/pull/7012)
#### OpenMPTarget:
* Honor user requested loop ordering in `MDRange` policy [\#6925](https://github.com/kokkos/kokkos/pull/6925)
* Prevent data races by guarding the scratch space used in `parallel_scan` [\#6998](https://github.com/kokkos/kokkos/pull/6998)
#### HPX:
* Workaround issue with template argument deduction to support compilation with NVCC [\#7015](https://github.com/kokkos/kokkos/pull/7015)
### General Enhancements
* Improve performance of view copies in host parallel regions [\#6730](https://github.com/kokkos/kokkos/pull/6730)
* Harmonize convertibility rules of `Kokkos::RandomAccessIterator` with `View`s [\#6929](https://github.com/kokkos/kokkos/pull/6929)
* Add a check precondition non-overlapping ranges for the `adjacent_difference` algorithm in debug mode [\#6922](https://github.com/kokkos/kokkos/pull/6922)
* Add deduction guides for `TeamPolicy` [\#7030](https://github.com/kokkos/kokkos/pull/7030)
* SIMD: Allow flexible vector width for 32 bit types [\#6802](https://github.com/kokkos/kokkos/pull/6802)
* Updates for `Kokkos::Array`: add `kokkos_swap(Array<T, N>)` specialization [\#6943](https://github.com/kokkos/kokkos/pull/6943), add `Kokkos::to_array` [\#6375](https://github.com/kokkos/kokkos/pull/6375), make `Kokkos::Array` equality-comparable [\#7148](https://github.com/kokkos/kokkos/pull/7148)
* Structured binding support for `Kokkos::complex` [\#7040](https://github.com/kokkos/kokkos/pull/7040)
### Build System Changes
* Do not require OpenMP support for languages other than CXX [\#6965](https://github.com/kokkos/kokkos/pull/6965)
* Update Intel GPU architectures in Makefile [\#6895](https://github.com/kokkos/kokkos/pull/6895)
* Fix use of OpenMP with Cuda or HIP as compile language [\#6972](https://github.com/kokkos/kokkos/pull/6972)
* Define and enforce new minimum compiler versions for C++20 support [\#7128](https://github.com/kokkos/kokkos/pull/7128), [\#7123](https://github.com/kokkos/kokkos/pull/7123)
* Add nvidia Grace CPU architecture: `Kokkos_ARCH_ARMV9_GRACE` [\#7158](https://github.com/kokkos/kokkos/pull/7158)
* Fix Makefile.kokkos for Threads [\#6896](https://github.com/kokkos/kokkos/pull/6896)
* Remove support for NVHPC as CUDA device compiler [\#6987](https://github.com/kokkos/kokkos/pull/6987)
* Fix using CUDAToolkit for CMake 3.28.4 and higher [\#7062](https://github.com/kokkos/kokkos/pull/7062)
### Incompatibilities (i.e. breaking changes)
* Drop `Kokkos::Array` special treatment in `View`s [\#6906](https://github.com/kokkos/kokkos/pull/6906)
* Drop `Experimental::RawMemoryAllocationFailure` [\#7145](https://github.com/kokkos/kokkos/pull/7145)
### Deprecations
* Remove `Experimental::LayoutTiled` class template and deprecate `is_layouttiled` trait [\#6907](https://github.com/kokkos/kokkos/pull/6907)
* Deprecate `Kokkos::layout_iterate_type_selector` [\#7076](https://github.com/kokkos/kokkos/pull/7076)
* Deprecate specialization of `Kokkos::pair` for a single element [\#6947](https://github.com/kokkos/kokkos/pull/6947)
* Deprecate `deep_copy` of `UnorderedMap` of different size [\#6812](https://github.com/kokkos/kokkos/pull/6812)
* Deprecate trailing `Proxy` template argument of `Kokkos::Array` [\#6934](https://github.com/kokkos/kokkos/pull/6934)
* Deprecate implicit conversions of integers to `ChunkSize` [\#7151](https://github.com/kokkos/kokkos/pull/7151)
* Deprecate implicit conversions to execution spaces [\#7156](https://github.com/kokkos/kokkos/pull/7156)
### Bug Fixes
* Do not return a copy of the input functor in `Experimental::for_each` [\#6910](https://github.com/kokkos/kokkos/pull/6910)
* Fix `realloc` on views of non-default constructible element types [\#6993](https://github.com/kokkos/kokkos/pull/6993)
* Fix undefined behavior in `View` initialization or fill with zeros [\#7014](https://github.com/kokkos/kokkos/pull/7014)
* Fix `sort_by_key` on host execution spaces when building with NVCC [\#7059](https://github.com/kokkos/kokkos/pull/7059)
* Fix using shared libraries and -fvisibility=hidden [\#7065](https://github.com/kokkos/kokkos/pull/7065)
* Fix view reference counting when functor copy constructor throws in parallel dispatch [\#6289](https://github.com/kokkos/kokkos/pull/6289)
* Fix `initialize(InitializationSetting)` for handling `print_configuration` setting [\#7098](https://github.com/kokkos/kokkos/pull/7098)
* Thread safety fixes for the Serial and OpenMP backend [\#7080](https://github.com/kokkos/kokkos/pull/7080), [\#6151](https://github.com/kokkos/kokkos/pull/6151)
## [4.3.01](https://github.com/kokkos/kokkos/tree/4.3.01)
[Full Changelog](https://github.com/kokkos/kokkos/compare/4.3.00...4.3.01)
### Backend and Architecture Enhancements:
#### HIP:
* MI300 support unified memory support [\#6877](https://github.com/kokkos/kokkos/pull/6877)
* MI300 support unified memory [\#6877](https://github.com/kokkos/kokkos/pull/6877)
### Bug Fixes
* Serial: Use the provided execution space instance in TeamPolicy [\#6951](https://github.com/kokkos/kokkos/pull/6951)

