Merge branch 'master' into master
This commit is contained in:
TD Swinburne (Tom)
@ -15,75 +15,93 @@ if(BUILD_DOC)
|
|||||||
endif()
|
endif()
|
||||||
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
|
set(VIRTUALENV ${Python3_EXECUTABLE} -m virtualenv -p ${Python3_EXECUTABLE})
|
||||||
endif()
|
endif()
|
||||||
|
find_package(Doxygen 1.8.10 REQUIRED)
|
||||||
|
|
||||||
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
|
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
|
||||||
|
|
||||||
|
|
||||||
add_custom_command(
|
add_custom_command(
|
||||||
OUTPUT docenv
|
OUTPUT docenv
|
||||||
COMMAND ${VIRTUALENV} docenv
|
COMMAND ${VIRTUALENV} docenv
|
||||||
)
|
)
|
||||||
|
|
||||||
set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
|
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)
|
||||||
|
|
||||||
|
# configuration and static files are copied to binary dir to avoid collisions with parallel builds
|
||||||
|
set(DOC_BUILD_DIR ${CMAKE_CURRENT_BINARY_DIR}/doc)
|
||||||
|
set(DOC_BUILD_CONFIG_FILE ${DOC_BUILD_DIR}/conf.py)
|
||||||
|
set(DOC_BUILD_STATIC_DIR ${DOC_BUILD_DIR}/_static)
|
||||||
|
set(DOXYGEN_BUILD_DIR ${DOC_BUILD_DIR}/doxygen)
|
||||||
|
set(DOXYGEN_XML_DIR ${DOXYGEN_BUILD_DIR}/xml)
|
||||||
|
|
||||||
|
# copy entire configuration folder to doc build directory
|
||||||
|
# files in _static are automatically copied during sphinx-build, so no need to copy them individually
|
||||||
|
file(COPY ${SPHINX_CONFIG_DIR}/ DESTINATION ${DOC_BUILD_DIR})
|
||||||
|
|
||||||
|
# configure paths in conf.py, since relative paths change when file is copied
|
||||||
|
configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
|
||||||
|
|
||||||
add_custom_command(
|
add_custom_command(
|
||||||
OUTPUT requirements.txt
|
OUTPUT ${DOC_BUILD_DIR}/requirements.txt
|
||||||
DEPENDS docenv
|
DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
|
||||||
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
|
COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
|
||||||
|
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
|
||||||
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
|
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
|
||||||
COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r requirements.txt --upgrade
|
COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
|
||||||
)
|
)
|
||||||
|
|
||||||
# download mathjax distribution and unpack to folder "mathjax"
|
# download mathjax distribution and unpack to folder "mathjax"
|
||||||
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5)
|
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
|
||||||
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
|
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
|
||||||
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
|
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
|
||||||
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
|
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
|
||||||
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||||
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
|
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
|
||||||
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
|
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
|
||||||
endif()
|
endif()
|
||||||
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
|
|
||||||
file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
|
|
||||||
|
|
||||||
# for increased browser compatibility
|
# for increased browser compatibility
|
||||||
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js)
|
if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)
|
||||||
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
|
file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
|
||||||
"${CMAKE_CURRENT_BINARY_DIR}/html/_static/polyfill.js")
|
"${DOC_BUILD_STATIC_DIR}/polyfill.js")
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
# note, this may run in parallel with other tasks, so we must not use multiple processes here
|
# set up doxygen and add targets to run it
|
||||||
|
file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})
|
||||||
|
file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)
|
||||||
|
configure_file(${LAMMPS_DOC_DIR}/doxygen/Doxyfile.in ${DOXYGEN_BUILD_DIR}/Doxyfile)
|
||||||
|
get_target_property(LAMMPS_SOURCES lammps SOURCES)
|
||||||
add_custom_command(
|
add_custom_command(
|
||||||
OUTPUT html
|
OUTPUT ${DOXYGEN_XML_DIR}/index.xml
|
||||||
DEPENDS ${DOC_SOURCES} docenv requirements.txt
|
DEPENDS ${DOC_SOURCES} ${LAMMPS_SOURCES}
|
||||||
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
|
COMMAND Doxygen::doxygen ${DOXYGEN_BUILD_DIR}/Doxyfile WORKING_DIRECTORY ${DOXYGEN_BUILD_DIR}
|
||||||
COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${CMAKE_CURRENT_BINARY_DIR}/html/index.html
|
COMMAND ${CMAKE_COMMAND} -E touch ${DOXYGEN_XML_DIR}/run.stamp
|
||||||
)
|
)
|
||||||
|
|
||||||
# copy selected image files to html output tree
|
if(EXISTS ${DOXYGEN_XML_DIR}/run.stamp)
|
||||||
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/html/JPG)
|
set(SPHINX_EXTRA_OPTS "-E")
|
||||||
set(HTML_EXTRA_IMAGES balance_nonuniform.jpg balance_rcb.jpg
|
else()
|
||||||
balance_uniform.jpg bow_tutorial_01.png bow_tutorial_02.png
|
set(SPHINX_EXTRA_OPTS "")
|
||||||
bow_tutorial_03.png bow_tutorial_04.png bow_tutorial_05.png
|
endif()
|
||||||
dump1.jpg dump2.jpg examples_mdpd.gif gran_funnel.png gran_mixer.png
|
|
||||||
hop1.jpg hop2.jpg saed_ewald_intersect.jpg saed_mesh.jpg
|
|
||||||
screenshot_atomeye.jpg screenshot_gl.jpg screenshot_pymol.jpg
|
|
||||||
screenshot_vmd.jpg sinusoid.jpg xrd_mesh.jpg)
|
|
||||||
set(HTML_IMAGE_TARGETS "")
|
|
||||||
foreach(_IMG ${HTML_EXTRA_IMAGES})
|
|
||||||
string(PREPEND _IMG JPG/)
|
|
||||||
list(APPEND HTML_IMAGE_TARGETS "${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}")
|
|
||||||
add_custom_command(
|
add_custom_command(
|
||||||
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
|
OUTPUT html
|
||||||
DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_CURRENT_BINARY_DIR}/html/JPG
|
DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
|
||||||
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
|
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
|
||||||
|
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
|
||||||
)
|
)
|
||||||
endforeach()
|
|
||||||
|
|
||||||
add_custom_target(
|
add_custom_target(
|
||||||
doc ALL
|
doc ALL
|
||||||
DEPENDS html ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
|
DEPENDS html ${DOC_BUILD_STATIC_DIR}/mathjax/es5
|
||||||
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
|
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
|
||||||
)
|
)
|
||||||
|
|
||||||
install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
|
install(DIRECTORY ${DOC_BUILD_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -75,7 +75,7 @@ if(GPU_API STREQUAL "CUDA")
|
|||||||
endif()
|
endif()
|
||||||
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
|
# Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
|
||||||
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
|
if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
|
||||||
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35]")
|
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
|
||||||
endif()
|
endif()
|
||||||
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
|
# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
|
||||||
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
|
if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
|
||||||
|
|||||||
@ -35,8 +35,8 @@ if(DOWNLOAD_KOKKOS)
|
|||||||
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
|
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
|
||||||
include(ExternalProject)
|
include(ExternalProject)
|
||||||
ExternalProject_Add(kokkos_build
|
ExternalProject_Add(kokkos_build
|
||||||
URL https://github.com/kokkos/kokkos/archive/3.1.01.tar.gz
|
URL https://github.com/kokkos/kokkos/archive/3.2.00.tar.gz
|
||||||
URL_MD5 3ccb2100f7fc316891e7dad3bc33fa37
|
URL_MD5 81569170fe232e5e64ab074f7cca5e50
|
||||||
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
|
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
|
||||||
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
|
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
|
||||||
)
|
)
|
||||||
@ -50,7 +50,7 @@ if(DOWNLOAD_KOKKOS)
|
|||||||
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
|
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
|
||||||
add_dependencies(LAMMPS::KOKKOS kokkos_build)
|
add_dependencies(LAMMPS::KOKKOS kokkos_build)
|
||||||
elseif(EXTERNAL_KOKKOS)
|
elseif(EXTERNAL_KOKKOS)
|
||||||
find_package(Kokkos 3.1.01 REQUIRED CONFIG)
|
find_package(Kokkos 3.2.00 REQUIRED CONFIG)
|
||||||
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
|
||||||
else()
|
else()
|
||||||
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
|
||||||
|
|||||||
7
doc/.gitignore
vendored
7
doc/.gitignore
vendored
@ -1,6 +1,7 @@
|
|||||||
/old
|
/old
|
||||||
/html
|
/html
|
||||||
/html-offline
|
/html-offline
|
||||||
|
/epub
|
||||||
/latex
|
/latex
|
||||||
/mathjax
|
/mathjax
|
||||||
/spelling
|
/spelling
|
||||||
@ -10,3 +11,9 @@
|
|||||||
/Developer.pdf
|
/Developer.pdf
|
||||||
/doctrees
|
/doctrees
|
||||||
/docenv
|
/docenv
|
||||||
|
/doxygen-warn.log
|
||||||
|
/utils/sphinx-config/conf.py
|
||||||
|
/doxygen/Doxyfile
|
||||||
|
*.el
|
||||||
|
/utils/sphinx-config/_static/mathjax
|
||||||
|
/utils/sphinx-config/_static/polyfill.js
|
||||||
|
|||||||
104
doc/Makefile
104
doc/Makefile
@ -4,20 +4,28 @@ SHELL = /bin/bash
|
|||||||
BUILDDIR = ${CURDIR}
|
BUILDDIR = ${CURDIR}
|
||||||
RSTDIR = $(BUILDDIR)/src
|
RSTDIR = $(BUILDDIR)/src
|
||||||
VENV = $(BUILDDIR)/docenv
|
VENV = $(BUILDDIR)/docenv
|
||||||
MATHJAX = $(BUILDDIR)/mathjax
|
|
||||||
TXT2RST = $(VENV)/bin/txt2rst
|
TXT2RST = $(VENV)/bin/txt2rst
|
||||||
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
|
ANCHORCHECK = $(VENV)/bin/rst_anchor_check
|
||||||
|
SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config
|
||||||
|
MATHJAX = $(SPHINXCONFIG)/_static/mathjax
|
||||||
|
POLYFILL = $(SPHINXCONFIG)/_static/polyfill.js
|
||||||
|
|
||||||
PYTHON = $(shell which python3)
|
PYTHON = $(shell which python3)
|
||||||
|
DOXYGEN = $(shell which doxygen)
|
||||||
VIRTUALENV = virtualenv
|
VIRTUALENV = virtualenv
|
||||||
HAS_PYTHON3 = NO
|
HAS_PYTHON3 = NO
|
||||||
HAS_VIRTUALENV = NO
|
HAS_VIRTUALENV = NO
|
||||||
|
HAS_DOXYGEN = NO
|
||||||
HAS_PDFLATEX = NO
|
HAS_PDFLATEX = NO
|
||||||
|
|
||||||
ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
|
ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
|
||||||
HAS_PYTHON3 = YES
|
HAS_PYTHON3 = YES
|
||||||
endif
|
endif
|
||||||
|
|
||||||
|
ifeq ($(shell which doxygen >/dev/null 2>&1; echo $$?), 0)
|
||||||
|
HAS_DOXYGEN = YES
|
||||||
|
endif
|
||||||
|
|
||||||
ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
|
ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
|
||||||
VIRTUALENV = virtualenv-3
|
VIRTUALENV = virtualenv-3
|
||||||
HAS_VIRTUALENV = YES
|
HAS_VIRTUALENV = YES
|
||||||
@ -33,16 +41,20 @@ HAS_PDFLATEX = YES
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
|
|
||||||
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
|
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
|
||||||
|
|
||||||
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check
|
# grab list of sources from doxygen config file.
|
||||||
|
# we only want to use explicitly listed files.
|
||||||
|
DOXYFILES = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//')
|
||||||
|
|
||||||
|
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check xmlgen
|
||||||
|
|
||||||
# ------------------------------------------
|
# ------------------------------------------
|
||||||
|
|
||||||
help:
|
help:
|
||||||
@echo "Please use \`make <target>' where <target> is one of"
|
@echo "Please use \`make <target>' where <target> is one of"
|
||||||
@echo " html create HTML doc pages in html dir"
|
@echo " html create HTML doc pages in html dir"
|
||||||
@echo " pdf create Developer.pdf and Manual.pdf in this dir"
|
@echo " pdf create Manual.pdf in this dir"
|
||||||
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
|
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
|
||||||
@echo " epub create ePUB format manual for e-book readers"
|
@echo " epub create ePUB format manual for e-book readers"
|
||||||
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
|
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
|
||||||
@ -57,23 +69,32 @@ help:
|
|||||||
# ------------------------------------------
|
# ------------------------------------------
|
||||||
|
|
||||||
clean-all: clean
|
clean-all: clean
|
||||||
rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax Manual.pdf Developer.pdf
|
rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
|
||||||
|
|
||||||
clean: clean-spelling
|
clean: clean-spelling
|
||||||
rm -rf html epub latex
|
rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py
|
||||||
|
|
||||||
clean-spelling:
|
clean-spelling:
|
||||||
rm -rf spelling
|
rm -rf $(BUILDDIR)/spelling
|
||||||
|
|
||||||
html: $(ANCHORCHECK) $(MATHJAX)
|
$(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
|
||||||
|
sed -e 's,@DOXYGEN_XML_DIR@,$(BUILDDIR)/doxygen/xml,g' \
|
||||||
|
-e 's,@LAMMPS_SOURCE_DIR@,$(BUILDDIR)/../src,g' \
|
||||||
|
-e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
|
||||||
|
-e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
|
||||||
|
|
||||||
|
html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
|
||||||
|
@$(MAKE) $(MFLAGS) -C graphviz all
|
||||||
@(\
|
@(\
|
||||||
. $(VENV)/bin/activate ;\
|
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
|
||||||
sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
|
sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
|
||||||
|
ln -sf Manual.html html/index.html;\
|
||||||
|
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||||
echo "############################################" ;\
|
echo "############################################" ;\
|
||||||
rst_anchor_check src/*.rst ;\
|
rst_anchor_check src/*.rst ;\
|
||||||
python utils/check-packages.py -s ../src -d src ;\
|
python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
|
||||||
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
|
||||||
python utils/check-styles.py -s ../src -d src ;\
|
python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
|
||||||
echo "############################################" ;\
|
echo "############################################" ;\
|
||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
@ -82,30 +103,28 @@ html: $(ANCHORCHECK) $(MATHJAX)
|
|||||||
@rm -rf html/USER
|
@rm -rf html/USER
|
||||||
@rm -rf html/JPG
|
@rm -rf html/JPG
|
||||||
@cp -r src/PDF html/PDF
|
@cp -r src/PDF html/PDF
|
||||||
@mkdir -p html/JPG
|
|
||||||
@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target: JPG' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
|
|
||||||
@rm -rf html/PDF/.[sg]*
|
@rm -rf html/PDF/.[sg]*
|
||||||
@mkdir -p html/_static/mathjax
|
|
||||||
@cp -r $(MATHJAX)/es5 html/_static/mathjax/
|
|
||||||
@echo "Build finished. The HTML pages are in doc/html."
|
@echo "Build finished. The HTML pages are in doc/html."
|
||||||
|
|
||||||
spelling: $(VENV) utils/sphinx-config/false_positives.txt
|
spelling: xmlgen $(VENV) $(SPHINXCONFIG)/false_positives.txt
|
||||||
@(\
|
@(\
|
||||||
. $(VENV)/bin/activate ;\
|
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
|
||||||
cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
|
cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
|
||||||
sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
|
sphinx-build -b spelling -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
|
||||||
|
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
@echo "Spell check finished."
|
@echo "Spell check finished."
|
||||||
|
|
||||||
epub: $(VENV)
|
epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
|
||||||
|
@$(MAKE) $(MFLAGS) -C graphviz all
|
||||||
@mkdir -p epub/JPG
|
@mkdir -p epub/JPG
|
||||||
@rm -f LAMMPS.epub
|
@rm -f LAMMPS.epub
|
||||||
@cp src/JPG/lammps-logo.png epub/
|
|
||||||
@cp src/JPG/*.* epub/JPG
|
@cp src/JPG/*.* epub/JPG
|
||||||
@(\
|
@(\
|
||||||
. $(VENV)/bin/activate ;\
|
. $(VENV)/bin/activate ;\
|
||||||
sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
|
sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
|
||||||
|
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
@mv epub/LAMMPS.epub .
|
@mv epub/LAMMPS.epub .
|
||||||
@ -117,18 +136,13 @@ mobi: epub
|
|||||||
@ebook-convert LAMMPS.epub LAMMPS.mobi
|
@ebook-convert LAMMPS.epub LAMMPS.mobi
|
||||||
@echo "Conversion finished. The MOBI manual file is created."
|
@echo "Conversion finished. The MOBI manual file is created."
|
||||||
|
|
||||||
pdf: $(ANCHORCHECK)
|
pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
|
||||||
|
@$(MAKE) $(MFLAGS) -C graphviz all
|
||||||
@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
|
@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
|
||||||
@(\
|
@(\
|
||||||
cd src/Developer; \
|
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
|
||||||
pdflatex developer; \
|
sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||||
pdflatex developer; \
|
rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
|
||||||
mv developer.pdf ../../Developer.pdf; \
|
|
||||||
cd ../../; \
|
|
||||||
)
|
|
||||||
@(\
|
|
||||||
. $(VENV)/bin/activate ;\
|
|
||||||
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
|
||||||
echo "############################################" ;\
|
echo "############################################" ;\
|
||||||
rst_anchor_check src/*.rst ;\
|
rst_anchor_check src/*.rst ;\
|
||||||
python utils/check-packages.py -s ../src -d src ;\
|
python utils/check-packages.py -s ../src -d src ;\
|
||||||
@ -154,12 +168,11 @@ pdf: $(ANCHORCHECK)
|
|||||||
@rm -rf latex/USER
|
@rm -rf latex/USER
|
||||||
@cp -r src/PDF latex/PDF
|
@cp -r src/PDF latex/PDF
|
||||||
@rm -rf latex/PDF/.[sg]*
|
@rm -rf latex/PDF/.[sg]*
|
||||||
@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
|
@echo "Build finished. Manual.pdf is in this directory."