65
lib/kokkos/CITATION.cff Normal file
View File

@ -0,0 +1,65 @@
cff-version: 1.2.0
title: Kokkos
message: >-
If you use this software, please cite the overview paper
type: software
authors:
- name: The Kokkos authors
website: https://kokkos.org/community/team/
identifiers:
- type: url
website: https://kokkos.org/kokkos-core-wiki/citation.html
repository-code: 'https://github.com/kokkos/kokkos'
url: 'https://kokkos.org/'
license: Apache-2.0
preferred-citation:
type: article
authors:
- given-names: Christian R.
family-names: Trott
- given-names: Damien
family-names: Lebrun-Grandié
- given-names: Daniel
family-names: Arndt
- family-names: Ciesko
given-names: Jan
- given-names: Vinh
family-names: Dang
- family-names: Ellingwood
given-names: Nathan
- given-names: Rahulkumar
family-names: Gayatri
- given-names: Evan
family-names: Harvey
- given-names: Daisy S.
family-names: Hollman
- given-names: Dan
family-names: Ibanez
- given-names: Nevin
family-names: Liber
- given-names: Jonathan
family-names: Madsen
- given-names: Jeff
family-names: Miles
- given-names: David
family-names: Poliakoff
- given-names: Amy
family-names: Powell
- given-names: Sivasankaran
family-names: Rajamanickam
- given-names: Mikael
family-names: Simberg
- given-names: Dan
family-names: Sunderland
- given-names: Bruno
family-names: Turcksin
- given-names: Jeremiah
family-names: Wilke
doi: 10.1109/TPDS.2021.3097283
journal: IEEE Transactions on Parallel and Distributed Systems
start: 805
end: 817
title: "Kokkos 3: Programming Model Extensions for the Exascale Era"
volume: 33
issue: 4
year: 2022

2
lib/kokkos/CMakeLists.txt
View File

@ -150,7 +150,7 @@ ENDIF()
set(Kokkos_VERSION_MAJOR 4)
set(Kokkos_VERSION_MINOR 3)
set(Kokkos_VERSION_MINOR 4)
set(Kokkos_VERSION_PATCH 1)
set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
message(STATUS "Kokkos version: ${Kokkos_VERSION}")

62
lib/kokkos/Makefile.kokkos
View File

@ -11,7 +11,7 @@ CXXFLAGS += $(SHFLAGS)
endif
KOKKOS_VERSION_MAJOR = 4
KOKKOS_VERSION_MINOR = 3
KOKKOS_VERSION_MINOR = 4
KOKKOS_VERSION_PATCH = 1
KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc)
@ -21,11 +21,11 @@ KOKKOS_DEVICES ?= "OpenMP"
# Options:
# Intel: KNC,KNL,SNB,HSW,BDW,SKL,SKX,ICL,ICX,SPR
# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80,Ampere86,Ada89,Hopper90
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX,ARMv9-Grace
# IBM: Power8,Power9
# AMD-GPUS: AMD_GFX906,AMD_GFX908,AMD_GFX90A,AMD_GFX940,AMD_GFX942,AMD_GFX1030,AMD_GFX1100,AMD_GFX1103
# AMD-GPUS: AMD_GFX906,AMD_GFX908,AMD_GFX90A,AMD_GFX940,AMD_GFX942,AMD_GFX1030,AMD_GFX1100
# AMD-CPUS: AMDAVX,Zen,Zen2,Zen3
# Intel-GPUs: Gen9,Gen11,Gen12LP,DG1,XeHP,PVC
# Intel-GPUs: Intel_Gen,Intel_Gen9,Intel_Gen11,Intel_Gen12LP,Intel_DG1,Intel_XeHP,Intel_PVC
KOKKOS_ARCH ?= ""
# Options: yes,no
KOKKOS_DEBUG ?= "no"
@ -41,7 +41,7 @@ KOKKOS_STANDALONE_CMAKE ?= "no"
# Default settings specific options.
# Options: force_uvm,use_ldg,rdc,enable_lambda,enable_constexpr,disable_malloc_async
KOKKOS_CUDA_OPTIONS ?= "enable_lambda"
KOKKOS_CUDA_OPTIONS ?= "disable_malloc_async"
# Options: rdc
KOKKOS_HIP_OPTIONS ?= ""
@ -328,12 +328,43 @@ KOKKOS_INTERNAL_USE_ARCH_ICL := $(call kokkos_has_string,$(KOKKOS_ARCH),ICL)
KOKKOS_INTERNAL_USE_ARCH_ICX := $(call kokkos_has_string,$(KOKKOS_ARCH),ICX)
KOKKOS_INTERNAL_USE_ARCH_SPR := $(call kokkos_has_string,$(KOKKOS_ARCH),SPR)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen)
# Traditionally, we supported, e.g., IntelGen9 instead of Intel_Gen9. The latter
# matches the CMake option but we also accept the former for backward-compatibility.
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen9)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9 := $(call kokkos_has_string,$(KOKKOS_ARCH),Intel_Gen9)
endif
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen11)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11 := $(call kokkos_has_string,$(KOKKOS_ARCH),Intel_Gen11)
endif
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen12LP)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP := $(call kokkos_has_string,$(KOKKOS_ARCH),Intel_Gen12LP)
endif
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen9)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9 := $(call kokkos_has_string,$(KOKKOS_ARCH),Intel_Gen9)
endif
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN_SET := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN9) \
+ $(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN11) \
+ $(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN12LP))
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN_SET), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelGen)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_GEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Intel_Gen)
endif
endif
KOKKOS_INTERNAL_USE_ARCH_INTEL_DG1 := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelDG1)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_DG1), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_DG1 := $(call kokkos_has_string,$(KOKKOS_ARCH),Intel_DG1)
endif
KOKKOS_INTERNAL_USE_ARCH_INTEL_XEHP := $(call kokkos_has_string,$(KOKKOS_ARCH),IntelXeHP)
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_INTEL_XEHP), 0)
KOKKOS_INTERNAL_USE_ARCH_INTEL_XEHP := $(call kokkos_has_string,$(KOKKOS_ARCH),Intel_XeHP)
endif
# Traditionally the architecture was called PVC instead of Intel_PVC. This
# version makes us accept IntelPVC and Intel_PVC as well.
KOKKOS_INTERNAL_USE_ARCH_INTEL_PVC := $(call kokkos_has_string,$(KOKKOS_ARCH),PVC)
# NVIDIA based.
@ -394,7 +425,8 @@ KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8
KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-ThunderX)
KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-TX2)
KOKKOS_INTERNAL_USE_ARCH_A64FX := $(call kokkos_has_string,$(KOKKOS_ARCH),A64FX)
KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2)+$(KOKKOS_INTERNAL_USE_ARCH_A64FX) | bc))
KOKKOS_INTERNAL_USE_ARCH_ARMV9_GRACE := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv9-Grace)
KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2)+$(KOKKOS_INTERNAL_USE_ARCH_A64FX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV9_GRACE) | bc))
# IBM based.
KOKKOS_INTERNAL_USE_ARCH_POWER8 := $(call kokkos_has_string,$(KOKKOS_ARCH),Power8)
@ -433,7 +465,6 @@ KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100 := $(call kokkos_has_string,$(KOKKOS_ARCH),
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100), 0)
KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100 := $(call kokkos_has_string,$(KOKKOS_ARCH),NAVI1100)
endif
KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1103 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX1103)
# Any AVX?
KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX))
@ -758,6 +789,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_A64FX), 1)
endif
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV9_GRACE), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV9_GRACE")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARM_NEON")
KOKKOS_CXXFLAGS += -mcpu=neoverse-v2 -msve-vector-bits=128
KOKKOS_LDFLAGS += -mcpu=neoverse-v2 -msve-vector-bits=128
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_ZEN")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX2")
@ -1119,11 +1158,6 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GPU")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --offload-arch=gfx1100
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1103), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GFX1103")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GPU")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --offload-arch=gfx1103
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
@ -1216,6 +1250,8 @@ ifeq ($(KOKKOS_INTERNAL_DISABLE_BUNDLED_MDSPAN), 0)
endif
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_IMPL_MDSPAN")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_IMPL_REF_COUNT_BRANCH_UNLIKELY")
KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h 2>&1)
ifeq ($(KOKKOS_INTERNAL_LS_CONFIG), KokkosCore_config.h)

2
lib/kokkos/Makefile.targets
View File

@ -81,7 +81,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_THREADS), 1)
Kokkos_Threads_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_Threads_Instance.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_Threads_Instance.cpp
Kokkos_Threads_Spinwait.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_Threads_Spinwait.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_Spinwait.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_Threads_Spinwait.cpp
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)