|
||||||
|
|
||||||
fetch:
|
fetch:
|
||||||
@rm -rf html_www Manual_www.pdf Developer_www.pdf
|
@rm -rf html_www Manual_www.pdf
|
||||||
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
|
@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
|
||||||
@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
|
|
||||||
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
|
@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
|
||||||
@tar xzf lammps-doc.tar.gz
|
@tar xzf lammps-doc.tar.gz
|
||||||
@rm -f lammps-doc.tar.gz
|
@rm -f lammps-doc.tar.gz
|
||||||
@ -185,21 +198,32 @@ package_check : $(VENV)
|
|||||||
deactivate ;\
|
deactivate ;\
|
||||||
)
|
)
|
||||||
|
|
||||||
|
xmlgen : doxygen/xml/index.xml
|
||||||
|
|
||||||
|
doxygen/Doxyfile: doxygen/Doxyfile.in
|
||||||
|
sed -e 's/@LAMMPS_SOURCE_DIR@/..\/..\/src/g' $< > $@
|
||||||
|
|
||||||
|
doxygen/xml/index.xml : $(VENV) doxygen/Doxyfile $(DOXYFILES)
|
||||||
|
@(cd doxygen; $(DOXYGEN) Doxyfile && touch xml/run.stamp)
|
||||||
# ------------------------------------------
|
# ------------------------------------------
|
||||||
|
|
||||||
$(VENV):
|
$(VENV):
|
||||||
@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
|
@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "python3 was not found! Please see README for further instructions" 1>&2; exit 1; fi
|
||||||
@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
|
@if [ "$(HAS_DOXYGEN)" == "NO" ] ; then echo "doxygen was not found! Please see README for further instructions" 1>&2; exit 1; fi
|
||||||
|
@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please see README for further instructions" 1>&2; exit 1; fi
|
||||||
@( \
|
@( \
|
||||||
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
|
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
|
||||||
. $(VENV)/bin/activate; \
|
. $(VENV)/bin/activate; \
|
||||||
pip install --upgrade pip; \
|
pip install --upgrade pip; \
|
||||||
pip install --use-feature=2020-resolver -r requirements.txt; \
|
pip install --use-feature=2020-resolver -r $(BUILDDIR)/utils/requirements.txt; \
|
||||||
deactivate;\
|
deactivate;\
|
||||||
)
|
)
|
||||||
|
|
||||||
$(MATHJAX):
|
$(MATHJAX):
|
||||||
@git clone --depth 1 https://github.com/mathjax/MathJax.git mathjax
|
@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
|
||||||
|
|
||||||
|
$(POLYFILL): $(MATHJAX)
|
||||||
|
@curl -s -o $@ "https://polyfill.io/v3/polyfill.min.js?features=es6"
|
||||||
|
|
||||||
$(TXT2RST) $(ANCHORCHECK): $(VENV)
|
$(TXT2RST) $(ANCHORCHECK): $(VENV)
|
||||||
@( \
|
@( \
|
||||||
|
|||||||
140
doc/README
140
doc/README
@ -1,97 +1,60 @@
|
|||||||
LAMMPS Documentation
|
LAMMPS Documentation
|
||||||
|
|
||||||
Depending on how you obtained LAMMPS, this directory has 2 or 3
|
Depending on how you obtained LAMMPS and whether you have built
|
||||||
sub-directories and optionally 2 PDF files and an ePUB file:
|
the manual yourself, this directory has a varying number of
|
||||||
|
sub-directories and files. Here is a list with descriptions:
|
||||||
|
|
||||||
|
README this file
|
||||||
src content files for LAMMPS documentation
|
src content files for LAMMPS documentation
|
||||||
html HTML version of the LAMMPS manual (see html/Manual.html)
|
html HTML version of the LAMMPS manual (see html/Manual.html)
|
||||||
utils utilities and settings for building the documentation
|
utils utilities and settings for building the documentation
|
||||||
Manual.pdf large PDF version of entire manual
|
Manual.pdf PDF version of entire manual
|
||||||
Developer.pdf small PDF with info about how LAMMPS is structured
|
Developer.pdf PDF with info about how LAMMPS is structured
|
||||||
LAMMPS.epub Manual in ePUB format
|
LAMMPS.epub Manual in ePUB format
|
||||||
|
LAMMPS.mobi Manual in MOBI (Kindle) format
|
||||||
|
lammps.1 man page for the lammps command
|
||||||
|
msi2lmp.1 man page for the msi2lmp command
|
||||||
|
mathjax code and fonts for rendering math in html
|
||||||
|
doctree temporary data
|
||||||
|
docenv python virtual environment for generating the manual
|
||||||
|
doxygen Doxygen configuration and output
|
||||||
|
.gitignore list of files and folders to be ignored by git
|
||||||
|
doxygen-warn.log logfile with warnings from running doxygen
|
||||||
|
|
||||||
If you downloaded LAMMPS as a tarball from the web site, all these
|
and:
|
||||||
directories and files should be included.
|
|
||||||
|
|
||||||
If you downloaded LAMMPS from the public SVN or Git repositories, then
|
github-development-workflow.md notes on the LAMMPS development workflow
|
||||||
the HTML and PDF files are not included. Instead you need to create
|
include-file-conventions.md notes on LAMMPS' include file conventions
|
||||||
them, in one of three ways:
|
documentation_conventions.md notes on writing documentation for LAMMPS
|
||||||
|
|
||||||
|
If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
|
||||||
|
folder and the PDF manual should be included. If you downloaded LAMMPS
|
||||||
|
from GitHub then you either need to download them or build them.
|
||||||
|
|
||||||
(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
|
(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
|
||||||
site. Just type "make fetch". This should create a html_www dir and
|
site. Just type "make fetch". This should create a html_www dir and
|
||||||
Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS
|
Manual_www.pdf/Developer_www.pdf files. These files will always
|
||||||
features have been added more recently than the date of your version,
|
represent the latest published patch/development version of LAMMPS.
|
||||||
the fetched documentation will include those changes (but your source
|
|
||||||
code will not, unless you update your local repository).
|
|
||||||
|
|
||||||
(b) You can build the HTML and PDF files yourself, by typing "make
|
(b) You can build the HTML and PDF files yourself, by typing "make html"
|
||||||
html" or by "make pdf", respectively. This requires various tools
|
or by "make pdf", respectively. This requires various tools and files.
|
||||||
including the Python documentation processing tool Sphinx, which the
|
Some of them have to be installed (more on that below). For the rest the
|
||||||
build process will attempt to download and install on your system into
|
build process will attempt to download and install into a python virtual
|
||||||
a python virtual environment, if not already available. The PDF file
|
environment and local folders.
|
||||||
will require a working LaTeX installation with several add-on packages
|
|
||||||
in addition to the Python/Sphinx setup. See more details below.
|
|
||||||
|
|
||||||
----------------
|
----------------
|
||||||
|
|
||||||
The generation of all documentation is managed by the Makefile in this
|
Installing prerequisites for the documentation build
|
||||||
dir.
|
|
||||||
|
|
||||||
Options:
|
To run the HTML documention build toolchain, python 3.x, doxygen, git,
|
||||||
|
and virtualenv have to be installed. Also internet access is initially
|
||||||
|
required to download external files and tools.
|
||||||
|
|
||||||
make html # generate HTML in html dir using Sphinx
|
Building the PDF format manual requires in addition a compatible LaTeX
|
||||||
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
|
installation with support for PDFLaTeX and several add-on LaTeX packages
|
||||||
# in this dir via Sphinx and PDFLaTeX
|
installed. This includes:
|
||||||
make fetch # fetch HTML doc pages and 2 PDF files from web site
|
|
||||||
# as a tarball and unpack into html dir and 2 PDFs
|
|
||||||
make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
|
||||||
make clean # remove intermediate RST files created by HTML build
|
|
||||||
make clean-all # remove entire build folder and any cached data
|
|
||||||
|
|
||||||
----------------
|
|
||||||
|
|
||||||
Installing prerequisites for HTML build
|
|
||||||
|
|
||||||
To run the HTML documention build toolchain, Python 3 and virtualenv
|
|
||||||
have to be installed. Here are instructions for common setups:
|
|
||||||
|
|
||||||
# Ubuntu
|
|
||||||
|
|
||||||
sudo apt-get install python-virtualenv
|
|
||||||
|
|
||||||
# Fedora (up to version 21)
|
|
||||||
# Red Hat Enterprise Linux or CentOS (up to version 7.x)
|
|
||||||
|
|
||||||
sudo yum install python3-virtualenv
|
|
||||||
|
|
||||||
# Fedora (since version 22)
|
|
||||||
|
|
||||||
sudo dnf install python3-virtualenv
|
|
||||||
|
|
||||||
# MacOS X
|
|
||||||
|
|
||||||
## Python 3
|
|
||||||
|
|
||||||
Download the latest Python 3 MacOS X package from
|
|
||||||
https://www.python.org and install it. This will install both Python
|
|
||||||
3 and pip3.
|
|
||||||
|
|
||||||
## virtualenv
|
|
||||||
|
|
||||||
Once Python 3 is installed, open a Terminal and type
|
|
||||||
|
|
||||||
pip3 install virtualenv
|
|
||||||
|
|
||||||
This will install virtualenv from the Python Package Index.
|
|
||||||
|
|
||||||
----------------
|
|
||||||
|
|
||||||
Installing prerequisites for PDF build
|
|
||||||
|
|
||||||
Same as for HTML plus a compatible LaTeX installation with
|
|
||||||
support for PDFLaTeX. Also the following LaTeX packages need
|
|
||||||
to be installed (e.g. from texlive):
|
|
||||||
- amsmath
|
- amsmath
|
||||||
|
- anysize
|
||||||
- babel
|
- babel
|
||||||
- capt-of
|
- capt-of
|
||||||
- cmap
|
- cmap
|
||||||
@ -105,24 +68,13 @@ to be installed (e.g. from texlive):
|
|||||||
- tabulary
|
- tabulary
|
||||||
- upquote
|
- upquote
|
||||||
- wrapfig
|
- wrapfig
|
||||||
|
|
||||||
|
Building the EPUB format requires LaTeX installation with the same packages
|
||||||
|
as for the PDF format plus the 'dvipng' command to convert the embedded math
|
||||||
|
into images. The MOBI format is generated from the EPUB format file by using
|
||||||
|
the tool 'ebook-convert' from the 'calibre' e-book management software
|
||||||
|
(https://calibre-ebook.com).
|
||||||
----------------
|
----------------
|
||||||
|
|
||||||
Installing prerequisites for epub build
|
More details this can be found in the manual itself. The online
|
||||||
|
version is at: https://lammps.sandia.gov/doc/Manual_build.html
|
||||||
## ePUB
|
|
||||||
|
|
||||||
Same as for HTML. This uses the same tools and configuration
|
|
||||||
files as the HTML tree. The ePUB format conversion currently
|
|
||||||
does not support processing mathematical expressions via MathJAX,
|
|
||||||
so there will be limitations on some pages. For the time being
|
|
||||||
until this is resolved, building and using the PDF format file
|
|
||||||
is recommended instead.
|
|
||||||
|
|
||||||
For converting the generated ePUB file to a mobi format file
|
|
||||||
(for e-book readers like Kindle, that cannot read ePUB), you
|
|
||||||
also need to have the 'ebook-convert' tool from the "calibre"
|
|
||||||
software installed. http://calibre-ebook.com/
|
|
||||||
You first create the ePUB file with 'make epub' and then do:
|
|
||||||
|
|
||||||
ebook-convert LAMMPS.epub LAMMPS.mobi
|
|
||||||
|
|
||||||
|
|||||||
93
doc/documentation_conventions.md
Normal file
93
doc/documentation_conventions.md
Normal file
@ -0,0 +1,93 @@
|
|||||||
|
# Outline of LAMMPS documentation file conventions
|
||||||
|
|
||||||
|
This purpose of this document is to provide a point of reference
|
||||||
|
for LAMMPS developers and contributors as to what conventions
|
||||||
|
should be used to structure and format files in the LAMMPS manual.
|
||||||
|
|
||||||
|
Last change: 2020-04-23
|
||||||
|
|
||||||
|
## File format and tools
|
||||||
|
|
||||||
|
In fall 2019, the LAMMPS documentation file format has changed from
|
||||||
|
a home grown minimal markup designed to generate HTML format files
|
||||||
|
from a mostly plain text format to using the reStructuredText file
|
||||||
|
format. For a transition period all files in the old .txt format
|
||||||
|
were transparently converted to .rst and then processed. The txt2rst
|
||||||
|
tool is still included in the distribution to obtain an initial .rst
|
||||||
|
file for integration into the manual. Since the transition to
|
||||||
|
reStructured text as source format, many of the artifacts or the
|
||||||
|
translation have been removed though and parts of the documentation
|
||||||
|
refactored and expanded to take advantage of the capabilities
|
||||||
|
reStructuredText and associated tools. The conversion from the
|
||||||
|
source to the final formats (HTML, PDF, and optionally e-book
|
||||||
|
reader formats ePUB and MOBI) is mostly automated and controlled
|
||||||
|
by a Makefile in the `doc` folder. This makefile assumes that the
|
||||||
|
processing is done on a Unix-like machine and Python 3.5 or later
|
||||||
|
and a matching virtualenv module are available. Additional Python
|
||||||
|
packages (like the Sphinx tool and several extensions) are
|
||||||
|
transparently installed into a virtual environment over the
|
||||||
|
internet using the `pip` package manager. Further requirements
|
||||||
|
and details are discussed in the manual.
|
||||||
|
|
||||||
|
## Work in progress
|
||||||
|
|
||||||
|
The refactoring and improving of the documentation is an ongoing
|
||||||
|
process, so statements in this document may not always be fully
|
||||||
|
up-to-date. If in doubt, contact the LAMMPS developers.
|
||||||
|
|
||||||
|
## General structure
|
||||||
|
|
||||||
|
The layout and formatting of added files should follow the example
|
||||||
|
of the existing files. Since those are directly derived from their
|
||||||
|
former .txt format versions and the manual has been maintained in
|
||||||
|
that format for many years, there is a large degree of consistency
|
||||||
|
already, so comparision with similar files should give you a good
|
||||||
|
idea what kind of information and sections are needed.
|
||||||
|
|
||||||
|
## Formatting conventions
|
||||||
|
|
||||||
|
Filenames, folders, paths, (shell) commands, definitions, makefile
|
||||||
|
settings and similar should be formatted as "literals" with
|
||||||
|
double backward quotes bracketing the item: \`\`path/to/some/file\`\`
|
||||||
|
|
||||||
|
Keywords and options are formatted in italics: \*option\*
|
||||||
|
|
||||||
|
Mathematical expressions, equations, symbols are typeset using
|
||||||
|
either a `.. math:`` block or the `:math:` role.
|
||||||
|
|
||||||
|
Groups of shell commands or LAMMPS input script or C/C++ source
|
||||||
|
code should be typeset into a `.. code-block::` section. A syntax
|
||||||
|
highlighting extension for LAMMPS input scripts is provided, so
|
||||||
|
`LAMMPS` can be used to indicate the language in the code block
|
||||||
|
in addition to `bash`, `c`, or `python`. When no syntax style
|
||||||
|
is indicated, no syntax highlighting is performed.
|
||||||
|
|
||||||
|
As an alternative, e.g. to typeset the syntax of file formats
|
||||||
|
a `.. parsed-literal::` block can be used, which allows some
|
||||||
|
formatting directives, which means that related characters need
|
||||||
|
to be escaped with a preceding backslash: `\*`.
|
||||||
|
|
||||||
|
Special remarks can be highlighted with a `.. note::` block and
|
||||||
|
strong warnings can be put into a `.. warning::` block.
|
||||||
|
|
||||||
|
## Required steps when adding a custom style to LAMMPS
|
||||||
|
|
||||||
|
When adding a new style (e.g. pair style or a compute or a fix)
|
||||||
|
or a new command, it is **required** to include the corresponding
|
||||||
|
documentation. Those are often new files that need to be added.
|
||||||
|
In order to be included in the documentation, those new files
|
||||||
|
need to be reference in a `.. toctree::` block. Most of those
|
||||||
|
use patterns with wildcards, so the addition will be automatic.
|
||||||
|
However, those additions also need to be added to some lists of
|
||||||
|
styles or commands. The `make style\_check` command will perform
|
||||||
|
a test and report any missing entries and list the affected files.
|
||||||
|
Any references defined with `.. \_refname:` have to be unique
|
||||||
|
across all documentation files and this can be checked for with
|
||||||
|
`make anchor\_check`. Finally, a spell-check should be done,
|
||||||
|
which is triggered via `make spelling`. Any offenses need to
|
||||||
|
be corrected and false positives should be added to the file
|
||||||
|
`utils/sphinx-config/false\_positives.txt`.
|
||||||
|
|
||||||
|
## Required additional steps when adding a new package to LAMMPS
|
||||||
|
|
||||||
|
TODO
|
||||||
1
doc/doxygen/.gitignore
vendored
Normal file
1
doc/doxygen/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
|||||||
|
/xml
|
||||||
528
doc/doxygen/Doxyfile.in
Normal file
528
doc/doxygen/Doxyfile.in
Normal file
@ -0,0 +1,528 @@
|
|||||||
|
# Doxyfile 1.8.15 -*- makefile -*-
|
||||||
|
|
||||||
|
DOXYFILE_ENCODING = UTF-8
|
||||||
|
PROJECT_NAME = "LAMMPS Programmer's Guide"
|
||||||
|
PROJECT_NUMBER = "24 August 2020"
|
||||||
|
PROJECT_BRIEF = "Documentation of the LAMMPS library interface and Python wrapper"