65
lib/kokkos/README.md
View File

@ -1,4 +1,4 @@
![Kokkos](https://avatars2.githubusercontent.com/u/10199860?s=200&v=4)
[![Kokkos](https://avatars2.githubusercontent.com/u/10199860?s=200&v=4)](https://kokkos.org)
# Kokkos: Core Libraries
@ -10,43 +10,66 @@ hierarchies and multiple types of execution resources. It currently can use
CUDA, HIP, SYCL, HPX, OpenMP and C++ threads as backend programming models with several other
backends in development.
**Kokkos Core is part of the Kokkos C++ Performance Portability Programming EcoSystem.**
**Kokkos Core is part of the [Kokkos C++ Performance Portability Programming Ecosystem](https://kokkos.org/about/abstract/).**
For the complete documentation, click below:
Kokkos is a [Linux Foundation](https://linuxfoundation.org) project.
# [kokkos.github.io/kokkos-core-wiki](https://kokkos.github.io/kokkos-core-wiki)
# Learning about Kokkos
## Learning about Kokkos
To start learning about Kokkos:
- [Kokkos Lectures](https://kokkos.github.io/kokkos-core-wiki/videolectures.html): they contain a mix of lecture videos and hands-on exercises covering all the important Kokkos Ecosystem capabilities.
- [Kokkos Lectures](https://kokkos.org/kokkos-core-wiki/videolectures.html): they contain a mix of lecture videos and hands-on exercises covering all the important capabilities.
- [Programming guide](https://kokkos.github.io/kokkos-core-wiki/programmingguide.html): contains in "narrative" form a technical description of the programming model, machine model, and the main building blocks like the Views and parallel dispatch.
- [Programming guide](https://kokkos.org/kokkos-core-wiki/programmingguide.html): contains in "narrative" form a technical description of the programming model, machine model, and the main building blocks like the Views and parallel dispatch.
- [API reference](https://kokkos.github.io/kokkos-core-wiki/): organized by category, i.e., [core](https://kokkos.github.io/kokkos-core-wiki/API/core-index.html), [algorithms](https://kokkos.github.io/kokkos-core-wiki/API/algorithms-index.html) and [containers](https://kokkos.github.io/kokkos-core-wiki/API/containers-index.html) or, if you prefer, in [alphabetical order](https://kokkos.github.io/kokkos-core-wiki/API/alphabetical.html).
- [API reference](https://kokkos.org/kokkos-core-wiki/): organized by category, i.e., [core](https://kokkos.org/kokkos-core-wiki/API/core-index.html), [algorithms](https://kokkos.org/kokkos-core-wiki/API/algorithms-index.html) and [containers](https://kokkos.org/kokkos-core-wiki/API/containers-index.html) or, if you prefer, in [alphabetical order](https://kokkos.org/kokkos-core-wiki/API/alphabetical.html).
- [Use cases and Examples](https://kokkos.github.io/kokkos-core-wiki/usecases.html): a series of examples ranging from how to use Kokkos with MPI to Fortran interoperability.
- [Use cases and Examples](https://kokkos.org/kokkos-core-wiki/usecases.html): a serie of examples ranging from how to use Kokkos with MPI to Fortran interoperability.
## Obtaining Kokkos
The latest release of Kokkos can be obtained from the [GitHub releases page](https://github.com/kokkos/kokkos/releases/latest).
The current release is [4.3.01](https://github.com/kokkos/kokkos/releases/tag/4.3.01).
```bash
curl -OJ -L https://github.com/kokkos/kokkos/archive/refs/tags/4.3.01.tar.gz
# Or with wget
wget https://github.com/kokkos/kokkos/archive/refs/tags/4.3.01.tar.gz
```
To clone the latest development version of Kokkos from GitHub:
```bash
git clone -b develop https://github.com/kokkos/kokkos.git
```
### Building Kokkos
To build Kokkos, you will need to have a C++ compiler that supports C++17 or later.
All requirements including minimum and primary tested compiler versions can be found [here](https://kokkos.org/kokkos-core-wiki/requirements.html).
Building and installation instructions are described [here](https://kokkos.org/kokkos-core-wiki/building.html).
You can also install Kokkos using [Spack](https://spack.io/): `spack install kokkos`. [Available configuration options](https://packages.spack.io/package.html?name=kokkos) can be displayed using `spack info kokkos`.
## For the complete documentation: [kokkos.org/kokkos-core-wiki/](https://kokkos.org/kokkos-core-wiki/)
## Support
For questions find us on Slack: https://kokkosteam.slack.com or open a GitHub issue.
For non-public questions send an email to: *crtrott(at)sandia.gov*
# Contributing to Kokkos
## Contributing
Please see [this page](https://kokkos.github.io/kokkos-core-wiki/contributing.html) for details on how to contribute.
Please see [this page](https://kokkos.org/kokkos-core-wiki/contributing.html) for details on how to contribute.
# Requirements, Building and Installing
## Citing Kokkos
All requirements including minimum and primary tested compiler versions can be found [here](https://kokkos.github.io/kokkos-core-wiki/requirements.html).
Please see the [following page](https://kokkos.org/kokkos-core-wiki/citation.html).
Building and installation instructions are described [here](https://kokkos.github.io/kokkos-core-wiki/building.html).
# Citing Kokkos
Please see the [following page](https://kokkos.github.io/kokkos-core-wiki/citation.html).
# License
## License
[![License](https://img.shields.io/badge/License-Apache--2.0_WITH_LLVM--exception-blue)](https://spdx.org/licenses/LLVM-exception.html)