|
||||||
|
PROJECT_LOGO = lammps-logo.png
|
||||||
|
CREATE_SUBDIRS = NO
|
||||||
|
ALLOW_UNICODE_NAMES = NO
|
||||||
|
OUTPUT_LANGUAGE = English
|
||||||
|
OUTPUT_TEXT_DIRECTION = LTR
|
||||||
|
|
||||||
|
BRIEF_MEMBER_DESC = YES
|
||||||
|
REPEAT_BRIEF = YES
|
||||||
|
|
||||||
|
ALWAYS_DETAILED_SEC = NO
|
||||||
|
INLINE_INHERITED_MEMB = NO
|
||||||
|
FULL_PATH_NAMES = NO
|
||||||
|
INHERIT_DOCS = YES
|
||||||
|
TAB_SIZE = 2
|
||||||
|
|
||||||
|
# When enabled doxygen tries to link words that correspond to documented
|
||||||
|
# classes, or namespaces to their corresponding documentation. Such a link can
|
||||||
|
# be prevented in individual cases by putting a % sign in front of the word or
|
||||||
|
# globally by setting AUTOLINK_SUPPORT to NO.
|
||||||
|
# The default value is: YES.
|
||||||
|
AUTOLINK_SUPPORT = YES
|
||||||
|
|
||||||
|
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
|
||||||
|
# to include (a tag file for) the STL sources as input, then you should set this
|
||||||
|
# tag to YES in order to let doxygen match functions declarations and
|
||||||
|
# definitions whose arguments contain STL classes (e.g. func(std::string);
|
||||||
|
# versus func(std::string) {}). This also make the inheritance and collaboration
|
||||||
|
# diagrams that involve STL classes more complete and accurate.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
BUILTIN_STL_SUPPORT = YES
|
||||||
|
IDL_PROPERTY_SUPPORT = NO
|
||||||
|
|
||||||
|
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
|
||||||
|
# cache is used to resolve symbols given their name and scope. Since this can be
|
||||||
|
# an expensive process and often the same symbol appears multiple times in the
|
||||||
|
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
|
||||||
|
# doxygen will become slower. If the cache is too large, memory is wasted. The
|
||||||
|
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
|
||||||
|
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
|
||||||
|
# symbols. At the end of a run doxygen will report the cache usage and suggest
|
||||||
|
# the optimal cache size from a speed point of view.
|
||||||
|
# Minimum value: 0, maximum value: 9, default value: 0.
|
||||||
|
|
||||||
|
LOOKUP_CACHE_SIZE = 2
|
||||||
|
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Build related configuration options
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
|
||||||
|
# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
|
||||||
|
# documentation are documented, even if no documentation was available. Private
|
||||||
|
# class members and static file members will be hidden unless the
|
||||||
|
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
|
||||||
|
# Note: This will also disable the warnings about undocumented members that are
|
||||||
|
# normally produced when WARNINGS is set to YES.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
EXTRACT_ALL = NO
|
||||||
|
|
||||||
|
# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
|
||||||
|
# be included in the documentation.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
EXTRACT_PRIVATE = YES
|
||||||
|
|
||||||
|
# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
|
||||||
|
# scope will be included in the documentation.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
EXTRACT_PACKAGE = YES
|
||||||
|
|
||||||
|
# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
|
||||||
|
# included in the documentation.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
EXTRACT_STATIC = YES
|
||||||
|
|
||||||
|
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
|
||||||
|
# locally in source files will be included in the documentation. If set to NO,
|
||||||
|
# only classes defined in header files are included. Does not have any effect
|
||||||
|
# for Java sources.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
EXTRACT_LOCAL_CLASSES = YES
|
||||||
|
|
||||||
|
# If this flag is set to YES, the members of anonymous namespaces will be
|
||||||
|
# extracted and appear in the documentation as a namespace called
|
||||||
|
# 'anonymous_namespace{file}', where file will be replaced with the base name of
|
||||||
|
# the file that contains the anonymous namespace. By default anonymous namespace
|
||||||
|
# are hidden.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
EXTRACT_ANON_NSPACES = YES
|
||||||
|
|
||||||
|
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
|
||||||
|
# undocumented members inside documented classes or files. If set to NO these
|
||||||
|
# members will be included in the various overviews, but no documentation
|
||||||
|
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
HIDE_UNDOC_MEMBERS = YES
|
||||||
|
|
||||||
|
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
|
||||||
|
# undocumented classes that are normally visible in the class hierarchy. If set
|
||||||
|
# to NO, these classes will be included in the various overviews. This option
|
||||||
|
# has no effect if EXTRACT_ALL is enabled.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
HIDE_UNDOC_CLASSES = YES
|
||||||
|
|
||||||
|
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
|
||||||
|
# (class|struct|union) declarations. If set to NO, these declarations will be
|
||||||
|
# included in the documentation.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
HIDE_FRIEND_COMPOUNDS = NO
|
||||||
|
|
||||||
|
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
|
||||||
|
# documentation blocks found inside the body of a function. If set to NO, these
|
||||||
|
# blocks will be appended to the function's detailed documentation block.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
HIDE_IN_BODY_DOCS = NO
|
||||||
|
|
||||||
|
# The INTERNAL_DOCS tag determines if documentation that is typed after a
|
||||||
|
# \internal command is included. If the tag is set to NO then the documentation
|
||||||
|
# will be excluded. Set it to YES to include the internal documentation.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
INTERNAL_DOCS = NO
|
||||||
|
|
||||||
|
# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
|
||||||
|
# names in lower-case letters. If set to YES, upper-case letters are also
|
||||||
|
# allowed. This is useful if you have classes or files whose names only differ
|
||||||
|
# in case and if your file system supports case sensitive file names. Windows
|
||||||
|
# and Mac users are advised to set this option to NO.
|
||||||
|
# The default value is: system dependent.
|
||||||
|
|
||||||
|
CASE_SENSE_NAMES = YES
|
||||||
|
|
||||||
|
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
|
||||||
|
# their full class and namespace scopes in the documentation. If set to YES, the
|
||||||
|
# scope will be hidden.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
HIDE_SCOPE_NAMES = YES
|
||||||
|
|
||||||
|
# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
|
||||||
|
# append additional text to a page's title, such as Class Reference. If set to
|
||||||
|
# YES the compound reference will be hidden.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
HIDE_COMPOUND_REFERENCE= NO
|
||||||
|
|
||||||
|
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
|
||||||
|
# the files that are included by a file in the documentation of that file.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
SHOW_INCLUDE_FILES = NO
|
||||||
|
|
||||||
|
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
|
||||||
|
# grouped member an include statement to the documentation, telling the reader
|
||||||
|
# which file to include in order to use the member.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
SHOW_GROUPED_MEMB_INC = NO
|
||||||
|
|
||||||
|
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
|
||||||
|
# files with double quotes in the documentation rather than with sharp brackets.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
FORCE_LOCAL_INCLUDES = NO
|
||||||
|
|
||||||
|
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
|
||||||
|
# documentation for inline members.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
INLINE_INFO = YES
|
||||||
|
|
||||||
|
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
|
||||||
|
# (detailed) documentation of file and class members alphabetically by member
|
||||||
|
# name. If set to NO, the members will appear in declaration order.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
SORT_MEMBER_DOCS = NO
|
||||||
|
|
||||||
|
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
|
||||||
|
# descriptions of file, namespace and class members alphabetically by member
|
||||||
|
# name. If set to NO, the members will appear in declaration order. Note that
|
||||||
|
# this will also influence the order of the classes in the class list.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
SORT_BRIEF_DOCS = NO
|
||||||
|
|
||||||
|
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
|
||||||
|
# (brief and detailed) documentation of class members so that constructors and
|
||||||
|
# destructors are listed first. If set to NO the constructors will appear in the
|
||||||
|
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
|
||||||
|
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
|
||||||
|
# member documentation.
|
||||||
|
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
|
||||||
|
# detailed member documentation.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
SORT_MEMBERS_CTORS_1ST = NO
|
||||||
|
|
||||||
|
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
|
||||||
|
# of group names into alphabetical order. If set to NO the group names will
|
||||||
|
# appear in their defined order.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
SORT_GROUP_NAMES = NO
|
||||||
|
|
||||||
|
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
|
||||||
|
# fully-qualified names, including namespaces. If set to NO, the class list will
|
||||||
|
# be sorted only by class name, not including the namespace part.
|
||||||
|
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
|
||||||
|
# Note: This option applies only to the class list, not to the alphabetical
|
||||||
|
# list.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
SORT_BY_SCOPE_NAME = NO
|
||||||
|
|
||||||
|
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
|
||||||
|
# type resolution of all parameters of a function it will reject a match between
|
||||||
|
# the prototype and the implementation of a member function even if there is
|
||||||
|
# only one candidate or it is obvious which candidate to choose by doing a
|
||||||
|
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
|
||||||
|
# accept a match between prototype and implementation in such cases.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
STRICT_PROTO_MATCHING = NO
|
||||||
|
|
||||||
|
# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
|
||||||
|
# list. This list is created by putting \todo commands in the documentation.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
GENERATE_TODOLIST = YES
|
||||||
|
|
||||||
|
# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
|
||||||
|
# list. This list is created by putting \test commands in the documentation.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
GENERATE_TESTLIST = YES
|
||||||
|
|
||||||
|
# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
|
||||||
|
# list. This list is created by putting \bug commands in the documentation.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
GENERATE_BUGLIST = YES
|
||||||
|
|
||||||
|
# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
|
||||||
|
# the deprecated list. This list is created by putting \deprecated commands in
|
||||||
|
# the documentation.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
GENERATE_DEPRECATEDLIST= YES
|
||||||
|
|
||||||
|
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
|
||||||
|
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
|
||||||
|
# ... \endcond blocks.
|
||||||
|
|
||||||
|
ENABLED_SECTIONS =
|
||||||
|
|
||||||
|
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
|
||||||
|
# initial value of a variable or macro / define can have for it to appear in the
|
||||||
|
# documentation. If the initializer consists of more lines than specified here
|
||||||
|
# it will be hidden. Use a value of 0 to hide initializers completely. The
|
||||||
|
# appearance of the value of individual variables and macros / defines can be
|
||||||
|
# controlled using \showinitializer or \hideinitializer command in the
|
||||||
|
# documentation regardless of this setting.
|
||||||
|
# Minimum value: 0, maximum value: 10000, default value: 30.
|
||||||
|
|
||||||
|
MAX_INITIALIZER_LINES = 30
|
||||||
|
|
||||||
|
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
|
||||||
|
# the bottom of the documentation of classes and structs. If set to YES, the
|
||||||
|
# list will mention the files that were used to generate the documentation.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
SHOW_USED_FILES = YES
|
||||||
|
|
||||||
|
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
|
||||||
|
# will remove the Files entry from the Quick Index and from the Folder Tree View
|
||||||
|
# (if specified).
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
SHOW_FILES = NO
|
||||||
|
|
||||||
|
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
|
||||||
|
# page. This will remove the Namespaces entry from the Quick Index and from the
|
||||||
|
# Folder Tree View (if specified).
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
SHOW_NAMESPACES = YES
|
||||||
|
|
||||||
|
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
|
||||||
|
# doxygen should invoke to get the current version for each file (typically from
|
||||||
|
# the version control system). Doxygen will invoke the program by executing (via
|
||||||
|
# popen()) the command command input-file, where command is the value of the
|
||||||
|
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
|
||||||
|
# by doxygen. Whatever the program writes to standard output is used as the file
|
||||||
|
# version. For an example see the documentation.
|
||||||
|
|
||||||
|
FILE_VERSION_FILTER =
|
||||||
|
|
||||||
|
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
|
||||||
|
# by doxygen. The layout file controls the global structure of the generated
|
||||||
|
# output files in an output format independent way. To create the layout file
|
||||||
|
# that represents doxygen's defaults, run doxygen with the -l option. You can
|
||||||
|
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
|
||||||
|
# will be used as the name of the layout file.
|
||||||
|
#
|
||||||
|
# Note that if you run doxygen from a directory containing a file called
|
||||||
|
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
|
||||||
|
# tag is left empty.
|
||||||
|
|
||||||
|
LAYOUT_FILE =
|
||||||
|
|
||||||
|
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
|
||||||
|
# the reference definitions. This must be a list of .bib files. The .bib
|
||||||
|
# extension is automatically appended if omitted. This requires the bibtex tool
|
||||||
|
# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
|
||||||
|
# For LaTeX the style of the bibliography can be controlled using
|
||||||
|
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
|
||||||
|
# search path. See also \cite for info how to create references.
|
||||||
|
|
||||||
|
CITE_BIB_FILES =
|
||||||
|
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration options related to warning and progress messages
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
|
||||||
|
# The QUIET tag can be used to turn on/off the messages that are generated to
|
||||||
|
# standard output by doxygen. If QUIET is set to YES this implies that the
|
||||||
|
# messages are off.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
QUIET = NO
|
||||||
|
|
||||||
|
# The WARNINGS tag can be used to turn on/off the warning messages that are
|
||||||
|
# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
|
||||||
|
# this implies that the warnings are on.
|
||||||
|
#
|
||||||
|
# Tip: Turn warnings on while writing the documentation.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
WARNINGS = YES
|
||||||
|
|
||||||
|
# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
|
||||||
|
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
|
||||||
|
# will automatically be disabled.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
WARN_IF_UNDOCUMENTED = YES
|
||||||
|
|
||||||
|
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
|
||||||
|
# potential errors in the documentation, such as not documenting some parameters
|
||||||
|
# in a documented function, or documenting parameters that don't exist or using
|
||||||
|
# markup commands wrongly.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
WARN_IF_DOC_ERROR = YES
|
||||||
|
|
||||||
|
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
|
||||||
|
# are documented, but have no documentation for their parameters or return
|
||||||
|
# value. If set to NO, doxygen will only warn about wrong or incomplete
|
||||||
|
# parameter documentation, but not about the absence of documentation. If
|
||||||
|
# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
WARN_NO_PARAMDOC = YES
|
||||||
|
|
||||||
|
# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
|
||||||
|
# a warning is encountered.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
WARN_AS_ERROR = NO
|
||||||
|
|
||||||
|
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
|
||||||
|
# can produce. The string should contain the $file, $line, and $text tags, which
|
||||||
|
# will be replaced by the file and line number from which the warning originated
|
||||||
|
# and the warning text. Optionally the format may contain $version, which will
|
||||||
|
# be replaced by the version of the file (if it could be obtained via
|
||||||
|
# FILE_VERSION_FILTER)
|
||||||
|
# The default value is: $file:$line: $text.
|
||||||
|
|
||||||
|
WARN_FORMAT = "$file:$line: $text"
|
||||||
|
|
||||||
|
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
|
||||||
|
# messages should be written. If left blank the output is written to standard
|
||||||
|
# error (stderr).
|
||||||
|
|
||||||
|
WARN_LOGFILE = "../doxygen-warn.log"
|
||||||
|
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration options related to the input files
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
|
||||||
|
# The INPUT tag is used to specify the files and/or directories that contain
|
||||||
|
# documented source files. You may enter file names like myfile.cpp or
|
||||||
|
# directories like /usr/src/myproject. Separate the files or directories with
|
||||||
|
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
|
||||||
|
# Note: If this tag is empty the current directory is searched.
|
||||||
|
|
||||||
|
INPUT = @LAMMPS_SOURCE_DIR@/utils.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/utils.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/library.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/library.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/lammps.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/lammps.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/lmptype.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/pointers.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/atom.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/atom.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/input.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/input.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/tokenizer.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/tokenizer.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/text_file_reader.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/text_file_reader.h \
|
||||||
|
@LAMMPS_SOURCE_DIR@/potential_file_reader.cpp \
|
||||||
|
@LAMMPS_SOURCE_DIR@/potential_file_reader.h \
|
||||||
|
|
||||||
|
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
|
||||||
|
# directories that are symbolic links (a Unix file system feature) are excluded
|
||||||
|
# from the input.
|
||||||
|
# The default value is: NO.
|
||||||
|
|
||||||
|
EXCLUDE_SYMLINKS = YES
|
||||||
|
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration options related to output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
|
||||||
|
GENERATE_HTML = NO
|
||||||
|
GENERATE_LATEX = NO
|
||||||
|
GENERATE_XML = YES
|
||||||
|
XML_OUTPUT = xml
|
||||||
|
XML_PROGRAMLISTING = YES
|
||||||
|
XML_NS_MEMB_FILE_SCOPE = NO
|
||||||
|
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration options related to the preprocessor
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
|
||||||
|
# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
|
||||||
|
# C-preprocessor directives found in the sources and include files.
|
||||||
|
# The default value is: YES.
|
||||||
|
|
||||||
|
#ENABLE_PREPROCESSING = YES
|
||||||
|
ENABLE_PREPROCESSING = NO
|
||||||
|
|
||||||
|
# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
|
||||||
|
# in the source code. If set to NO, only conditional compilation will be
|
||||||
|
# performed. Macro expansion can be done in a controlled way by setting
|
||||||
|
# EXPAND_ONLY_PREDEF to YES.
|
||||||
|
# The default value is: NO.
|
||||||
|
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
|
||||||
|
|
||||||
|
MACRO_EXPANSION = NO
|
||||||
|
|
||||||
|
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
|
||||||
|
# the macro expansion is limited to the macros specified with the PREDEFINED and
|
||||||
|
# EXPAND_AS_DEFINED tags.
|
||||||
|
# The default value is: NO.
|
||||||
|
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
|
||||||
|
|
||||||
|
EXPAND_ONLY_PREDEF = NO
|
||||||
|
|
||||||
|
# If the SEARCH_INCLUDES tag is set to YES, the include files in the
|
||||||
|
# INCLUDE_PATH will be searched if a #include is found.
|
||||||
|
# The default value is: YES.
|
||||||
|
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
|
||||||
|
|
||||||
|
SEARCH_INCLUDES = YES
|
||||||
|
|
||||||
|
# The INCLUDE_PATH tag can be used to specify one or more directories that
|
||||||
|
# contain include files that are not input files but should be processed by the
|
||||||
|
# preprocessor.
|
||||||
|
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
|
||||||
|
|
||||||
|
INCLUDE_PATH =
|
||||||
|
|
||||||
|
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
|
||||||
|
# patterns (like *.h and *.hpp) to filter out the header-files in the
|
||||||
|
# directories. If left blank, the patterns specified with FILE_PATTERNS will be
|
||||||
|
# used.
|
||||||
|
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
|
||||||
|
|
||||||
|
INCLUDE_FILE_PATTERNS =
|
||||||
|
|
||||||
|
# The PREDEFINED tag can be used to specify one or more macro names that are
|
||||||
|
# defined before the preprocessor is started (similar to the -D option of e.g.
|
||||||
|
# gcc). The argument of the tag is a list of macros of the form: name or
|
||||||
|
# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
|
||||||
|
# is assumed. To prevent a macro definition from being undefined via #undef or
|
||||||
|
# recursively expanded use the := operator instead of the = operator.
|
||||||
|
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
|
||||||
|
|
||||||
|
PREDEFINED =
|
||||||
|
|
||||||
|
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
|
||||||
|
# tag can be used to specify a list of macro names that should be expanded. The
|
||||||
|
# macro definition that is found in the sources will be used. Use the PREDEFINED
|
||||||
|
# tag if you want to use a different macro definition that overrules the
|
||||||
|
# definition found in the source code.
|
||||||
|
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
|
||||||
|
|
||||||
|
EXPAND_AS_DEFINED =
|
||||||
|
|
||||||
|
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
|
||||||
|
# remove all references to function-like macros that are alone on a line, have
|
||||||
|
# an all uppercase name, and do not end with a semicolon. Such function macros
|
||||||
|
# are typically used for boiler-plate code, and will confuse the parser if not
|
||||||
|
# removed.
|
||||||
|
# The default value is: YES.
|
||||||
|
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
|
||||||
|
|
||||||
|
SKIP_FUNCTION_MACROS = YES
|
||||||
|
|
||||||
BIN
doc/doxygen/lammps-logo.png
Normal file
BIN
doc/doxygen/lammps-logo.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 13 KiB |
3
doc/graphviz/.gitignore
vendored
Normal file
3
doc/graphviz/.gitignore
vendored
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
/*.png
|
||||||
|
/*.svg
|
||||||
|
/*.pdf
|
||||||
30
doc/graphviz/Makefile
Normal file
30
doc/graphviz/Makefile
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
# Makefile for generating images with graphviz
|
||||||
|
#
|
||||||
|
SHELL = /bin/bash
|
||||||
|
BUILDDIR = ${CURDIR}/..