55
lib/kokkos/algorithms/src/sorting/impl/Kokkos_SortByKeyImpl.hpp
View File

@ -189,6 +189,33 @@ void applyPermutation(const ExecutionSpace& space,
KOKKOS_LAMBDA(int i) { view(i) = view_copy(permutation(i)); });
}
// FIXME_NVCC: nvcc has trouble compiling lambdas inside a function with
// variadic templates (sort_by_key_via_sort). Switch to using functors instead.
template <typename Permute>
struct IotaFunctor {
Permute _permute;
KOKKOS_FUNCTION void operator()(int i) const { _permute(i) = i; }
};
template <typename Keys>
struct LessFunctor {
Keys _keys;
KOKKOS_FUNCTION bool operator()(int i, int j) const {
return _keys(i) < _keys(j);
}
};
// FIXME_NVCC+MSVC: We can't use a lambda instead of a functor which gave us
// "For this host platform/dialect, an extended lambda cannot be defined inside
// the 'if' or 'else' block of a constexpr if statement"
template <typename Keys, typename Comparator>
struct KeyComparisonFunctor {
Keys m_keys;
Comparator m_comparator;
KOKKOS_FUNCTION bool operator()(int i, int j) const {
return m_comparator(m_keys(i), m_keys(j));
}
};
template <class ExecutionSpace, class KeysDataType, class... KeysProperties,
class ValuesDataType, class... ValuesProperties,
class... MaybeComparator>
@ -207,10 +234,9 @@ void sort_by_key_via_sort(
n);
// iota
Kokkos::parallel_for(
"Kokkos::sort_by_key_via_sort::iota",
Kokkos::RangePolicy<ExecutionSpace>(exec, 0, n),
KOKKOS_LAMBDA(int i) { permute(i) = i; });
Kokkos::parallel_for("Kokkos::sort_by_key_via_sort::iota",
Kokkos::RangePolicy<ExecutionSpace>(exec, 0, n),
IotaFunctor<decltype(permute)>{permute});
using Layout =
typename Kokkos::View<unsigned int*, ExecutionSpace>::array_layout;
@ -228,16 +254,15 @@ void sort_by_key_via_sort(
Kokkos::DefaultHostExecutionSpace host_exec;
if constexpr (sizeof...(MaybeComparator) == 0) {
Kokkos::sort(
host_exec, host_permute,
KOKKOS_LAMBDA(int i, int j) { return host_keys(i) < host_keys(j); });
Kokkos::sort(host_exec, host_permute,
LessFunctor<decltype(host_keys)>{host_keys});
} else {
auto keys_comparator =
std::get<0>(std::tuple<MaybeComparator...>(maybeComparator...));
Kokkos::sort(
host_exec, host_permute, KOKKOS_LAMBDA(int i, int j) {
return keys_comparator(host_keys(i), host_keys(j));
});
host_exec, host_permute,
KeyComparisonFunctor<decltype(host_keys), decltype(keys_comparator)>{
host_keys, keys_comparator});
}
host_exec.fence("Kokkos::Impl::sort_by_key_via_sort: after host sort");
Kokkos::deep_copy(exec, permute, host_permute);
@ -262,16 +287,14 @@ void sort_by_key_via_sort(
}
#else
if constexpr (sizeof...(MaybeComparator) == 0) {
Kokkos::sort(
exec, permute,
KOKKOS_LAMBDA(int i, int j) { return keys(i) < keys(j); });
Kokkos::sort(exec, permute, LessFunctor<decltype(keys)>{keys});
} else {
auto keys_comparator =
std::get<0>(std::tuple<MaybeComparator...>(maybeComparator...));
Kokkos::sort(
exec, permute, KOKKOS_LAMBDA(int i, int j) {
return keys_comparator(keys(i), keys(j));
});
exec, permute,
KeyComparisonFunctor<decltype(keys), decltype(keys_comparator)>{
keys, keys_comparator});
}
#endif
}