|
||||||
|
IMGDIR = $(BUILDDIR)/src/JPG
|
||||||
|
IMGSRC = $(wildcard *.dot)
|
||||||
|
IMGPNG = $(IMGSRC:%.dot=$(IMGDIR)/%.png)
|
||||||
|
|
||||||
|
HAS_DOT = NO
|
||||||
|
ifeq ($(shell which dot >/dev/null 2>&1; echo $$?), 0)
|
||||||
|
HAS_DOT = YES
|
||||||
|
endif
|
||||||
|
|
||||||
|
all: $(IMGPNG)
|
||||||
|
|
||||||
|
clean:
|
||||||
|
rm -f $(IMGSVG) $(IMGPDF) $(IMGPNG) *~
|
||||||
|
|
||||||
|
ifeq ($(HAS_DOT),YES)
|
||||||
|
$(IMGDIR)/%.png: %.dot
|
||||||
|
dot -Tpng -o $@ $<
|
||||||
|
endif
|
||||||
|
|
||||||
|
ifeq ($(HAS_DOT),NO)
|
||||||
|
$(IMGDIR)/%.png: %.dot
|
||||||
|
@echo '###################################################'
|
||||||
|
@echo '# Need to install "graphviz" to regenerate graphs #'
|
||||||
|
@echo '###################################################'
|
||||||
|
endif
|
||||||
|
|
||||||
90
doc/graphviz/lammps-classes.dot
Normal file
90
doc/graphviz/lammps-classes.dot
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
// LAMMPS Class topology
|
||||||
|
digraph lammps {
|
||||||
|
rankdir="LR"
|
||||||
|
La [shape=circle label="LAMMPS"]
|
||||||
|
At [shape=box label="Atom" color=blue]
|
||||||
|
Ci [shape=box label="CiteMe"]
|
||||||
|
Co [shape=box label="Comm" color=blue]
|
||||||
|
Do [shape=box label="Domain" color=blue]
|
||||||
|
Er [shape=box label="Error" color=blue]
|
||||||
|
Fo [shape=box label="Force" color=blue]
|
||||||
|
Gr [shape=box label="Group" color=blue]
|
||||||
|
In [shape=box label="Input" color=blue]
|
||||||
|
Ko [shape=box label="KokkosLMP"]
|
||||||
|
Ak [shape=box label="AtomKK" color=blue]
|
||||||
|
Mk [shape=box label="MemoryKK" color=blue]
|
||||||
|
Me [shape=box label="Memory" color=blue]
|
||||||
|
Mo [shape=box label="Modify" color=blue]
|
||||||
|
Ne [shape=box label="Neighbor" color=blue]
|
||||||
|
Ou [shape=box label="Output" color=blue]
|
||||||
|
Py [shape=box label="Python" color=blue]
|
||||||
|
Up [shape=box label="Update" color=blue]
|
||||||
|
Un [shape=box label="Universe" color=blue]
|
||||||
|
Ti [shape=box label="Timer" color=blue]
|
||||||
|
Rg [label="Region" color=red]
|
||||||
|
Rb [shape=box label="RegionBlock"]
|
||||||
|
Rs [shape=box label="RegionSphere"]
|
||||||
|
Av [label="AtomVec" color=red]
|
||||||
|
It [label="Integrate" color=red]
|
||||||
|
Mi [label="Min" color=red]
|
||||||
|
Pa [label="Pair" color=red]
|
||||||
|
Bo [label="Bond" color=red]
|
||||||
|
An [label="Angle" color=red]
|
||||||
|
Di [label="Dihedral" color=red]
|
||||||
|
Im [label="Improper" color=red]
|
||||||
|
Ks [label="Kspace" color=red]
|
||||||
|
Du [label="Dump" color=red]
|
||||||
|
Fi [label="Fix" color=red]
|
||||||
|
Cp [label="Compute" color=red]
|
||||||
|
Th [label="Thermo"]
|
||||||
|
Va [label="Variable"]
|
||||||
|
Ew [shape=box label="Ewald"]
|
||||||
|
Pp [shape=box label="PPPM"]
|
||||||
|
Ff [label="FFT3d"]
|
||||||
|
Re [label="Remap"]
|
||||||
|
Gc [label="GridComm"]
|
||||||
|
Cb [shape=box label="CommBrick"]
|
||||||
|
Ct [shape=box label="CommTiled"]
|
||||||
|
Aa [shape=box label="AtomVecAtomic"]
|
||||||
|
Am [shape=box label="AtomVecMolecular"]
|
||||||
|
Lj [shape=box label="PairLJCut"]
|
||||||
|
Lo [shape=box label="PairLJCutOMP"]
|
||||||
|
Lg [shape=box label="PairLJCutGPU"]
|
||||||
|
Te [shape=box label="PairTersoff"]
|
||||||
|
Bh [shape=box label="BondHarmonic"]
|
||||||
|
Bf [shape=box label="BondFENE"]
|
||||||
|
Fa [shape=box label="FixAveTime"]
|
||||||
|
Fn [shape=box label="FixNVE"]
|
||||||
|
Fh [shape=box label="FixNH"]
|
||||||
|
Fp [shape=box label="FixNPT"]
|
||||||
|
Ft [shape=box label="FixNVT"]
|
||||||
|
Da [shape=box label="DumpAtom"]
|
||||||
|
Dc [shape=box label="DumpCustom"]
|
||||||
|
Dg [shape=box label="DumpCFG"]
|
||||||
|
Ve [shape=box label="Verlet"]
|
||||||
|
Rr [shape=box label="Respa"]
|
||||||
|
Po [shape=box label="PPPMOmp"]
|
||||||
|
La -> {At Ci Co Do Er Fo Gr In Ko Ak Mk Me Mo Ne Ou Py Ti Up Un} [penwidth=2]
|
||||||
|
Do -> {Rg} [penwidth=2]
|
||||||
|
Co -> {Cb Ct} [style=dashed penwidth=2]
|
||||||
|
Rg -> {Rb Rs} [style=dashed penwidth=2]
|
||||||
|
In -> Va [penwidth=2]
|
||||||
|
Mo -> {Fi Cp} [penwidth=2]
|
||||||
|
Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
|
||||||
|
Ks -> {Ew Pp} [style=dashed penwidth=2]
|
||||||
|
Pp -> {Ff Re Gc} [penwidth=2]
|
||||||
|
Pp -> {Po} [style=dashed penwidth=2]
|
||||||
|
Up -> {It Mi} [penwidth=2]
|
||||||
|
It -> {Ve Rr} [style=dashed penwidth=2]
|
||||||
|
Ou -> {Du Th} [penwidth=2]
|
||||||
|
Du -> {Da Dc} [style=dashed penwidth=2]
|
||||||
|
Dc -> {Dg} [style=dashed penwidth=2]
|
||||||
|
At -> Av [penwidth=2]
|
||||||
|
Av -> {Aa Am} [style=dashed penwidth=2]
|
||||||
|
Pa -> {Lj Te} [style=dashed penwidth=2]
|
||||||
|
Lj -> {Lo Lg} [style=dashed penwidth=2]
|
||||||
|
Bo -> {Bh Bf} [style=dashed penwidth=2]
|
||||||
|
Fi -> {Fa Fn Fh} [style=dashed penwidth=2]
|
||||||
|
Fh -> {Fp Ft} [style=dashed penwidth=2]
|
||||||
|
}
|
||||||
|
|
||||||
@ -3,7 +3,7 @@
|
|||||||
This purpose of this document is to provide a point of reference
|
This purpose of this document is to provide a point of reference
|
||||||
for LAMMPS developers and contributors as to what include files
|
for LAMMPS developers and contributors as to what include files
|
||||||
and definitions to put where into LAMMPS source.
|
and definitions to put where into LAMMPS source.
|
||||||
Last change 2019-07-05
|
Last change 2020-08-31
|
||||||
|
|
||||||
## Table of Contents
|
## Table of Contents
|
||||||
|
|
||||||
@ -99,10 +99,13 @@ Include files should be included in this order:
|
|||||||
|
|
||||||
#### pointers.h
|
#### pointers.h
|
||||||
|
|
||||||
The `pointer.h` header file also includes `cstdio` and `lmptype.h`
|
The `pointer.h` header file also includes `cstdio`, `cstddef`,
|
||||||
(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
|
`string`, `lmptype.h`, and `utils.h` (and through those indirectly
|
||||||
|
`stdint.h`, `intttypes.h`, cstdlib, and `climits`).
|
||||||
This means any header including `pointers.h` can assume that `FILE`,
|
This means any header including `pointers.h` can assume that `FILE`,
|
||||||
`NULL`, `INT_MAX` are defined.
|
`NULL`, `INT_MAX` are defined, they may freely use std::string
|
||||||
|
and functions from the utils namespace without including the
|
||||||
|
corresponding header files.
|
||||||
|
|
||||||
## Tools
|
## Tools
|
||||||
|
|
||||||
|
|||||||
@ -1,4 +1,4 @@
|
|||||||
.TH LAMMPS "21 August 2020" "2020-08-21"
|
.TH LAMMPS "24 August 2020" "2020-08-24"
|
||||||
.SH NAME
|
.SH NAME
|
||||||
.B LAMMPS
|
.B LAMMPS
|
||||||
\- Molecular Dynamics Simulator.
|
\- Molecular Dynamics Simulator.
|
||||||
|
|||||||
@ -1,4 +0,0 @@
|
|||||||
Sphinx
|
|
||||||
sphinxcontrib-spelling
|
|
||||||
breathe
|
|
||||||
Pygments
|
|
||||||
@ -471,7 +471,7 @@ LAMMPS source distribution.
|
|||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
make html # create HTML doc pages in html directory
|
make html # create HTML doc pages in html directory
|
||||||
make pdf # create Developer.pdf and Manual.pdf in this directory
|
make pdf # create Manual.pdf in this directory
|
||||||
make fetch # fetch HTML and PDF files from LAMMPS web site
|
make fetch # fetch HTML and PDF files from LAMMPS web site
|
||||||
make clean # remove all intermediate files
|
make clean # remove all intermediate files
|
||||||
make clean-all # reset the entire doc build environment
|
make clean-all # reset the entire doc build environment
|
||||||
|
|||||||
@ -378,22 +378,22 @@ The images below illustrate how the data is presented.
|
|||||||
.. list-table::
|
.. list-table::
|
||||||
|
|
||||||
* - .. figure:: JPG/coverage-overview-top.png
|
* - .. figure:: JPG/coverage-overview-top.png
|
||||||
:target: JPG/coverage-overview-top.png
|
:scale: 25%
|
||||||
|
|
||||||
Top of the overview page
|
Top of the overview page
|
||||||
|
|
||||||
- .. figure:: JPG/coverage-overview-manybody.png
|
- .. figure:: JPG/coverage-overview-manybody.png
|
||||||
:target: JPG/coverage-overview-manybody.png
|
:scale: 25%
|
||||||
|
|
||||||
Styles with good coverage
|
Styles with good coverage
|
||||||
|
|
||||||
- .. figure:: JPG/coverage-file-top.png
|
- .. figure:: JPG/coverage-file-top.png
|
||||||
:target: JPG/coverage-file-top.png
|
:scale: 25%
|
||||||
|
|
||||||
Top of individual source page
|
Top of individual source page
|
||||||
|
|
||||||
- .. figure:: JPG/coverage-file-branches.png
|
- .. figure:: JPG/coverage-file-branches.png
|
||||||
:target: JPG/coverage-file-branches.png
|
:scale: 25%
|
||||||
|
|
||||||
Source page with branches
|
Source page with branches
|
||||||
|
|
||||||
|
|||||||
@ -361,9 +361,12 @@ be specified in uppercase.
|
|||||||
* - AMDAVX
|
* - AMDAVX
|
||||||
- HOST
|
- HOST
|
||||||
- AMD 64-bit x86 CPU (AVX 1)
|
- AMD 64-bit x86 CPU (AVX 1)
|
||||||
* - EPYC
|
* - ZEN
|
||||||
- HOST
|
- HOST
|
||||||
- AMD EPYC Zen class CPU (AVX 2)
|
- AMD Zen class CPU (AVX 2)
|
||||||
|
* - ZEN2
|
||||||
|
- HOST
|
||||||
|
- AMD Zen2 class CPU (AVX 2)
|
||||||
* - ARMV80
|
* - ARMV80
|
||||||
- HOST
|
- HOST
|
||||||
- ARMv8.0 Compatible CPU
|
- ARMv8.0 Compatible CPU
|
||||||
@ -445,12 +448,18 @@ be specified in uppercase.
|
|||||||
* - TURING75
|
* - TURING75
|
||||||
- GPU
|
- GPU
|
||||||
- NVIDIA Turing generation CC 7.5 GPU
|
- NVIDIA Turing generation CC 7.5 GPU
|
||||||
|
* - AMPERE80
|
||||||
|
- GPU
|
||||||
|
- NVIDIA Ampere generation CC 8.0 GPU
|
||||||
* - VEGA900
|
* - VEGA900
|
||||||
- GPU
|
- GPU
|
||||||
- AMD GPU MI25 GFX900
|
- AMD GPU MI25 GFX900
|
||||||
* - VEGA906
|
* - VEGA906
|
||||||
- GPU
|
- GPU
|
||||||
- AMD GPU MI50/MI60 GFX906
|
- AMD GPU MI50/MI60 GFX906
|
||||||
|
* - INTEL_GEN
|
||||||
|
- GPU
|
||||||
|
- Intel GPUs Gen9+
|
||||||
|
|
||||||
Basic CMake build settings:
|
Basic CMake build settings:
|
||||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|||||||
3
doc/src/Developer/.gitignore
vendored
3
doc/src/Developer/.gitignore
vendored
@ -1,3 +0,0 @@
|
|||||||
/developer.aux
|
|
||||||
/developer.log
|
|
||||||
/developer.toc
|
|
||||||
@ -1,198 +0,0 @@
|
|||||||
#FIG 3.2 Produced by xfig version 3.2.5a
|
|
||||||
Portrait
|
|
||||||
Center
|
|
||||||
Inches
|
|
||||||
Letter
|
|
||||||
100.00
|
|
||||||
Single
|
|
||||||
-2
|
|
||||||
1200 2
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2232 1170 3540 1170 3540 1505 2232 1505 2232 1170
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2220 1830 3015 1830 3015 2219 2220 2219 2220 1830
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2226 3285 3300 3285 3300 3665 2226 3665 2226 3285
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2223 5190 3225 5190 3225 5525 2223 5525 2223 5190
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2232 7125 3090 7125 3090 7478 2232 7478 2232 7125
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2226 10230 3300 10230 3300 10565 2226 10565 2226 10230
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4026 10305 4980 10305 4980 10592 4026 10592 4026 10305
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4029 9900 5205 9900 5205 10250 4029 10250 4029 9900
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4038 9315 5370 9315 5370 9659 4038 9659 4038 9315
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4023 8955 4530 8955 4530 9278 4023 9278 4023 8955
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4029 8475 5190 8475 5190 8762 4029 8762 4029 8475
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4008 8115 5430 8115 5430 8408 4008 8408 4008 8115
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4026 7425 4995 7425 4995 7712 4026 7712 4026 7425
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4035 6720 4650 6720 4650 7025 4035 7025 4035 6720
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4044 7080 4830 7080 4830 7358 4044 7358 4044 7080
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4032 6105 5205 6105 5205 6419 4032 6419 4032 6105
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4026 5715 5115 5715 5115 6062 4026 6062 4026 5715
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4023 3585 4605 3585 4605 3872 4023 3872 4023 3585
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
3954 1680 5175 1680 5175 1997 3954 1997 3954 1680
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
1620 5235 2100 615
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
1605 5445 2070 10695
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3120 1935 3855 1800
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3150 2115 3765 2250
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3135 7230 3945 6840
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3150 7335 3945 8610
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
5265 8610 6195 8400
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
5280 8655 6180 8820
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3345 10290 3930 10020
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3360 10395 3930 10425
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3360 10455 3930 10755
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2193 360 3435 360 3435 647 2193 647 2193 360
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3398 3472 3923 3307
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3413 3601 3923 3721
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3285 2806 3870 2802
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3315 5372 3900 5368
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
6354 2280 7470 2280 7470 2585 6354 2585 6354 2280
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
6348 1875 7320 1875 7320 2222 6348 2222 6348 1875
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
3954 2070 5505 2070 5505 2372 3954 2372 3954 2070
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
5634 2137 6230 2045
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
5670 2310 6265 2418
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
3900 2640 5400 2640 5400 2975 3900 2975 3900 2640
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4038 3165 5385 3165 5385 3497 4038 3497 4038 3165
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4245 4110 5730 4110 5730 4499 4245 4499 4245 4110
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4233 4545 6390 4545 6390 4862 4233 4862 4233 4545
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4026 5190 5385 5190 5385 5525 4026 5525 4026 5190
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4038 7755 5310 7755 5310 8075 4038 8075 4038 7755
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
6270 8250 7365 8250 7365 8610 6270 8610 6270 8250
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
6273 8655 7380 8655 7380 8978 6273 8978 6273 8655
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
4041 10620 5985 10620 5985 10943 4041 10943 4041 10620
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2217 10830 3135 10830 3135 11156 2217 11156 2217 10830
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2229 9780 3240 9780 3240 10118 2229 10118 2229 9780
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2214 9015 3285 9015 3285 9362 2214 9362 2214 9015
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2208 5850 3420 5850 3420 6209 2208 6209 2208 5850
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2217 4275 3615 4275 3615 4634 2217 4634 2217 4275
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2235 2655 3150 2655 3150 3000 2235 3000 2235 2655
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
60 5115 1500 5115 1500 5610 60 5610 60 5115
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3486 6018 4011 5853
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3486 6129 3996 6249
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3361 9291 3991 9531
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3345 9129 4005 9099
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3691 4412 4216 4277
|
|
||||||
2 1 0 2 0 7 50 -1 -1 0.000 0 0 -1 1 0 2
|
|
||||||
1 1 2.00 120.00 240.00
|
|
||||||
3695 4561 4175 4711
|
|
||||||
2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5
|
|
||||||
2220 735 3129 735 3129 1043 2220 1043 2220 735
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 225 1275 2265 1455 Universe\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 285 735 2265 2175 Input\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 225 780 2265 2925 Atom\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 285 1020 2265 3600 Update\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 285 1320 2265 4575 Neighbor\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 225 945 2265 5475 Comm\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 225 1110 2265 6150 Domain\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 225 810 2265 7425 Force\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 285 975 2265 9300 Modify\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 285 900 2265 10050 Group\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 285 990 2265 10500 Output\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 225 825 2265 11100 Timer\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 225 1170 3990 1950 Variable\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 225 1470 3990 2325 Command\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 285 1275 4065 3450 Integrate\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 225 525 4065 3825 Min\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 285 1230 4065 5475 Irregular\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 285 1020 4065 6000 Region\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 225 975 4065 6375 Lattice\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 225 435 4065 9225 Fix\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 285 1305 4065 9600 Compute\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 225 570 4065 6975 Pair\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 285 840 4065 7665 Angle\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 225 1215 4065 8010 Dihedral\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 285 1305 4065 8355 Improper\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 285 1095 4065 8700 KSpace\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 285 855 4065 10545 Dump\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 225 1815 4065 10890 WriteRestart\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 225 930 6315 8550 FFT3D\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 285 1005 6315 8925 Remap\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 225 885 6390 2175 Finish\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 285 1050 6390 2550 Special\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 225 1305 3990 2925 AtomVec\001
|
|
||||||
4 0 4 50 -1 18 18 0.0000 4 225 765 4065 7320 Bond\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 225 1095 4065 10200 Thermo\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 285 1380 4305 4425 NeighList\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 285 2025 4305 4800 NeighRequest\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 285 1155 2250 600 Memory\001
|
|
||||||
4 0 0 50 -1 18 18 0.0000 4 225 1305 120 5475 LAMMPS\001
|
|
||||||
4 0 1 50 -1 18 18 0.0000 4 225 735 2265 1005 Error\001
|
|
||||||
Binary file not shown.
@ -1,699 +0,0 @@
|
|||||||
\documentclass{article}
|
|
||||||
\usepackage{graphicx}
|
|
||||||
|
|
||||||
\begin{document}
|
|
||||||
|
|
||||||
\centerline{\Large \bf LAMMPS Developer Guide}
|
|
||||||
\centerline{\bf 23 Aug 2011}
|
|
||||||
|
|
||||||
\vspace{0.5in}
|
|
||||||
|
|
||||||
This document is a developer guide to the LAMMPS molecular dynamics
|
|
||||||
package, whose WWW site is at lammps.sandia.gov. It describes the
|
|
||||||
internal structure and algorithms of the code. Sections will be added
|
|
||||||
as we have time, and in response to requests from developers and
|
|
||||||
users.
|
|
||||||
|
|
||||||
\tableofcontents
|
|
||||||
|
|
||||||
\pagebreak
|
|
||||||
\section{LAMMPS source files}
|
|
||||||
|
|
||||||
LAMMPS source files are in two directories of the distribution
|
|
||||||
tarball. The src directory has the majority of them, all of which are
|
|
||||||
C++ files (*.cpp and *.h). Many of these files are in the src
|
|
||||||
directory itself. There are also dozens of ``packages'', which can be
|
|
||||||
included or excluded when LAMMPS is built. See the
|
|
||||||
doc/Section\_build.html section of the manual for more information
|
|
||||||
about packages, or type ``make'' from within the src directory, which
|
|
||||||
lists package-related commands, such as ``make package-status''. The
|
|
||||||
source files for each package are in an all-uppercase sub-directory of
|
|
||||||
src, like src/MOLECULE or src/USER-CUDA. If the package is currently
|
|
||||||
installed, copies of the package source files will also exist in the
|
|
||||||
src directory itself. The src/STUBS sub-directory is not a package
|
|
||||||
but contains a dummy version of the MPI library, used when building a
|
|
||||||
serial version of the code.
|
|
||||||
|
|
||||||
The lib directory also contains source code for external libraries,
|
|
||||||
used by a few of the packages. Each sub-directory, like meam or gpu,
|
|
||||||
contains the source files, some of which are in different languages
|
|
||||||
such as Fortran. The files are compiled into libraries from within
|
|
||||||
each sub-directory, e.g. performing a ``make'' in the lib/meam directory
|
|
||||||
creates a libmeam.a file. These libraries are linked to during a
|
|
||||||
LAMMPS build, if the corresponding package is installed.
|
|
||||||
|
|
||||||
LAMMPS C++ source files almost always come in pairs, such as run.cpp
|
|
||||||
and run.h. The pair of files defines a C++ class, the Run class in
|
|
||||||
this case, which contains the code invoked by the ``run'' command in a
|
|
||||||
LAMMPS input script. As this example illustrates, source file and
|
|
||||||
class names often have a one-to-one correspondence with a command used
|
|
||||||
in a LAMMPS input script. Some source files and classes do not have a
|
|
||||||
corresponding input script command, e.g. ``force.cpp'' and the Force
|
|
||||||
class. They are discussed in the next section.
|
|
||||||
|
|
||||||
\pagebreak
|
|
||||||
\section{Class hierarchy of LAMMPS}
|
|
||||||
|
|
||||||
Though LAMMPS has a lot of source files and classes, its class
|
|
||||||
hierarchy is quite simple, as outlined in Fig \ref{fig:classes}. Each
|
|
||||||
boxed name refers to a class and has a pair of associated source files
|
|
||||||
in lammps/src, e.g. ``memory.cpp'' and ``memory.h''. More details on the
|
|
||||||
class and its methods and data structures can be found by examining
|
|
||||||
its *.h file.
|
|
||||||
|
|
||||||
LAMMPS (lammps.cpp/h) is the top-level class for the entire code. It
|
|
||||||
holds an ``instance'' of LAMMPS and can be instantiated one or more
|
|
||||||
times by a calling code. For example, the file src/main.cpp simply
|
|
||||||
instantiates one instance of LAMMPS and passes it the input script.
|
|
||||||
|
|
||||||
The file src/library.cpp contains a C-style library interface to the
|
|
||||||
LAMMPS class. See the lammps/couple and lammps/python directories for
|
|
||||||
examples of simple programs that use LAMMPS through its library
|
|
||||||
interface. A driver program can instantiate the LAMMPS class multiple
|
|
||||||
times, e.g. to embed several atomistic simulation regions within a
|
|
||||||
mesoscale or continuum simulation domain.
|
|
||||||
|
|
||||||
There are a dozen or so top-level classes within the LAMMPS class that
|
|
||||||
are visible everywhere in the code. They are shaded blue in Fig
|
|
||||||
\ref{fig:classes}. Thus any class can refer to the y-coordinate of
|
|
||||||
local atom $I$ as atom$\rightarrow$x[i][1]. This visibility is
|
|
||||||
enabled by a bit of cleverness in the Pointers class (see
|
|
||||||
src/pointers.h) which every class inherits from.
|
|
||||||
|
|
||||||
There are a handful of virtual parent classes in LAMMPS that define
|
|
||||||
what LAMMPS calls ``styles''. They are shaded red in Fig
|
|
||||||
\ref{fig:classes}. Each of these are parents of a number of child
|
|
||||||
classes that implement the interface defined by the parent class. For
|
|
||||||
example, the fix style has around 100 child classes. They are the
|
|
||||||
possible fixes that can be specified by the fix command in an input
|
|
||||||
script, e.g. fix nve, fix shake, fix ave/time, etc. The corresponding
|
|
||||||
classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
|
|
||||||
etc. The source files for these classes are easy to identify in the
|
|
||||||
src directory, since they begin with the word ``fix'', e,g,
|
|
||||||
fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
|
|
||||||
|
|
||||||
The one exception is child class files for the ``command'' style. These
|
|
||||||
implement specific commands in the input script that can be invoked
|
|
||||||
before/after/between runs or which launch a simulation. Examples are
|
|
||||||
the create\_box, minimize, run, and velocity commands which encode the
|
|
||||||
CreateBox, Minimize, Run, and Velocity classes. The corresponding
|
|
||||||
files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
|
|
||||||
The list of command style files can be found by typing ``grep
|
|
||||||
COMMAND\_CLASS *.h'' from within the src directory, since that word in
|
|
||||||
the header file identifies the class as an input script command.
|
|
||||||
Similar words can be grepped to list files for the other LAMMPS
|
|
||||||
styles. E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
|
|
||||||
FIX\_CLASS, COMPUTE\_CLASS, DUMP\_CLASS, etc.
|
|
||||||
|
|
||||||
\begin{figure}[htb]
|
|
||||||
\begin{center}
|
|
||||||
\includegraphics[height=4in]{classes.pdf}
|
|
||||||
\end{center}
|
|
||||||
\caption{Class hierarchy within LAMMPS source code.}
|
|
||||||
\label{fig:classes}
|
|
||||||
\end{figure}
|
|
||||||
|
|
||||||
More details on individual classes in Fig \ref{fig:classes} are as
|
|
||||||
follows:
|
|
||||||
|
|
||||||
\begin{itemize}
|
|
||||||
|
|
||||||
\item The Memory class handles allocation of all large vectors and
|
|
||||||
arrays.
|
|
||||||
|
|
||||||
\item The Error class prints all error and warning messages.
|
|
||||||
|
|
||||||
\item The Universe class sets up partitions of processors so that
|
|
||||||
multiple simulations can be run, each on a subset of the processors
|
|
||||||
allocated for a run, e.g. by the mpirun command.
|
|
||||||
|
|
||||||
\item The Input class reads an input script, stores variables, and
|
|
||||||
invokes stand-alone commands that are child classes of the Command
|
|
||||||
class.
|
|
||||||
|
|
||||||
\item As discussed above, the Command class is a parent class for
|
|
||||||
certain input script commands that perform a one-time operation
|
|
||||||
before/after/between simulations or which invoke a simulation. They
|
|
||||||
are instantiated from within the Input class, invoked, then
|
|
||||||
immediately destructed.
|
|
||||||
|
|
||||||
\item The Finish class is instantiated to print statistics to the
|
|
||||||
screen after a simulation is performed, by commands like run and
|
|
||||||
minimize.
|
|
||||||
|
|
||||||
\item The Special class walks the bond topology of a molecular system
|
|
||||||
to find first, second, third neighbors of each atom. It is invoked by
|
|
||||||
several commands, like read\_data, read\_restart, and replicate.
|
|
||||||
|
|
||||||
\item The Atom class stores all per-atom arrays. More precisely, they
|
|
||||||
are allocated and stored by the AtomVec class, and the Atom class
|
|
||||||
simply stores a pointer to them. The AtomVec class is a parent
|
|
||||||
class for atom styles, defined by the atom\_style command.
|
|
||||||
|
|
||||||
\item The Update class holds an integrator and a minimizer. The
|
|
||||||
Integrate class is a parent style for the Verlet and rRESPA time
|
|
||||||
integrators, as defined by the run\_style input command. The Min
|
|
||||||
class is a parent style for various energy minimizers.
|
|
||||||
|
|
||||||
\item The Neighbor class builds and stores neighbor lists. The
|
|
||||||
NeighList class stores a single list (for all atoms). The
|
|
||||||
NeighRequest class is called by pair, fix, or compute styles when
|
|
||||||
they need a particular kind of neighbor list.
|
|
||||||
|
|
||||||
\item The Comm class performs interprocessor communication, typically
|
|
||||||
of ghost atom information. This usually involves MPI message
|
|
||||||
exchanges with 6 neighboring processors in the 3d logical grid of
|
|
||||||
processors mapped to the simulation box. Sometimes the Irregular
|
|
||||||
class is used, when atoms may migrate to arbitrary processors.
|
|
||||||
|
|
||||||
\item The Domain class stores the simulation box geometry, as well as
|
|
||||||
geometric Regions and any user definition of a Lattice. The latter
|
|
||||||
are defined by region and lattice commands in an input script.
|
|
||||||
|
|
||||||
\item The Force class computes various forces between atoms. The Pair
|
|
||||||
parent class is for non-bonded or pair-wise forces, which in LAMMPS
|
|
||||||
lingo includes many-body forces such as the Tersoff 3-body
|
|
||||||
potential. The Bond, Angle, Dihedral, Improper parent classes are
|
|
||||||
styles for bonded interactions within a static molecular topology.
|
|
||||||
The KSpace parent class is for computing long-range Coulombic
|
|
||||||
interactions. One of its child classes, PPPM, uses the FFT3D and
|
|
||||||
Remap classes to communicate grid-based information with neighboring
|
|
||||||
processors.
|
|
||||||
|
|
||||||
\item The Modify class stores lists of Fix and Compute classes, both
|
|
||||||
of which are parent styles.
|
|
||||||
|
|
||||||
\item The Group class manipulates groups that atoms are assigned to
|
|
||||||
via the group command. It also computes various attributes of
|
|
||||||
groups of atoms.
|
|
||||||
|
|
||||||
\item The Output class is used to generate 3 kinds of output from a
|
|
||||||
LAMMPS simulation: thermodynamic information printed to the screen
|
|
||||||
and log file, dump file snapshots, and restart files. These
|
|
||||||
correspond to the Thermo, Dump, and WriteRestart classes
|
|
||||||
respectively. The Dump class is a parent style.
|
|
||||||
|
|
||||||
\item The Timer class logs MPI timing information, output at the end
|
|
||||||
of a run.
|
|
||||||
|
|
||||||
\end{itemize}
|
|
||||||
|
|
||||||
%%\pagebreak
|
|
||||||
%%\section{Spatial decomposition and parallel operations}
|
|
||||||
%%distributed memory
|
|
||||||
%%Ref to JCP paper
|
|
||||||
%%diagram of 3d grid of procs and spatial decomp
|
|
||||||
%%6-way comm
|
|
||||||
%%ghost atoms, PBC added when comm (in atom class)
|
|
||||||
|
|
||||||
%%\pagebreak
|
|
||||||
%%\section{Fixes, computes, variables}
|
|
||||||
%%fixes intercolate in timestep, store per-atom info
|
|
||||||
%%computes based on current snapshot
|
|
||||||
%%equal- and atom-style variables
|
|
||||||
%%output they produce - see write-up in HowTo
|
|
||||||
|
|
||||||
\pagebreak
|
|
||||||
\section{How a timestep works}
|
|
||||||
|
|
||||||
The first and most fundamental operation within LAMMPS to understand
|
|
||||||
is how a timestep is structured. Timestepping is performed by the
|
|
||||||
Integrate class within the Update class. Since Integrate is a parent
|
|
||||||
class, corresponding to the run\_style input script command, it has
|
|
||||||
child classes. In this section, the timestep implemented by the
|
|
||||||
Verlet child class is described. A similar timestep is implemented by
|
|
||||||
the Respa child class, for the rRESPA hierarchical timestepping
|
|
||||||
method. The Min parent class performs energy minimization, so does
|
|
||||||
not perform a literal timestep. But it has logic similar to what is
|
|
||||||
described here, to compute forces and invoke fixes at each iteration
|
|
||||||
of a minimization. Differences between time integration and
|
|
||||||
minimization are highlighted at the end of this section.
|
|
||||||
|
|
||||||
The Verlet class is encoded in the src/verlet.cpp and verlet.h files.
|
|
||||||
It implements the velocity-Verlet timestepping algorithm. The
|
|
||||||
workhorse method is Verlet::run(), but first we highlight several
|
|
||||||
other methods in the class.
|
|
||||||
|
|
||||||
\begin{itemize}
|
|
||||||
|
|
||||||
\item The init() method is called at the beginning of each dynamics
|
|
||||||
run. It simply sets some internal flags, based on user settings in
|
|
||||||
other parts of the code.
|
|
||||||
|
|
||||||
\item The setup() or setup\_minimal() methods are also called before
|
|
||||||
each run. The velocity-Verlet method requires current forces be
|
|
||||||
calculated before the first timestep, so these routines compute
|
|
||||||
forces due to all atomic interactions, using the same logic that
|
|
||||||
appears in the timestepping described next. A few fixes are also
|
|
||||||
invoked, using the mechanism described in the next section. Various
|
|
||||||
counters are also initialized before the run begins. The
|
|
||||||
setup\_minimal() method is a variant that has a flag for performing
|
|
||||||
less setup. This is used when runs are continued and information
|
|
||||||
from the previous run is still valid. For example, if repeated
|
|
||||||
short LAMMPS runs are being invoked, interleaved by other commands,
|
|
||||||
via the ``pre no'' and ``every'' options of the run command, the
|
|
||||||
setup\_minimal() method is used.
|
|
||||||
|
|
||||||
\item The force\_clear() method initializes force and other arrays to
|
|
||||||
zero before each timestep, so that forces (torques, etc) can be
|
|
||||||
accumulated.
|
|
||||||
|
|
||||||
\end{itemize}
|
|
||||||
|
|
||||||
Now for the Verlet::run() method. Its structure in hi-level pseudo
|
|
||||||
code is shown in Fig \ref{fig:verlet}. In the actual code in
|
|
||||||
src/verlet.cpp some of these operations are conditionally invoked.
|
|
||||||
|
|
||||||
\begin{figure}[htb]
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
loop over N timesteps:
|
|
||||||
ev_set()
|
|
||||||
|
|
||||||
fix->initial_integrate()
|
|
||||||
fix->post_integrate()
|
|
||||||
|
|
||||||
nflag = neighbor->decide()
|
|
||||||
if nflag:
|
|
||||||
fix->pre_exchange()
|
|
||||||
domain->pbc()
|
|
||||||
domain->reset_box()
|
|
||||||
comm->setup()
|
|
||||||
neighbor->setup_bins()
|
|
||||||
comm->exchange()
|
|
||||||
comm->borders()
|
|
||||||
fix->pre_neighbor()
|
|
||||||
neighbor->build()
|
|
||||||
else
|
|
||||||
comm->forward_comm()
|
|
||||||
|
|
||||||
force_clear()
|
|
||||||
fix->pre_force()
|
|
||||||
|
|
||||||
pair->compute()
|
|
||||||
bond->compute()
|
|
||||||
angle->compute()
|
|
||||||
dihedral->compute()
|
|
||||||
improper->compute()
|
|
||||||
kspace->compute()
|
|
||||||
|
|
||||||
comm->reverse_comm()
|
|
||||||
|
|
||||||
fix->post_force()
|
|
||||||
fix->final_integrate()
|
|
||||||
fix->end_of_step()
|
|
||||||
|
|
||||||
if any output on this step: output->write()
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
\caption{Pseudo-code for the Verlet::run() method.}
|
|
||||||
\label{fig:verlet}
|
|
||||||
\end{figure}
|
|
||||||
|
|
||||||
The ev\_set() method (in the parent Integrate class), sets two flags
|
|
||||||
({\em eflag} and {\em vflag}) for energy and virial computation. Each
|
|
||||||
flag encodes whether global and/or per-atom energy and virial should
|
|
||||||
be calculated on this timestep, because some fix or variable or output
|
|
||||||
will need it. These flags are passed to the various methods that
|
|
||||||
compute particle interactions, so that they can skip the extra
|
|
||||||
calculations if the energy and virial are not needed. See the
|
|
||||||
comments with the Integrate::ev\_set() method which document the flag
|
|
||||||
values.
|
|
||||||
|
|
||||||
At various points of the timestep, fixes are invoked,
|
|
||||||
e.g. fix$\rightarrow$initial\_integrate(). In the code, this is
|
|
||||||
actually done via the Modify class which stores all the Fix objects
|
|
||||||
and lists of which should be invoked at what point in the timestep.
|
|
||||||
Fixes are the LAMMPS mechanism for tailoring the operations of a
|
|
||||||
timestep for a particular simulation. As described elsewhere
|
|
||||||
(unwritten section), each fix has one or more methods, each of which
|
|
||||||
is invoked at a specific stage of the timestep, as in Fig
|
|
||||||
\ref{fig:verlet}. All the fixes defined in an input script with an
|
|
||||||
initial\_integrate() method are invoked at the beginning of each
|
|
||||||
timestep. Fix nve, nvt, npt are examples, since they perform the
|
|
||||||
start-of-timestep velocity-Verlet integration to update velocities by
|
|
||||||
a half-step, and coordinates by a full step. The post\_integrate()
|
|
||||||
method is next. Only a few fixes use this, e.g. to reflect particles
|
|
||||||
off box boundaries in the FixWallReflect class.
|
|
||||||
|
|
||||||
The decide() method in the Neighbor class determines whether neighbor
|
|
||||||
lists need to be rebuilt on the current timestep. If not, coordinates
|
|
||||||
of ghost atoms are acquired by each processor via the forward\_comm()
|
|
||||||
method of the Comm class. If neighbor lists need to be built, several
|
|
||||||
operations within the inner if clause of Fig \ref{fig:verlet} are
|
|
||||||
first invoked. The pre\_exchange() method of any defined fixes is
|
|
||||||
invoked first. Typically this inserts or deletes particles from the
|
|
||||||
system.
|
|
||||||
|
|
||||||
Periodic boundary conditions are then applied by the Domain class via
|
|
||||||
its pbc() method to remap particles that have moved outside the
|
|
||||||
simulation box back into the box. Note that this is not done every
|
|
||||||
timestep. but only when neighbor lists are rebuilt. This is so that
|
|
||||||
each processor's sub-domain will have consistent (nearby) atom
|
|
||||||
coordinates for its owned and ghost atoms. It is also why dumped atom
|
|
||||||
coordinates can be slightly outside the simulation box.
|
|
||||||
|
|
||||||
The box boundaries are then reset (if needed) via the reset\_box()
|
|
||||||
method of the Domain class, e.g. if box boundaries are shrink-wrapped
|
|
||||||
to current particle coordinates. A change in the box size or shape
|
|
||||||
requires internal information for communicating ghost atoms (Comm
|
|
||||||
class) and neighbor list bins (Neighbor class) be updated. The
|
|
||||||
setup() method of the Comm class and setup\_bins() method of the
|
|
||||||
Neighbor class perform the update.
|
|
||||||
|
|
||||||
The code is now ready to migrate atoms that have left a processor's
|
|
||||||
geometric sub-domain to new processors. The exchange() method of the
|
|
||||||
Comm class performs this operation. The borders() method of the Comm
|
|
||||||
class then identifies ghost atoms surrounding each processor's
|
|
||||||
sub-domain and communicates ghost atom information to neighboring
|
|
||||||
processors. It does this by looping over all the atoms owned by a
|
|
||||||
processor to make lists of those to send to each neighbor processor.
|
|
||||||
On subsequent timesteps, the lists are used by the
|
|
||||||
Comm::forward\_comm() method.
|
|
||||||
|
|
||||||
Fixes with a pre\_neighbor() method are then called. These typically
|
|
||||||
re-build some data structure stored by the fix that depends on the
|
|
||||||
current atoms owned by each processor.
|
|
||||||
|
|
||||||
Now that each processor has a current list of its owned and ghost
|
|
||||||
atoms, LAMMPS is ready to rebuild neighbor lists via the build()
|
|
||||||
method of the Neighbor class. This is typically done by binning all
|
|
||||||
owned and ghost atoms, and scanning a stencil of bins around each
|
|
||||||
owned atom's bin to make a Verlet list of neighboring atoms within the
|
|
||||||
force cutoff plus neighbor skin distance.
|
|
||||||
|
|
||||||
In the next portion of the timestep, all interaction forces between
|
|
||||||
particles are computed, after zeroing the per-atom force vector via
|
|
||||||
the force\_clear() method. If the newton flag is set to ``on'' by the
|
|
||||||
newton command, forces on both owned and ghost atoms are calculated.
|
|
||||||
|
|
||||||
Pairwise forces are calculated first, which enables the global virial
|
|
||||||
(if requested) to be calculated cheaply (at the end of the
|
|
||||||
Pair::compute() method), by a dot product of atom coordinates and
|
|
||||||
forces. By including owned and ghost atoms in the dot product, the
|
|
||||||
effect of periodic boundary conditions is correctly accounted for.
|
|
||||||
Molecular topology interactions (bonds, angles, dihedrals, impropers)
|
|
||||||
are calculated next. The final contribution is from long-range
|
|
||||||
Coulombic interactions, invoked by the KSpace class.
|
|
||||||
|
|
||||||
If the newton flag is on, forces on ghost atoms are communicated and
|
|
||||||
summed back to their corresponding owned atoms. The reverse\_comm()
|
|
||||||
method of the Comm class performs this operation, which is essentially
|
|
||||||
the inverse operation of sending copies of owned atom coordinates to
|
|
||||||
other processor's ghost atoms.