56
lib/kokkos/algorithms/src/std_algorithms/Kokkos_ForEach.hpp
View File

@ -29,49 +29,46 @@ namespace Experimental {
template <
class ExecutionSpace, class IteratorType, class UnaryFunctorType,
std::enable_if_t<Kokkos::is_execution_space_v<ExecutionSpace>, int> = 0>
UnaryFunctorType for_each(const std::string& label, const ExecutionSpace& ex,
IteratorType first, IteratorType last,
UnaryFunctorType functor) {
return Impl::for_each_exespace_impl(label, ex, first, last,
std::move(functor));
void for_each(const std::string& label, const ExecutionSpace& ex,
IteratorType first, IteratorType last, UnaryFunctorType functor) {
Impl::for_each_exespace_impl(label, ex, first, last, std::move(functor));
}
template <
class ExecutionSpace, class IteratorType, class UnaryFunctorType,
std::enable_if_t<Kokkos::is_execution_space_v<ExecutionSpace>, int> = 0>
UnaryFunctorType for_each(const ExecutionSpace& ex, IteratorType first,
IteratorType last, UnaryFunctorType functor) {
return Impl::for_each_exespace_impl("Kokkos::for_each_iterator_api_default",
ex, first, last, std::move(functor));
void for_each(const ExecutionSpace& ex, IteratorType first, IteratorType last,
UnaryFunctorType functor) {
Impl::for_each_exespace_impl("Kokkos::for_each_iterator_api_default", ex,
first, last, std::move(functor));
}
template <
class ExecutionSpace, class DataType, class... Properties,
class UnaryFunctorType,
std::enable_if_t<Kokkos::is_execution_space_v<ExecutionSpace>, int> = 0>
UnaryFunctorType for_each(const std::string& label, const ExecutionSpace& ex,
const ::Kokkos::View<DataType, Properties...>& v,
UnaryFunctorType functor) {
void for_each(const std::string& label, const ExecutionSpace& ex,
const ::Kokkos::View<DataType, Properties...>& v,
UnaryFunctorType functor) {
Impl::static_assert_is_admissible_to_kokkos_std_algorithms(v);
namespace KE = ::Kokkos::Experimental;
return Impl::for_each_exespace_impl(label, ex, KE::begin(v), KE::end(v),
std::move(functor));
Impl::for_each_exespace_impl(label, ex, KE::begin(v), KE::end(v),
std::move(functor));
}
template <
class ExecutionSpace, class DataType, class... Properties,
class UnaryFunctorType,
std::enable_if_t<Kokkos::is_execution_space_v<ExecutionSpace>, int> = 0>
UnaryFunctorType for_each(const ExecutionSpace& ex,
const ::Kokkos::View<DataType, Properties...>& v,
UnaryFunctorType functor) {
void for_each(const ExecutionSpace& ex,
const ::Kokkos::View<DataType, Properties...>& v,
UnaryFunctorType functor) {
Impl::static_assert_is_admissible_to_kokkos_std_algorithms(v);
namespace KE = ::Kokkos::Experimental;
return Impl::for_each_exespace_impl("Kokkos::for_each_view_api_default", ex,
KE::begin(v), KE::end(v),
std::move(functor));
Impl::for_each_exespace_impl("Kokkos::for_each_view_api_default", ex,
KE::begin(v), KE::end(v), std::move(functor));
}
//
@ -82,24 +79,23 @@ UnaryFunctorType for_each(const ExecutionSpace& ex,
template <class TeamHandleType, class IteratorType, class UnaryFunctorType,
std::enable_if_t<Kokkos::is_team_handle_v<TeamHandleType>, int> = 0>
KOKKOS_FUNCTION UnaryFunctorType for_each(const TeamHandleType& teamHandle,
IteratorType first, IteratorType last,
UnaryFunctorType functor) {
return Impl::for_each_team_impl(teamHandle, first, last, std::move(functor));
KOKKOS_FUNCTION void for_each(const TeamHandleType& teamHandle,
IteratorType first, IteratorType last,
UnaryFunctorType functor) {
Impl::for_each_team_impl(teamHandle, first, last, std::move(functor));
}
template <class TeamHandleType, class DataType, class... Properties,
class UnaryFunctorType,
std::enable_if_t<Kokkos::is_team_handle_v<TeamHandleType>, int> = 0>
KOKKOS_FUNCTION UnaryFunctorType
for_each(const TeamHandleType& teamHandle,
const ::Kokkos::View<DataType, Properties...>& v,
UnaryFunctorType functor) {
KOKKOS_FUNCTION void for_each(const TeamHandleType& teamHandle,
const ::Kokkos::View<DataType, Properties...>& v,
UnaryFunctorType functor) {
Impl::static_assert_is_admissible_to_kokkos_std_algorithms(v);
namespace KE = ::Kokkos::Experimental;
return Impl::for_each_team_impl(teamHandle, KE::begin(v), KE::end(v),
std::move(functor));
Impl::for_each_team_impl(teamHandle, KE::begin(v), KE::end(v),
std::move(functor));
}
} // namespace Experimental