|
|
||||||
|
|
||||||
At this point in the timestep, the total force on each atom is known.
|
|
||||||
Additional force constraints (external forces, SHAKE, etc) are applied
|
|
||||||
by Fixes that have a post\_force() method. The second half of the
|
|
||||||
velocity-Verlet integration is then performed (another half-step
|
|
||||||
update of the velocities) via fixes like nve, nvt, npt.
|
|
||||||
|
|
||||||
At the end of the timestep, fixes that define an end\_of\_step()
|
|
||||||
method are invoked. These typically perform a diagnostic calculation,
|
|
||||||
e.g. the ave/time and ave/spatial fixes. The final operation of the
|
|
||||||
timestep is to perform any requested output, via the write() method of
|
|
||||||
the Output class. There are 3 kinds of LAMMPS output: thermodynamic
|
|
||||||
output to the screen and log file, snapshots of atom data to a dump
|
|
||||||
file, and restart files. See the thermo\_style, dump, and restart
|
|
||||||
commands for more details.
|
|
||||||
|
|
||||||
The iteration performed by an energy minimization is similar to the
|
|
||||||
dynamics timestep of Fig \ref{fig:verlet}. Forces are computed,
|
|
||||||
neighbor lists are built as needed, atoms migrate to new processors,
|
|
||||||
and atom coordinates and forces are communicated to neighboring
|
|
||||||
processors. The only difference is what Fix class operations are
|
|
||||||
invoked when. Only a subset of LAMMPS fixes are useful during energy
|
|
||||||
minimization, as explained in their individual doc pages. The
|
|
||||||
relevant Fix class methods are min\_pre\_exchange(),
|
|
||||||
min\_pre\_force(), and min\_post\_force(). Each is invoked at the
|
|
||||||
appropriate place within the minimization iteration. For example, the
|
|
||||||
min\_post\_force() method is analogous to the post\_force() method for
|
|
||||||
dynamics; it is used to alter or constrain forces on each atom, which
|
|
||||||
affects the minimization procedure.
|
|
||||||
|
|
||||||
\pagebreak
|
|
||||||
\section{Extending LAMMPS}
|
|
||||||
|
|
||||||
The Section\_modify.html file in the doc directory of
|
|
||||||
the LAMMPS distribution gives an overview of how LAMMPS can
|
|
||||||
be extended by writing new classes that derive from existing
|
|
||||||
parent classes in LAMMPS. Here, some specific coding
|
|
||||||
details are provided for writing a new fix.
|
|
||||||
|
|
||||||
\subsection{New fixes}
|
|
||||||
|
|
||||||
(this section provided by Kirill Lykov)
|
|
||||||
\vspace{0.25cm}
|
|
||||||
|
|
||||||
Writing fixes is a flexible way of extending LAMMPS. Users can
|
|
||||||
implement many things using fixes:
|
|
||||||
|
|
||||||
\begin{itemize}
|
|
||||||
\item changing particles attributes (positions, velocities, forces, etc.).
|
|
||||||
Example: FixFreeze.
|
|
||||||
\item reading/writing data. Example: FixRestart.
|
|
||||||
\item implementing boundary conditions. Example: FixWall.
|
|
||||||
\item saving information about particles for future use (previous positions,
|
|
||||||
for instance). Example: FixStoreState.
|
|
||||||
\end{itemize}
|
|
||||||
|
|
||||||
All fixes are derived from class Fix and must have constructor with the
|
|
||||||
signature: FixMine(class LAMMPS *, int, char **).
|
|
||||||
|
|
||||||
Every fix must be registered in LAMMPS by writing the following lines
|
|
||||||
of code in the header before include guards:
|
|
||||||
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
#ifdef FIX_CLASS
|
|
||||||
FixStyle(your/fix/name,FixMine)
|
|
||||||
#else
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
|
|
||||||
Where ``your/fix/name'' is a name of your fix in the script and FixMine
|
|
||||||
is the name of the class. This code allows LAMMPS to find your fix
|
|
||||||
when it parses input script. In addition, your fix header must be
|
|
||||||
included in the file ``style\_fix.h''. In case if you use LAMMPS make,
|
|
||||||
this file is generated automatically - all files starting with prefix
|
|
||||||
fix\_ are included, so call your header the same way. Otherwise, don't
|
|
||||||
forget to add your include into ``style\_fix.h''.
|
|
||||||
|
|
||||||
Let's write a simple fix which will print average velocity at the end
|
|
||||||
of each timestep. First of all, implement a constructor:
|
|
||||||
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
|
|
||||||
: Fix(lmp, narg, arg)
|
|
||||||
{
|
|
||||||
if (narg < 4)
|
|
||||||
error->all(FLERR,"Illegal fix print command");
|
|
||||||
|
|
||||||
nevery = atoi(arg[3]);
|
|
||||||
if (nevery <= 0)
|
|
||||||
error->all(FLERR,"Illegal fix print command");
|
|
||||||
}
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
|
|
||||||
In the constructor you should parse your fix arguments which are
|
|
||||||
specified in the script. All fixes have pretty the same syntax: fix
|
|
||||||
[fix\_identifier] [group\_name] [fix\_name] [fix\_arguments]. The
|
|
||||||
first 3 parameters are parsed by Fix class constructor, while
|
|
||||||
[fix\_arguments] should be parsed by you. In our case, we need to
|
|
||||||
specify how often we want to print an average velocity. For instance,
|
|
||||||
once in 50 timesteps: fix 1 print/vel 50. There is a special variable
|
|
||||||
in Fix class called nevery which specifies how often method
|
|
||||||
end\_of\_step() is called. Thus all we need to do is just set it up.
|
|
||||||
|
|
||||||
The next method we need to implement is setmask():
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
int FixPrintVel::setmask()
|
|
||||||
{
|
|
||||||
int mask = 0;
|
|
||||||
mask |= FixConst::END_OF_STEP;
|
|
||||||
return mask;
|
|
||||||
}
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
|
|
||||||
Here user specifies which methods of your fix should be called during
|
|
||||||
the execution. For instance, END\_OF\_STEP corresponds to the
|
|
||||||
end\_of\_step() method. Overall, there are 8 most important methods,
|
|
||||||
methods are called in predefined order during the execution of the
|
|
||||||
verlet algorithm as was mentioned in the Section 3:
|
|
||||||
|
|
||||||
\begin{itemize}
|
|
||||||
\item initial\_integrate()
|
|
||||||
\item post\_integrate()
|
|
||||||
\item pre\_exchange()
|
|
||||||
\item pre\_neighbor()
|
|
||||||
\item pre\_force()
|
|
||||||
\item post\_force()
|
|
||||||
\item final\_integrate()
|
|
||||||
\item end\_of\_step()
|
|
||||||
\end{itemize}
|
|
||||||
|
|
||||||
Fix developer must understand when he wants to execute his code. In
|
|
||||||
case if we want to write FixPrintVel, we need only end\_of\_step():
|
|
||||||
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
void FixPrintVel::end_of_step()
|
|
||||||
{
|
|
||||||
// for add3, scale3
|
|
||||||
using namespace MathExtra;
|
|
||||||
|
|
||||||
double** v = atom->v;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
double localAvgVel[4]; // 4th element for particles count
|
|
||||||
memset(localAvgVel, 0, 4 * sizeof(double));
|
|
||||||
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
|
|
||||||
add3(localAvgVel, v[particleInd], localAvgVel);
|
|
||||||
}
|
|
||||||
localAvgVel[3] = nlocal;
|
|
||||||
double globalAvgVel[4];
|
|
||||||
memset(globalAvgVel, 0, 4 * sizeof(double));
|
|
||||||
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
|
|
||||||
scale3(1.0 / globalAvgVel[3], globalAvgVel);
|
|
||||||
if (comm->me == 0) {
|
|
||||||
printf("\%e, \%e, \%e\n",
|
|
||||||
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
|
|
||||||
In the code above, we use MathExtra routines defined in
|
|
||||||
``math\_extra.h''. There are bunch of math functions to work with
|
|
||||||
arrays of doubles as with math vectors.
|
|
||||||
|
|
||||||
In this code we use an instance of Atom class. This object is stored
|
|
||||||
in the Pointers class (see ``pointers.h''). This object contains all
|
|
||||||
global information about the simulation system. Data from Pointers
|
|
||||||
class available to all classes inherited from it using protected
|
|
||||||
inheritance. Hence when you write you own class, which is going to use
|
|
||||||
LAMMPS data, don't forget to inherit from Pointers. When writing
|
|
||||||
fixes we inherit from class Fix which is inherited from Pointers so
|
|
||||||
there is no need to inherit from it directly.
|
|
||||||
|
|
||||||
The code above computes average velocity for all particles in the
|
|
||||||
simulation. Yet you have one unused parameter in fix call from the
|
|
||||||
script - [group\_name]. This parameter specifies the group of atoms
|
|
||||||
used in the fix. So we should compute average for all particles in the
|
|
||||||
simulation if group\_name == all, but it can be any group. The group
|
|
||||||
information is specified by groupbit which is defined in class Fix:
|
|
||||||
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
|
|
||||||
if (atom->mask[particleInd] & groupbit) {
|
|
||||||
//Do all job here
|
|
||||||
}
|
|
||||||
}
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
|
|
||||||
Class Atom encapsulates atoms positions, velocities, forces, etc. User
|
|
||||||
can access them using particle index. Note, that particle indexes are
|
|
||||||
usually changed every timestep because of sorting.
|
|
||||||
|
|
||||||
Lets consider another Fix example. We want to have a fix which stores
|
|
||||||
atoms position from previous time step in your fix. The local atoms
|
|
||||||
indexes will not be valid on the next iteration. In order to handle
|
|
||||||
this situation there are several methods which should be implemented:
|
|
||||||
|
|
||||||
\begin{itemize}
|
|
||||||
\item \verb|double memory_usage| - return how much memory fix uses
|
|
||||||
\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
|
|
||||||
in your fix
|
|
||||||
\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle
|
|
||||||
information to j-th. Used when atoms sorting is performed. if delflag is set
|
|
||||||
and atom j owns a body, move the body information to atom i.
|
|
||||||
\item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
|
|
||||||
\end{itemize}
|
|
||||||
|
|
||||||
Note, that if your class implements these methods, it must call add calls of
|
|
||||||
add\_callback and delete\_callback to constructor and destructor:
|
|
||||||
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg) {
|
|
||||||
//...
|
|
||||||
atom->add_callback(0);
|
|
||||||
}
|
|
||||||
|
|
||||||
FixSavePos::~FixSavePos() {
|
|
||||||
atom->delete_callback(id, 0);
|
|
||||||
}
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
|
|
||||||
Since we want to store positions of atoms from previous timestep, we
|
|
||||||
need to add double** x to the header file. Than add allocation code to
|
|
||||||
constructor:
|
|
||||||
|
|
||||||
\verb|memory->create(this->x, atom->nmax, 3, "FixSavePos:x");|. Free memory
|
|
||||||
at destructor: \verb|memory->destroy(x);|
|
|
||||||
|
|
||||||
Finally, implement mentioned methods:
|
|
||||||
|
|
||||||
\begin{center}
|
|
||||||
\begin{verbatim}
|
|
||||||
double FixSavePos::memory_usage()
|
|
||||||
{
|
|
||||||
int nmax = atom->nmax;
|
|
||||||
double bytes = 0.0;
|
|
||||||
bytes += nmax * 3 * sizeof(double);
|
|
||||||
return bytes;
|
|
||||||
}
|
|
||||||
|
|
||||||
void FixSavePos::grow_arrays(int nmax)
|
|
||||||
{
|
|
||||||
memory->grow(this->x, nmax, 3, "FixSavePos:x");
|
|
||||||
}
|
|
||||||
|
|
||||||
void FixSavePos::copy_arrays(int i, int j, int delflag)
|
|
||||||
{
|
|
||||||
memcpy(this->x[j], this->x[i], sizeof(double) * 3);
|
|
||||||
}
|
|
||||||
|
|
||||||
void FixSavePos::set_arrays(int i)
|
|
||||||
{
|
|
||||||
memset(this->x[i], 0, sizeof(double) * 3);
|
|
||||||
}
|
|
||||||
|
|
||||||
int FixSavePos::pack_exchange(int i, double *buf)
|
|
||||||
{
|
|
||||||
int m = 0;
|
|
||||||
buf[m++] = x[i][0];
|
|
||||||
buf[m++] = x[i][1];
|
|
||||||
buf[m++] = x[i][2];
|
|
||||||
|
|
||||||
return m;
|
|
||||||
}
|
|
||||||
|
|
||||||
int FixSavePos::unpack_exchange(int nlocal, double *buf)
|
|
||||||
{
|
|
||||||
int m = 0;
|
|
||||||
x[nlocal][0] = buf[m++];
|
|
||||||
x[nlocal][1] = buf[m++];
|
|
||||||
x[nlocal][2] = buf[m++];
|
|
||||||
|
|
||||||
return m;
|
|
||||||
}
|
|
||||||
\end{verbatim}
|
|
||||||
\end{center}
|
|
||||||
|
|
||||||
Now, a little bit about memory allocation. We used Memory class which
|
|
||||||
is just a bunch of template functions for allocating 1D and 2D
|
|
||||||
arrays. So you need to add include ``memory.h'' to have access to them.
|
|
||||||
|
|
||||||
Finally, if you need to write/read some global information used in
|
|
||||||
your fix to the restart file, you might do it by setting flag
|
|
||||||
restart\_global = 1 in the constructor and implementing methods void
|
|
||||||
write\_restart(FILE *fp) and void restart(char *buf).
|
|
||||||
|
|
||||||
\end{document}
|
|
||||||
@ -502,7 +502,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
|
|||||||
*Bond/react: Unknown section in map file*
|
*Bond/react: Unknown section in map file*
|
||||||
Please ensure reaction map files are properly formatted.
|
Please ensure reaction map files are properly formatted.
|
||||||
|
|
||||||
*Bond/react: Atom affected by reaction too close to template edge*
|
*Bond/react: Atom/Bond type affected by reaction too close to template edge*
|
||||||
This means an atom which changes type or connectivity during the
|
This means an atom which changes type or connectivity during the
|
||||||
reaction is too close to an 'edge' atom defined in the map
|
reaction is too close to an 'edge' atom defined in the map
|
||||||
file. This could cause incorrect assignment of bonds, angle, etc.
|
file. This could cause incorrect assignment of bonds, angle, etc.
|
||||||
|
|||||||
@ -191,19 +191,19 @@ You start the command ``ccmake ../cmake`` in the ``build`` folder.
|
|||||||
.. list-table::
|
.. list-table::
|
||||||
|
|
||||||
* - .. figure:: JPG/ccmake-initial.png
|
* - .. figure:: JPG/ccmake-initial.png
|
||||||
:target: JPG/ccmake-initial.png
|
:scale: 33%
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
Initial ``ccmake`` screen
|
Initial ``ccmake`` screen
|
||||||
|
|
||||||
- .. figure:: JPG/ccmake-config.png
|
- .. figure:: JPG/ccmake-config.png
|
||||||
:target: JPG/ccmake-config.png
|
:scale: 33%
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
Configure output of ``ccmake``
|
Configure output of ``ccmake``
|
||||||
|
|
||||||
- .. figure:: JPG/ccmake-options.png
|
- .. figure:: JPG/ccmake-options.png
|
||||||
:target: JPG/ccmake-options.png
|
:scale: 33%
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
Options screen of ``ccmake``
|
Options screen of ``ccmake``
|
||||||
@ -236,19 +236,19 @@ not required, it can also be entered from the GUI.
|
|||||||
.. list-table::
|
.. list-table::
|
||||||
|
|
||||||
* - .. figure:: JPG/cmake-gui-initial.png
|
* - .. figure:: JPG/cmake-gui-initial.png
|
||||||
:target: JPG/cmake-gui-initial.png
|
:scale: 40%
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
Initial ``cmake-gui`` screen
|
Initial ``cmake-gui`` screen
|
||||||
|
|
||||||
- .. figure:: JPG/cmake-gui-popup.png
|
- .. figure:: JPG/cmake-gui-popup.png
|
||||||
:target: JPG/cmake-gui-popup.png
|
:scale: 60%
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
Generator selection in ``cmake-gui``
|
Generator selection in ``cmake-gui``
|
||||||
|
|
||||||
- .. figure:: JPG/cmake-gui-options.png
|
- .. figure:: JPG/cmake-gui-options.png
|
||||||
:target: JPG/cmake-gui-options.png
|
:scale: 40%
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
Options screen of ``cmake-gui``
|
Options screen of ``cmake-gui``
|
||||||
|
|||||||
@ -12,96 +12,52 @@ LAMMPS can be coupled to other codes in at least 4 ways. Each has
|
|||||||
advantages and disadvantages, which you will have to think about in the
|
advantages and disadvantages, which you will have to think about in the
|
||||||
context of your application.
|
context of your application.
|
||||||
|
|
||||||
----------
|
1. Define a new :doc:`fix <fix>` command that calls the other code. In
|
||||||
|
this scenario, LAMMPS is the driver code. During timestepping,
|
||||||
|
the fix is invoked, and can make library calls to the other code,
|
||||||
|
which has been linked to LAMMPS as a library. This is the way how the
|
||||||
|
:ref:`LATTE <PKG-LATTE>` package, which performs density-functional
|
||||||
|
tight-binding calculations using the `LATTE software <https://github.com/lanl/LATTE>`_
|
||||||
|
to compute forces, is hooked to LAMMPS.
|
||||||
|
See the :doc:`fix latte <fix_latte>` command for more details.
|
||||||
|
Also see the :doc:`Modify <Modify>` doc pages for info on how to
|
||||||
|
add a new fix to LAMMPS.
|
||||||
|
|
||||||
(1) Define a new :doc:`fix <fix>` command that calls the other code. In
|
.. spacer
|
||||||
this scenario, LAMMPS is the driver code. During its timestepping,
|
|
||||||
the fix is invoked, and can make library calls to the other code,
|
|
||||||
which has been linked to LAMMPS as a library. This is the way the
|
|
||||||
`POEMS <poems_>`_ package that performs constrained rigid-body motion on
|
|
||||||
groups of atoms is hooked to LAMMPS. See the :doc:`fix poems <fix_poems>` command for more details. See the
|
|
||||||
:doc:`Modify <Modify>` doc pages for info on how to add a new fix to
|
|
||||||
LAMMPS.
|
|
||||||
|
|
||||||
.. _poems: http://www.rpi.edu/~anderk5/lab
|
2. Define a new LAMMPS command that calls the other code. This is
|
||||||
|
conceptually similar to method (1), but in this case LAMMPS and the
|
||||||
|
other code are on a more equal footing. Note that now the other code
|
||||||
|
is not called during the timestepping of a LAMMPS run, but between
|
||||||
|
runs. The LAMMPS input script can be used to alternate LAMMPS runs
|
||||||
|
with calls to the other code, invoked via the new command. The
|
||||||
|
:doc:`run <run>` command facilitates this with its *every* option,
|
||||||
|
which makes it easy to run a few steps, invoke the command, run a few
|
||||||
|
steps, invoke the command, etc.
|
||||||
|
|
||||||
----------
|
In this scenario, the other code can be called as a library, as in
|
||||||
|
1., or it could be a stand-alone code, invoked by a system() call
|
||||||
|
made by the command (assuming your parallel machine allows one or
|
||||||
|
more processors to start up another program). In the latter case the
|
||||||
|
stand-alone code could communicate with LAMMPS through files that the
|
||||||
|
command writes and reads.
|
||||||
|
|
||||||
(2) Define a new LAMMPS command that calls the other code. This is
|
See the :doc:`Modify command <Modify_command>` doc page for info on how
|
||||||
conceptually similar to method (1), but in this case LAMMPS and the
|
to add a new command to LAMMPS.