10
lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_AdjacentDifference.hpp
View File

@ -82,6 +82,11 @@ OutputIteratorType adjacent_difference_exespace_impl(
return first_dest;
}
#ifdef KOKKOS_ENABLE_DEBUG
// check for overlapping iterators
Impl::expect_no_overlap(first_from, last_from, first_dest);
#endif
// run
const auto num_elements =
Kokkos::Experimental::distance(first_from, last_from);
@ -114,6 +119,11 @@ KOKKOS_FUNCTION OutputIteratorType adjacent_difference_team_impl(
return first_dest;
}
#ifdef KOKKOS_ENABLE_DEBUG
// check for overlapping iterators
Impl::expect_no_overlap(first_from, last_from, first_dest);
#endif
// run
const auto num_elements =
Kokkos::Experimental::distance(first_from, last_from);

61
lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_Constraints.hpp
View File

@ -24,18 +24,21 @@ namespace Kokkos {
namespace Experimental {
namespace Impl {
template <class T>
class RandomAccessIterator;
template <typename T, typename enable = void>
struct is_admissible_to_kokkos_std_algorithms : std::false_type {};
template <typename T>
struct is_admissible_to_kokkos_std_algorithms<
T, std::enable_if_t< ::Kokkos::is_view<T>::value && T::rank() == 1 &&
(std::is_same<typename T::traits::array_layout,
Kokkos::LayoutLeft>::value ||
std::is_same<typename T::traits::array_layout,
Kokkos::LayoutRight>::value ||
std::is_same<typename T::traits::array_layout,
Kokkos::LayoutStride>::value)> >
T, std::enable_if_t<::Kokkos::is_view<T>::value && T::rank() == 1 &&
(std::is_same<typename T::traits::array_layout,
Kokkos::LayoutLeft>::value ||
std::is_same<typename T::traits::array_layout,
Kokkos::LayoutRight>::value ||
std::is_same<typename T::traits::array_layout,
Kokkos::LayoutStride>::value)>>
: std::true_type {};
template <class ViewType>
@ -58,6 +61,18 @@ using is_iterator = Kokkos::is_detected<iterator_category_t, T>;
template <class T>
inline constexpr bool is_iterator_v = is_iterator<T>::value;
template <typename ViewType>
struct is_kokkos_iterator : std::false_type {};
template <typename ViewType>
struct is_kokkos_iterator<RandomAccessIterator<ViewType>> {
static constexpr bool value =
is_admissible_to_kokkos_std_algorithms<ViewType>::value;
};
template <class T>
inline constexpr bool is_kokkos_iterator_v = is_kokkos_iterator<T>::value;
//
// are_iterators
//
@ -215,6 +230,38 @@ KOKKOS_INLINE_FUNCTION void expect_valid_range(IteratorType first,
(void)last;
}
//
// Check if kokkos iterators are overlapping
//
template <typename IteratorType1, typename IteratorType2>
KOKKOS_INLINE_FUNCTION void expect_no_overlap(
[[maybe_unused]] IteratorType1 first, [[maybe_unused]] IteratorType1 last,
[[maybe_unused]] IteratorType2 s_first) {
if constexpr (is_kokkos_iterator_v<IteratorType1> &&
is_kokkos_iterator_v<IteratorType2>) {
auto const view1 = first.view();
auto const view2 = s_first.view();
std::size_t stride1 = view1.stride(0);
std::size_t stride2 = view2.stride(0);
ptrdiff_t first_diff = view1.data() - view2.data();
// FIXME If strides are not identical, checks may not be made
// with the cost of O(1)
// Currently, checks are made only if strides are identical
// If first_diff == 0, there is already an overlap
if (stride1 == stride2 || first_diff == 0) {
[[maybe_unused]] bool is_no_overlap = (first_diff % stride1);
auto* first_pointer1 = view1.data();
auto* first_pointer2 = view2.data();
[[maybe_unused]] auto* last_pointer1 = first_pointer1 + (last - first);
[[maybe_unused]] auto* last_pointer2 = first_pointer2 + (last - first);
KOKKOS_EXPECTS(first_pointer1 >= last_pointer2 ||
last_pointer1 <= first_pointer2 || is_no_overlap);
}
}
}
} // namespace Impl
} // namespace Experimental
} // namespace Kokkos

5
lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_CopyIf.hpp
View File

@ -150,8 +150,9 @@ KOKKOS_FUNCTION OutputIterator copy_if_team_impl(
return d_first + count;
}
#if defined KOKKOS_COMPILER_INTEL || \
(defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130)
#if defined KOKKOS_COMPILER_INTEL || \
(defined(KOKKOS_COMPILER_NVCC) && KOKKOS_COMPILER_NVCC >= 1130 && \
!defined(KOKKOS_COMPILER_MSVC))
__builtin_unreachable();
#endif
}