|
||||||
other code are on a more equal footing. Note that now the other code
|
|
||||||
is not called during the timestepping of a LAMMPS run, but between
|
|
||||||
runs. The LAMMPS input script can be used to alternate LAMMPS runs
|
|
||||||
with calls to the other code, invoked via the new command. The
|
|
||||||
:doc:`run <run>` command facilitates this with its *every* option, which
|
|
||||||
makes it easy to run a few steps, invoke the command, run a few steps,
|
|
||||||
invoke the command, etc.
|
|
||||||
|
|
||||||
In this scenario, the other code can be called as a library, as in
|
.. spacer
|
||||||
(1), or it could be a stand-alone code, invoked by a system() call
|
|
||||||
made by the command (assuming your parallel machine allows one or more
|
|
||||||
processors to start up another program). In the latter case the
|
|
||||||
stand-alone code could communicate with LAMMPS through files that the
|
|
||||||
command writes and reads.
|
|
||||||
|
|
||||||
See the :doc:`Modify command <Modify_command>` doc page for info on how
|
3. Use LAMMPS as a library called by another code. In this case the
|
||||||
to add a new command to LAMMPS.
|
other code is the driver and calls LAMMPS as needed. Or a wrapper
|
||||||
|
code could link and call both LAMMPS and another code as libraries.
|
||||||
|
Again, the :doc:`run <run>` command has options that allow it to be
|
||||||
|
invoked with minimal overhead (no setup or clean-up) if you wish to
|
||||||
|
do multiple short runs, driven by another program. Details about
|
||||||
|
using the library interface are given in the :doc:`library API
|
||||||
|
<pg_library>` documentation.
|
||||||
|
|
||||||
----------
|
.. spacer
|
||||||
|
|
||||||
(3) Use LAMMPS as a library called by another code. In this case the
|
4. Couple LAMMPS with another code in a client/server mode. This is
|
||||||
other code is the driver and calls LAMMPS as needed. Or a wrapper
|
described on the :doc:`Howto client/server <Howto_client_server>` doc
|
||||||
code could link and call both LAMMPS and another code as libraries.
|
page.
|
||||||
Again, the :doc:`run <run>` command has options that allow it to be
|
|
||||||
invoked with minimal overhead (no setup or clean-up) if you wish to do
|
|
||||||
multiple short runs, driven by another program.
|
|
||||||
|
|
||||||
Examples of driver codes that call LAMMPS as a library are included in
|
|
||||||
the examples/COUPLE directory of the LAMMPS distribution; see
|
|
||||||
examples/COUPLE/README for more details:
|
|
||||||
|
|
||||||
* simple: simple driver programs in C++ and C which invoke LAMMPS as a
|
|
||||||
library
|
|
||||||
* plugin: simple driver program in C which invokes LAMMPS as a plugin
|
|
||||||
from a shared library.
|
|
||||||
* lammps_quest: coupling of LAMMPS and `Quest <quest_>`_, to run classical
|
|
||||||
MD with quantum forces calculated by a density functional code
|
|
||||||
* lammps_spparks: coupling of LAMMPS and `SPPARKS <spparks_>`_, to couple
|
|
||||||
a kinetic Monte Carlo model for grain growth using MD to calculate
|
|
||||||
strain induced across grain boundaries
|
|
||||||
|
|
||||||
.. _quest: http://dft.sandia.gov/Quest
|
|
||||||
|
|
||||||
.. _spparks: http://www.sandia.gov/~sjplimp/spparks.html
|
|
||||||
|
|
||||||
The :doc:`Build basics <Build_basics>` doc page describes how to build
|
|
||||||
LAMMPS as a library. Once this is done, you can interface with LAMMPS
|
|
||||||
either via C++, C, Fortran, or Python (or any other language that
|
|
||||||
supports a vanilla C-like interface). For example, from C++ you could
|
|
||||||
create one (or more) "instances" of LAMMPS, pass it an input script to
|
|
||||||
process, or execute individual commands, all by invoking the correct
|
|
||||||
class methods in LAMMPS. From C or Fortran you can make function
|
|
||||||
calls to do the same things. See the :doc:`Python <Python_head>` doc
|
|
||||||
pages for a description of the Python wrapper provided with LAMMPS
|
|
||||||
that operates through the LAMMPS library interface.
|
|
||||||
|
|
||||||
The files src/library.cpp and library.h contain the C-style interface
|
|
||||||
to LAMMPS. See the :doc:`Howto library <Howto_library>` doc page for a
|
|
||||||
description of the interface and how to extend it for your needs.
|
|
||||||
|
|
||||||
Note that the lammps_open() function that creates an instance of
|
|
||||||
LAMMPS takes an MPI communicator as an argument. This means that
|
|
||||||
instance of LAMMPS will run on the set of processors in the
|
|
||||||
communicator. Thus the calling code can run LAMMPS on all or a subset
|
|
||||||
of processors. For example, a wrapper script might decide to
|
|
||||||
alternate between LAMMPS and another code, allowing them both to run
|
|
||||||
on all the processors. Or it might allocate half the processors to
|
|
||||||
LAMMPS and half to the other code and run both codes simultaneously
|
|
||||||
before syncing them up periodically. Or it might instantiate multiple
|
|
||||||
instances of LAMMPS to perform different calculations.
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
(4) Couple LAMMPS with another code in a client/server mode. This is
|
|
||||||
described on the :doc:`Howto client/server <Howto_client_server>` doc
|
|
||||||
page.
|
|
||||||
|
|||||||
@ -2,241 +2,36 @@ Library interface to LAMMPS
|
|||||||
===========================
|
===========================
|
||||||
|
|
||||||
As described on the :doc:`Build basics <Build_basics>` doc page, LAMMPS
|
As described on the :doc:`Build basics <Build_basics>` doc page, LAMMPS
|
||||||
can be built as a library, so that it can be called by another code,
|
can be built as a static or shared library, so that it can be called by
|
||||||
used in a :doc:`coupled manner <Howto_couple>` with other codes, or
|
another code, used in a :doc:`coupled manner <Howto_couple>` with other
|
||||||
driven through a :doc:`Python interface <Python_head>`.
|
codes, or driven through a :doc:`Python interface <Python_head>`.
|
||||||
|
|
||||||
All of these methodologies use a C-style interface to LAMMPS that is
|
At the core of LAMMPS is the ``LAMMPS`` class which encapsulates the
|
||||||
provided in the files src/library.cpp and src/library.h. The
|
state of the simulation program through the state of the various class
|
||||||
functions therein have a C-style argument list, but contain C++ code
|
instances that it is composed of. So a calculation using LAMMPS
|
||||||
you could write yourself in a C++ application that was invoking LAMMPS
|
requires to create an instance of the ``LAMMPS`` class and then send it
|
||||||
directly. The C++ code in the functions illustrates how to invoke
|
(text) commands, either individually or from a file, or perform other
|
||||||
internal LAMMPS operations. Note that LAMMPS classes are defined
|
operations that modify the state stored inside that instance or drive
|
||||||
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
|
simulations. This is essentially what the ``src/main.cpp`` file does
|
||||||
application.
|
as well for the standalone LAMMPS executable with reading commands
|
||||||
|
either from an input file or stdin.
|
||||||
|
|
||||||
The examples/COUPLE and python/examples directories have example C++
|
Creating a LAMMPS instance can be done by using C++ code directly or
|
||||||
and C and Python codes which show how a driver code can link to LAMMPS
|
through a C-style interface library to LAMMPS that is provided in the
|
||||||
as a library, run LAMMPS on a subset of processors, grab data from
|
files ``src/library.cpp`` and ``library.h``. This
|
||||||
LAMMPS, change it, and put it back into LAMMPS.
|
:ref:`C language API <lammps_c_api>`, can be used from C and C++,
|
||||||
|
and is also the basis for the :doc:`Python <pg_python>` and
|
||||||
|
:doc:`Fortran <pg_fortran>` interfaces or wrappers included in the
|
||||||
|
LAMMPS source code.
|
||||||
|
|
||||||
Thread-safety
|
The ``examples/COUPLE`` and ``python/examples`` directories contain some
|
||||||
-------------
|
example programs written in C++, C, Fortran, and Python, which show how
|
||||||
|
a driver code can link to LAMMPS as a library, run LAMMPS on a subset of
|
||||||
|
processors (so the others are available to run some other code
|
||||||
|
concurrently), grab data from LAMMPS, change it, and send it back into
|
||||||
|
LAMMPS.
|
||||||
|
|
||||||
LAMMPS has not initially been conceived as a thread-safe program, but
|
A detailed documentation of the available APIs and examples of how to
|
||||||
over the years changes have been applied to replace operations that
|
use them can be found in the :doc:`Programmer Documentation
|
||||||
collide with creating multiple LAMMPS instances from multiple-threads
|
<pg_library>` section of this manual.
|
||||||
of the same process with thread-safe alternatives. This primarily
|
|
||||||
applies to the core LAMMPS code and less so on add-on packages, especially
|
|
||||||
when those packages require additional code in the *lib* folder,
|
|
||||||
interface LAMMPS to Fortran libraries, or the code uses static variables
|
|
||||||
(like the USER-COLVARS package.
|
|
||||||
|
|
||||||
Another major issue to deal with is to correctly handle MPI. Creating
|
|
||||||
a LAMMPS instance requires passing an MPI communicator, or it assumes
|
|
||||||
the MPI_COMM_WORLD communicator, which spans all MPI processor ranks.
|
|
||||||
When creating multiple LAMMPS object instances from different threads,
|
|
||||||
this communicator has to be different for each thread or else collisions
|
|
||||||
can happen, or it has to be guaranteed, that only one thread at a time
|
|
||||||
is active. MPI communicators, however, are not a problem, if LAMMPS is
|
|
||||||
compiled with the MPI STUBS library, which implies that there is no MPI
|
|
||||||
communication and only 1 MPI rank.
|
|
||||||
|
|
||||||
Provided APIs
|
|
||||||
-------------
|
|
||||||
|
|
||||||
The file src/library.cpp contains the following functions for creating
|
|
||||||
and destroying an instance of LAMMPS and sending it commands to
|
|
||||||
execute. See the documentation in the src/library.cpp file for
|
|
||||||
details.
|
|
||||||
|
|
||||||
.. note::
|
|
||||||
|
|
||||||
You can write code for additional functions as needed to define
|
|
||||||
how your code talks to LAMMPS and add them to src/library.cpp and
|
|
||||||
src/library.h, as well as to the :doc:`Python interface <Python_head>`.
|
|
||||||
The added functions can access or change any internal LAMMPS data you
|
|
||||||
wish.
|
|
||||||
|
|
||||||
.. code-block:: c
|
|
||||||
|
|
||||||
void lammps_open(int, char **, MPI_Comm, void **)
|
|
||||||
void lammps_open_no_mpi(int, char **, void **)
|
|
||||||
void lammps_close(void *)
|
|
||||||
int lammps_version(void *)
|
|
||||||
void lammps_file(void *, char *)
|
|
||||||
char *lammps_command(void *, char *)
|
|
||||||
void lammps_commands_list(void *, int, char **)
|
|
||||||
void lammps_commands_string(void *, char *)
|
|
||||||
void lammps_free(void *)
|
|
||||||
|
|
||||||
The lammps_open() function is used to initialize LAMMPS, passing in a
|
|
||||||
list of strings as if they were :doc:`command-line arguments <Run_options>` when LAMMPS is run in stand-alone mode
|
|
||||||
from the command line, and a MPI communicator for LAMMPS to run under.
|
|
||||||
It returns a ptr to the LAMMPS object that is created, and which is
|
|
||||||
used in subsequent library calls. The lammps_open() function can be
|
|
||||||
called multiple times, to create multiple instances of LAMMPS.
|
|
||||||
|
|
||||||
LAMMPS will run on the set of processors in the communicator. This
|
|
||||||
means the calling code can run LAMMPS on all or a subset of
|
|
||||||
processors. For example, a wrapper script might decide to alternate
|
|
||||||
between LAMMPS and another code, allowing them both to run on all the
|
|
||||||
processors. Or it might allocate half the processors to LAMMPS and
|
|
||||||
half to the other code and run both codes simultaneously before
|
|
||||||
syncing them up periodically. Or it might instantiate multiple
|
|
||||||
instances of LAMMPS to perform different calculations.
|
|
||||||
|
|
||||||
The lammps_open_no_mpi() function is similar except that no MPI
|
|
||||||
communicator is passed from the caller. Instead, MPI_COMM_WORLD is
|
|
||||||
used to instantiate LAMMPS, and MPI is initialized if necessary.
|
|
||||||
|
|
||||||
The lammps_close() function is used to shut down an instance of LAMMPS
|
|
||||||
and free all its memory.
|
|
||||||
|
|
||||||
The lammps_version() function can be used to determined the specific
|
|
||||||
version of the underlying LAMMPS code. This is particularly useful
|
|
||||||
when loading LAMMPS as a shared library via dlopen(). The code using
|
|
||||||
the library interface can than use this information to adapt to
|
|
||||||
changes to the LAMMPS command syntax between versions. The returned
|
|
||||||
LAMMPS version code is an integer (e.g. 2 Sep 2015 results in
|
|
||||||
20150902) that grows with every new LAMMPS version.
|
|
||||||
|
|
||||||
The lammps_file(), lammps_command(), lammps_commands_list(), and
|
|
||||||
lammps_commands_string() functions are used to pass one or more
|
|
||||||
commands to LAMMPS to execute, the same as if they were coming from an
|
|
||||||
input script.
|
|
||||||
|
|
||||||
Via these functions, the calling code can read or generate a series of
|
|
||||||
LAMMPS commands one or multiple at a time and pass it through the library
|
|
||||||
interface to setup a problem and then run it in stages. The caller
|
|
||||||
can interleave the command function calls with operations it performs,
|
|
||||||
calls to extract information from or set information within LAMMPS, or
|
|
||||||
calls to another code's library.
|
|
||||||
|
|
||||||
The lammps_file() function passes the filename of an input script.
|
|
||||||
The lammps_command() function passes a single command as a string.
|
|
||||||
The lammps_commands_list() function passes multiple commands in a
|
|
||||||
char\*\* list. In both lammps_command() and lammps_commands_list(),
|
|
||||||
individual commands may or may not have a trailing newline. The
|
|
||||||
lammps_commands_string() function passes multiple commands
|
|
||||||
concatenated into one long string, separated by newline characters.
|
|
||||||
In both lammps_commands_list() and lammps_commands_string(), a single
|
|
||||||
command can be spread across multiple lines, if the last printable
|
|
||||||
character of all but the last line is "&", the same as if the lines
|
|
||||||
appeared in an input script.
|
|
||||||
|
|
||||||
The lammps_free() function is a clean-up function to free memory that
|
|
||||||
the library allocated previously via other function calls. See
|
|
||||||
comments in src/library.cpp file for which other functions need this
|
|
||||||
clean-up.
|
|
||||||
|
|
||||||
The file src/library.cpp also contains these functions for extracting
|
|
||||||
information from LAMMPS and setting value within LAMMPS. Again, see
|
|
||||||
the documentation in the src/library.cpp file for details, including
|
|
||||||
which quantities can be queried by name:
|
|
||||||
|
|
||||||
.. code-block:: c
|
|
||||||
|
|
||||||
int lammps_extract_setting(void *, char *)
|
|
||||||
void *lammps_extract_global(void *, char *)
|
|
||||||
void lammps_extract_box(void *, double *, double *,
|
|
||||||
double *, double *, double *, int *, int *)
|
|
||||||
void *lammps_extract_atom(void *, char *)
|
|
||||||
void *lammps_extract_compute(void *, char *, int, int)
|
|
||||||
void *lammps_extract_fix(void *, char *, int, int, int, int)
|
|
||||||
void *lammps_extract_variable(void *, char *, char *)
|
|
||||||
|
|
||||||
The extract_setting() function returns info on the size
|
|
||||||
of data types (e.g. 32-bit or 64-bit atom IDs) used
|
|
||||||
by the LAMMPS executable (a compile-time choice).
|
|
||||||
|
|
||||||
The other extract functions return a pointer to various global or
|
|
||||||
per-atom quantities stored in LAMMPS or to values calculated by a
|
|
||||||
compute, fix, or variable. The pointer returned by the
|
|
||||||
extract_global() function can be used as a permanent reference to a
|
|
||||||
value which may change. For the extract_atom() method, see the
|
|
||||||
extract() method in the src/atom.cpp file for a list of valid per-atom
|
|
||||||
properties. New names could easily be added if the property you want
|
|
||||||
is not listed. For the other extract functions, the underlying
|
|
||||||
storage may be reallocated as LAMMPS runs, so you need to re-call the
|
|
||||||
function to assure a current pointer or returned value(s).
|
|
||||||
|
|
||||||
.. code-block:: c
|
|
||||||
|
|
||||||
double lammps_get_thermo(void *, char *)
|
|
||||||
int lammps_get_natoms(void *)
|
|
||||||
|
|
||||||
int lammps_set_variable(void *, char *, char *)
|
|
||||||
void lammps_reset_box(void *, double *, double *, double, double, double)
|
|
||||||
|
|
||||||
The lammps_get_thermo() function returns the current value of a thermo
|
|
||||||
keyword as a double precision value.
|
|
||||||
|
|
||||||
The lammps_get_natoms() function returns the total number of atoms in
|
|
||||||
the system and can be used by the caller to allocate memory for the
|
|
||||||
lammps_gather_atoms() and lammps_scatter_atoms() functions.
|
|
||||||
|
|
||||||
The lammps_set_variable() function can set an existing string-style
|
|
||||||
variable to a new string value, so that subsequent LAMMPS commands can
|
|
||||||
access the variable.
|
|
||||||
|
|
||||||
The lammps_reset_box() function resets the size and shape of the
|
|
||||||
simulation box, e.g. as part of restoring a previously extracted and
|
|
||||||
saved state of a simulation.
|
|
||||||
|
|
||||||
.. code-block:: c
|
|
||||||
|
|
||||||
void lammps_gather_atoms(void *, char *, int, int, void *)
|
|
||||||
void lammps_gather_atoms_concat(void *, char *, int, int, void *)
|
|
||||||
void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
|
|
||||||
void lammps_scatter_atoms(void *, char *, int, int, void *)
|
|
||||||
void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *)
|
|
||||||
|
|
||||||
The gather functions collect peratom info of the requested type (atom
|
|
||||||
coords, atom types, forces, etc) from all processors, and returns the
|
|
||||||
same vector of values to each calling processor. The scatter
|
|
||||||
functions do the inverse. They distribute a vector of peratom values,
|
|
||||||
passed by all calling processors, to individual atoms, which may be
|
|
||||||
owned by different processors.
|
|
||||||
|
|
||||||
.. warning::
|
|
||||||
|
|
||||||
These functions are not compatible with the
|
|
||||||
-DLAMMPS_BIGBIG setting when compiling LAMMPS. Dummy functions
|
|
||||||
that result in an error message and abort will be substituted
|
|
||||||
instead of resulting in random crashes and memory corruption.
|
|
||||||
|
|
||||||
The lammps_gather_atoms() function does this for all N atoms in the
|
|
||||||
system, ordered by atom ID, from 1 to N. The
|
|
||||||
lammps_gather_atoms_concat() function does it for all N atoms, but
|
|
||||||
simply concatenates the subset of atoms owned by each processor. The
|
|
||||||
resulting vector is not ordered by atom ID. Atom IDs can be requested
|
|
||||||
by the same function if the caller needs to know the ordering. The
|
|
||||||
lammps_gather_subset() function allows the caller to request values
|
|
||||||
for only a subset of atoms (identified by ID).
|
|
||||||
For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
|
|
||||||
If the count is specified as 1, they are returned
|
|
||||||
in a packed format with all three image flags stored in a single integer.
|
|
||||||
If the count is specified as 3, the values are unpacked into xyz flags
|
|
||||||
by the library before returning them.