20
lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_ForEachForEachN.hpp
View File

@ -42,10 +42,9 @@ struct StdForEachFunctor {
};
template <class HandleType, class IteratorType, class UnaryFunctorType>
UnaryFunctorType for_each_exespace_impl(const std::string& label,
const HandleType& handle,
IteratorType first, IteratorType last,
UnaryFunctorType functor) {
void for_each_exespace_impl(const std::string& label, const HandleType& handle,
IteratorType first, IteratorType last,
UnaryFunctorType functor) {
// checks
Impl::static_assert_random_access_and_accessible(handle, first);
Impl::expect_valid_range(first, last);
@ -56,8 +55,6 @@ UnaryFunctorType for_each_exespace_impl(const std::string& label,
label, RangePolicy<HandleType>(handle, 0, num_elements),
StdForEachFunctor<IteratorType, UnaryFunctorType>(first, functor));
handle.fence("Kokkos::for_each: fence after operation");
return functor;
}
template <class ExecutionSpace, class IteratorType, class SizeType,
@ -75,7 +72,7 @@ IteratorType for_each_n_exespace_impl(const std::string& label,
}
for_each_exespace_impl(label, ex, first, last, std::move(functor));
// no neeed to fence since for_each_exespace_impl fences already
// no need to fence since for_each_exespace_impl fences already
return last;
}
@ -84,9 +81,9 @@ IteratorType for_each_n_exespace_impl(const std::string& label,
// team impl
//
template <class TeamHandleType, class IteratorType, class UnaryFunctorType>
KOKKOS_FUNCTION UnaryFunctorType
for_each_team_impl(const TeamHandleType& teamHandle, IteratorType first,
IteratorType last, UnaryFunctorType functor) {
KOKKOS_FUNCTION void for_each_team_impl(const TeamHandleType& teamHandle,
IteratorType first, IteratorType last,
UnaryFunctorType functor) {
// checks
Impl::static_assert_random_access_and_accessible(teamHandle, first);
Impl::expect_valid_range(first, last);
@ -96,7 +93,6 @@ for_each_team_impl(const TeamHandleType& teamHandle, IteratorType first,
TeamThreadRange(teamHandle, 0, num_elements),
StdForEachFunctor<IteratorType, UnaryFunctorType>(first, functor));
teamHandle.team_barrier();
return functor;
}
template <class TeamHandleType, class IteratorType, class SizeType,
@ -113,7 +109,7 @@ for_each_n_team_impl(const TeamHandleType& teamHandle, IteratorType first,
}
for_each_team_impl(teamHandle, first, last, std::move(functor));
// no neeed to fence since for_each_team_impl fences already
// no need to fence since for_each_team_impl fences already
return last;
}

31
lib/kokkos/algorithms/src/std_algorithms/impl/Kokkos_RandomAccessIterator.hpp
View File

@ -59,6 +59,30 @@ class RandomAccessIterator< ::Kokkos::View<DataType, Args...> > {
ptrdiff_t current_index)
: m_view(view), m_current_index(current_index) {}
#ifndef KOKKOS_ENABLE_CXX17 // C++20 and beyond
template <class OtherViewType>
requires(std::is_constructible_v<view_type, OtherViewType>) KOKKOS_FUNCTION
explicit(!std::is_convertible_v<OtherViewType, view_type>)
RandomAccessIterator(const RandomAccessIterator<OtherViewType>& other)
: m_view(other.m_view), m_current_index(other.m_current_index) {}
#else
template <
class OtherViewType,
std::enable_if_t<std::is_constructible_v<view_type, OtherViewType> &&
!std::is_convertible_v<OtherViewType, view_type>,
int> = 0>
KOKKOS_FUNCTION explicit RandomAccessIterator(
const RandomAccessIterator<OtherViewType>& other)
: m_view(other.m_view), m_current_index(other.m_current_index) {}
template <class OtherViewType,
std::enable_if_t<std::is_convertible_v<OtherViewType, view_type>,
int> = 0>
KOKKOS_FUNCTION RandomAccessIterator(
const RandomAccessIterator<OtherViewType>& other)
: m_view(other.m_view), m_current_index(other.m_current_index) {}
#endif
KOKKOS_FUNCTION
iterator_type& operator++() {
++m_current_index;
@ -152,9 +176,16 @@ class RandomAccessIterator< ::Kokkos::View<DataType, Args...> > {
KOKKOS_FUNCTION
reference operator*() const { return m_view(m_current_index); }
KOKKOS_FUNCTION
view_type view() const { return m_view; }
private:
view_type m_view;
ptrdiff_t m_current_index = 0;
// Needed for the converting constructor accepting another iterator
template <class>
friend class RandomAccessIterator;
};
} // namespace Impl

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