|
|
||||||
|
|
||||||
The lammps_scatter_atoms() function takes a list of values for all N
|
|
||||||
atoms in the system, ordered by atom ID, from 1 to N, and assigns
|
|
||||||
those values to each atom in the system. The
|
|
||||||
lammps_scatter_atoms_subset() function takes a subset of IDs as an
|
|
||||||
argument and only scatters those values to the owning atoms.
|
|
||||||
|
|
||||||
.. code-block:: c
|
|
||||||
|
|
||||||
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
|
|
||||||
imageint *, int)
|
|
||||||
|
|
||||||
The lammps_create_atoms() function takes a list of N atoms as input
|
|
||||||
with atom types and coords (required), an optionally atom IDs and
|
|
||||||
velocities and image flags. It uses the coords of each atom to assign
|
|
||||||
it as a new atom to the processor that owns it. This function is
|
|
||||||
useful to add atoms to a simulation or (in tandem with
|
|
||||||
lammps_reset_box()) to restore a previously extracted and saved state
|
|
||||||
of a simulation. Additional properties for the new atoms can then be
|
|
||||||
assigned via the lammps_scatter_atoms() or lammps_extract_atom()
|
|
||||||
functions.
|
|
||||||
|
|||||||
@ -79,13 +79,13 @@ To get a copy of the current potentials files:
|
|||||||
which will download the potentials files to
|
which will download the potentials files to
|
||||||
``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is
|
``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is
|
||||||
hard-coded to look for potential files in this directory (it does not
|
hard-coded to look for potential files in this directory (it does not
|
||||||
use the `LAMMPS_POTENTIALS` environment variable, as described
|
use the ``LAMMPS_POTENTIALS`` environment variable, as described
|
||||||
in :doc:`pair_coeff <pair_coeff>` command).
|
in :doc:`pair_coeff <pair_coeff>` command).
|
||||||
|
|
||||||
The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
|
The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
|
||||||
results in the above command also installing the `kim-api` binaries when LAMMPS
|
results in the above command also installing the ``kim-api`` binaries when LAMMPS
|
||||||
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
|
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
|
||||||
can install the `openkim-models` package
|
can install the ``openkim-models`` package
|
||||||
|
|
||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
|
|||||||
@ -23,7 +23,6 @@ this Intr are included in this list.
|
|||||||
* `Mail list <https://lammps.sandia.gov/mail.html>`_
|
* `Mail list <https://lammps.sandia.gov/mail.html>`_
|
||||||
* `Workshops <https://lammps.sandia.gov/workshops.html>`_
|
* `Workshops <https://lammps.sandia.gov/workshops.html>`_
|
||||||
* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_
|
* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_
|
||||||
* `Developer guide <https://lammps.sandia.gov/Developer.pdf>`_
|
|
||||||
|
|
||||||
* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_
|
* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_
|
||||||
* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_
|
* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_
|
||||||
|
|||||||
BIN
doc/src/JPG/lammps-classes.png
Normal file
BIN
doc/src/JPG/lammps-classes.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 245 KiB |
@ -27,8 +27,7 @@ all LAMMPS development is coordinated.
|
|||||||
The content for this manual is part of the LAMMPS distribution. You
|
The content for this manual is part of the LAMMPS distribution. You
|
||||||
can build a local copy of the Manual as HTML pages or a PDF file, by
|
can build a local copy of the Manual as HTML pages or a PDF file, by
|
||||||
following the steps on the :doc:`Manual build <Manual_build>` doc page.
|
following the steps on the :doc:`Manual build <Manual_build>` doc page.
|
||||||
There is also a `Developer.pdf <Developer.pdf>`_ document which gives
|
The manual is split into two parts: 1) User documentation and 2) Programmer documentation.
|
||||||
a brief description of the basic code structure of LAMMPS.
|
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -55,11 +54,24 @@ every LAMMPS command.
|
|||||||
Howto
|
Howto
|
||||||
Examples
|
Examples
|
||||||
Tools
|
Tools
|
||||||
Modify
|
|
||||||
Python_head
|
Python_head
|
||||||
Errors
|
Errors
|
||||||
Manual_build
|
Manual_build
|
||||||
|
|
||||||
|
.. _programmer_documentation:
|
||||||
|
.. toctree::
|
||||||
|
:maxdepth: 2
|
||||||
|
:numbered: 3
|
||||||
|
:caption: Programmer Documentation
|
||||||
|
:name: progdoc
|
||||||
|
:includehidden:
|
||||||
|
|
||||||
|
pg_library
|
||||||
|
Modify
|
||||||
|
pg_developer
|
||||||
|
.. pg_modify
|
||||||
|
.. pg_base
|
||||||
|
|
||||||
.. toctree::
|
.. toctree::
|
||||||
:caption: Index
|
:caption: Index
|
||||||
:name: index
|
:name: index
|
||||||
|
|||||||
@ -14,7 +14,6 @@ files. Here is a list with descriptions:
|
|||||||
lammps.1 # man page for the lammps command
|
lammps.1 # man page for the lammps command
|
||||||
msi2lmp.1 # man page for the msi2lmp command
|
msi2lmp.1 # man page for the msi2lmp command
|
||||||
Manual.pdf # large PDF version of entire manual
|
Manual.pdf # large PDF version of entire manual
|
||||||
Developer.pdf # small PDF with info about how LAMMPS is structured
|
|
||||||
LAMMPS.epub # Manual in ePUB e-book format
|
LAMMPS.epub # Manual in ePUB e-book format
|
||||||
LAMMPS.mobi # Manual in MOBI e-book format
|
LAMMPS.mobi # Manual in MOBI e-book format
|
||||||
docenv # virtualenv folder for processing the manual sources
|
docenv # virtualenv folder for processing the manual sources
|
||||||
@ -35,7 +34,7 @@ of two ways:
|
|||||||
|
|
||||||
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
|
a. You can "fetch" the current HTML and PDF files from the LAMMPS web
|
||||||
site. Just type ``make fetch``. This should download a html_www
|
site. Just type ``make fetch``. This should download a html_www
|
||||||
directory and Manual_www.pdf/Developer_www.pdf files. Note that if
|
directory and a Manual_www.pdf file. Note that if
|
||||||
new LAMMPS features have been added more recently than the date of
|
new LAMMPS features have been added more recently than the date of
|
||||||
your LAMMPS version, the fetched documentation will include those
|
your LAMMPS version, the fetched documentation will include those
|
||||||
changes (but your source code will not, unless you update your local
|
changes (but your source code will not, unless you update your local
|
||||||
@ -49,6 +48,11 @@ b. You can build the HTML or PDF files yourself, by typing ``make html``
|
|||||||
only once, unless you type ``make clean-all``. After that, viewing and
|
only once, unless you type ``make clean-all``. After that, viewing and
|
||||||
processing of the documentation can be done without internet access.
|
processing of the documentation can be done without internet access.
|
||||||
|
|
||||||
|
A current version of the manual (latest patch release, aka unstable branch)
|
||||||
|
is is available online at: `https://lammps.sandia.gov/doc/Manual.html <https://lammps.sandia.gov/doc/Manual.html>`_
|
||||||
|
A version of the manual corresponding to the ongoing development
|
||||||
|
(aka master branch) is available online at: `https://docs.lammps.org/ <https://docs.lammps.org/>`_
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The generation of all documentation is managed by the Makefile in the
|
The generation of all documentation is managed by the Makefile in the
|
||||||
@ -58,10 +62,9 @@ available:
|
|||||||
.. code-block:: bash
|
.. code-block:: bash
|
||||||
|
|
||||||
make html # generate HTML in html dir using Sphinx
|
make html # generate HTML in html dir using Sphinx
|
||||||
make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
|
make pdf # generate PDF as Manual.pdf using Sphinx and pdflatex
|
||||||
# in doc dir via htmldoc and pdflatex
|
make fetch # fetch HTML doc pages and PDF file from web site
|
||||||
make fetch # fetch HTML doc pages and 2 PDF files from web site
|
# as a tarball and unpack into html dir and PDF
|
||||||
# as a tarball and unpack into html dir and 2 PDFs
|
|
||||||
make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
make epub # generate LAMMPS.epub in ePUB format using Sphinx
|
||||||
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert
|
||||||
|
|
||||||
|
|||||||
@ -1,5 +1,5 @@
|
|||||||
Modify & extend LAMMPS
|
Modifying & extending LAMMPS
|
||||||
**********************
|
****************************
|
||||||
|
|
||||||
LAMMPS is designed in a modular fashion so as to be easy to modify and
|
LAMMPS is designed in a modular fashion so as to be easy to modify and
|
||||||
extend with new functionality. In fact, about 95% of its source code
|
extend with new functionality. In fact, about 95% of its source code
|
||||||
|
|||||||
@ -1692,7 +1692,7 @@ USER-MEAMC package
|
|||||||
**Contents:**
|
**Contents:**
|
||||||
|
|
||||||
A pair style for the modified embedded atom (MEAM) potential
|
A pair style for the modified embedded atom (MEAM) potential
|
||||||
translated from the Fortran version in the (obsolete) "MEAM" package
|
translated from the Fortran version in the (obsolete) MEAM package
|
||||||
to plain C++. The USER-MEAMC fully replaces the MEAM package, which
|
to plain C++. The USER-MEAMC fully replaces the MEAM package, which
|
||||||
has been removed from LAMMPS after the 12 December 2018 version.
|
has been removed from LAMMPS after the 12 December 2018 version.
|
||||||
|
|
||||||
|
|||||||
@ -6,7 +6,7 @@ name gives more details.
|
|||||||
|
|
||||||
User packages have been contributed by users, and begin with the
|
User packages have been contributed by users, and begin with the
|
||||||
"user" prefix. If a contribution is a single command (single file),
|
"user" prefix. If a contribution is a single command (single file),
|
||||||
it is typically in the user-misc package. User packages don't
|
it is typically in the USER-MISC package. User packages don't
|
||||||
necessarily meet the requirements of the :doc:`standard packages <Packages_standard>`. This means the developers will try
|
necessarily meet the requirements of the :doc:`standard packages <Packages_standard>`. This means the developers will try
|
||||||
to keep things working and usually can answer technical questions
|
to keep things working and usually can answer technical questions
|
||||||
about compiling the package. If you have problems using a specific
|
about compiling the package. If you have problems using a specific
|
||||||
|
|||||||
@ -89,7 +89,6 @@ Miscellaneous tools
|
|||||||
:columns: 6
|
:columns: 6
|
||||||
|
|
||||||
* :ref:`CMake <cmake>`
|
* :ref:`CMake <cmake>`
|
||||||
* :ref:`doxygen <doxygen>`
|
|
||||||
* :ref:`emacs <emacs>`
|
* :ref:`emacs <emacs>`
|
||||||
* :ref:`i-pi <ipi>`
|
* :ref:`i-pi <ipi>`
|
||||||
* :ref:`kate <kate>`
|
* :ref:`kate <kate>`
|
||||||
@ -254,21 +253,6 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _doxygen:
|
|
||||||
|
|
||||||
doxygen tool
|
|
||||||
--------------------------
|
|
||||||
|
|
||||||
The tools/doxygen directory contains a shell script called
|
|
||||||
doxygen.sh which can generate a call graph and API lists using
|
|
||||||
the `Doxygen software <http://doxygen.org>`_.
|
|
||||||
|
|
||||||
See the included README file for details.
|
|
||||||
|
|
||||||
The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
.. _drude:
|
.. _drude:
|
||||||
|
|
||||||
drude tool
|
drude tool
|
||||||
|
|||||||
@ -14,19 +14,22 @@ Syntax
|
|||||||
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
|
||||||
...
|
...
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command. Group-ID is ignored.
|
* ID, group-ID are documented in :doc:`fix <fix>` command.
|
||||||
* bond/react = style name of this fix command
|
* bond/react = style name of this fix command
|
||||||
* the common keyword/values may be appended directly after 'bond/react'
|
* the common keyword/values may be appended directly after 'bond/react'
|
||||||
* this applies to all reaction specifications (below)
|
* this applies to all reaction specifications (below)
|
||||||
* common_keyword = *stabilization*
|
* common_keyword = *stabilization* or *reset_mol_ids*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
*stabilization* values = *no* or *yes* *group-ID* *xmax*
|
*stabilization* values = *no* or *yes* *group-ID* *xmax*
|
||||||
*no* = no reaction site stabilization
|
*no* = no reaction site stabilization (default)
|
||||||
*yes* = perform reaction site stabilization
|
*yes* = perform reaction site stabilization
|
||||||
*group-ID* = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
|
*group-ID* = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
|
||||||
*xmax* = xmax value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
|
*xmax* = xmax value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
|
||||||
|
*reset_mol_ids* values = *yes* or *no*
|
||||||
|
*yes* = update molecule IDs based on new global topology (default)
|
||||||
|
*no* = do not update molecule IDs
|
||||||
|
|
||||||
* react = mandatory argument indicating new reaction specification
|
* react = mandatory argument indicating new reaction specification
|
||||||
* react-ID = user-assigned name for the reaction
|
* react-ID = user-assigned name for the reaction
|
||||||
@ -50,9 +53,9 @@ Syntax
|
|||||||
*stabilize_steps* value = timesteps
|
*stabilize_steps* value = timesteps
|
||||||
timesteps = number of timesteps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms
|
timesteps = number of timesteps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms
|
||||||
*update_edges* value = *none* or *charges* or *custom*
|
*update_edges* value = *none* or *charges* or *custom*
|
||||||
none = do not update topology near the edges of reaction templates
|
*none* = do not update topology near the edges of reaction templates
|
||||||
charges = update atomic charges of all atoms in reaction templates
|
*charges* = update atomic charges of all atoms in reaction templates
|
||||||
custom = force the update of user-specified atomic charges
|
*custom* = force the update of user-specified atomic charges
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
@ -154,6 +157,13 @@ due to the internal dynamic grouping performed by fix bond/react.
|
|||||||
If the group-ID is an existing static group, react-group-IDs
|
If the group-ID is an existing static group, react-group-IDs
|
||||||
should also be specified as this static group, or a subset.
|
should also be specified as this static group, or a subset.
|
||||||
|
|
||||||
|
The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>`
|
||||||
|
command after a reaction occurs, to ensure that molecule IDs are
|
||||||
|
consistent with the new bond topology. The group-ID used for
|
||||||
|
:doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix.
|
||||||
|
Resetting molecule IDs is necessarily a global operation, and so can
|
||||||
|
be slow for very large systems.
|
||||||
|
|
||||||
The following comments pertain to each *react* argument (in other
|
The following comments pertain to each *react* argument (in other
|
||||||
words, can be customized for each reaction, or reaction step):
|
words, can be customized for each reaction, or reaction step):
|
||||||
|
|
||||||
@ -203,9 +213,10 @@ surrounding topology. As described below, the bonding atom pairs of
|
|||||||
the pre-reacted template are specified by atom ID in the map file. The
|
the pre-reacted template are specified by atom ID in the map file. The
|
||||||
pre-reacted molecule template should contain as few atoms as possible
|
pre-reacted molecule template should contain as few atoms as possible
|
||||||
while still completely describing the topology of all atoms affected
|
while still completely describing the topology of all atoms affected
|
||||||
by the reaction. For example, if the force field contains dihedrals,
|
by the reaction (which includes all atoms that change atom type or
|
||||||
the pre-reacted template should contain any atom within three bonds of
|
connectivity, and all bonds that change bond type). For example, if
|
||||||
reacting atoms.
|
the force field contains dihedrals, the pre-reacted template should
|
||||||
|
contain any atom within three bonds of reacting atoms.
|
||||||
|
|
||||||
Some atoms in the pre-reacted template that are not reacting may have
|
Some atoms in the pre-reacted template that are not reacting may have
|
||||||
missing topology with respect to the simulation. For example, the
|
missing topology with respect to the simulation. For example, the
|
||||||
@ -300,8 +311,8 @@ either 'none' or 'charges.' Further details are provided in the
|
|||||||
discussion of the 'update_edges' keyword. The fifth optional section
|
discussion of the 'update_edges' keyword. The fifth optional section
|
||||||
begins with the keyword 'Constraints' and lists additional criteria
|
begins with the keyword 'Constraints' and lists additional criteria
|
||||||
that must be satisfied in order for the reaction to occur. Currently,
|
that must be satisfied in order for the reaction to occur. Currently,
|
||||||
there are four types of constraints available, as discussed below:
|
there are five types of constraints available, as discussed below:
|
||||||
'distance', 'angle', 'dihedral', and 'arrhenius'.
|
'distance', 'angle', 'dihedral', 'arrhenius', and 'rmsd'.
|
||||||
|
|
||||||
A sample map file is given below:
|
A sample map file is given below:
|
||||||
|
|
||||||
@ -421,6 +432,25 @@ temperature calculations. A uniform random number between 0 and 1 is
|
|||||||
generated using *seed*\ ; if this number is less than the result of the
|
generated using *seed*\ ; if this number is less than the result of the
|
||||||
Arrhenius equation above, the reaction is permitted to occur.
|
Arrhenius equation above, the reaction is permitted to occur.
|
||||||
|
|
||||||
|
The constraint of type 'rmsd' has the following syntax:
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
rmsd *RMSDmax* *molfragment*
|
||||||
|
|
||||||
|
where 'rmsd' is the required keyword, and *RMSDmax* is the maximum
|
||||||
|
root-mean-square deviation between atom positions of the pre-reaction
|
||||||
|
template and the local reaction site (distance units), after optimal
|
||||||
|
translation and rotation of the pre-reaction template. Optionally, the
|
||||||
|
name of a molecule fragment (of the pre-reaction template) can be
|
||||||
|
specified by *molfragment*\ . If a molecule fragment is specified,
|
||||||
|
only atoms that are part of this molecule fragment are used to
|
||||||
|
determine the RMSD. A molecule fragment must have been defined in the
|
||||||
|
:doc:`molecule <molecule>` command for the pre-reaction template. For
|
||||||
|
example, the molecule fragment could consist of only the backbone
|
||||||
|
atoms of a polymer chain. This constraint can be used to enforce a
|
||||||
|
specific relative position and orientation between reacting molecules.
|
||||||
|
|
||||||
Once a reaction site has been successfully identified, data structures
|
Once a reaction site has been successfully identified, data structures
|
||||||
within LAMMPS that store bond topology are updated to reflect the
|
within LAMMPS that store bond topology are updated to reflect the
|
||||||
post-reacted molecule template. All force fields with fixed bonds,
|
post-reacted molecule template. All force fields with fixed bonds,
|
||||||
@ -554,7 +584,7 @@ Default
|
|||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
|
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
|
||||||
update_edges = none
|
reset_mol_ids = yes, update_edges = none
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
|||||||
@ -13,7 +13,7 @@ Syntax
|
|||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
* restrain = style name of this fix command
|
* restrain = style name of this fix command
|
||||||
* one or more keyword/arg pairs may be appended
|
* one or more keyword/arg pairs may be appended
|
||||||
* keyword = *bond* or *angle* or *dihedral*
|
* keyword = *bond* or *lbound* or *angle* or *dihedral*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -23,7 +23,7 @@ Syntax
|
|||||||
r0start = equilibrium bond distance at start of run (distance units)
|
r0start = equilibrium bond distance at start of run (distance units)
|
||||||
r0stop = equilibrium bond distance at end of run (optional) (distance units). If not
|
r0stop = equilibrium bond distance at end of run (optional) (distance units). If not
|
||||||
specified it is assumed to be equal to r0start
|
specified it is assumed to be equal to r0start
|
||||||
*lbond* args = atom1 atom2 Kstart Kstop r0start (r0stop)
|
*lbound* args = atom1 atom2 Kstart Kstop r0start (r0stop)
|
||||||
atom1,atom2 = IDs of 2 atoms in bond
|
atom1,atom2 = IDs of 2 atoms in bond
|
||||||
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
|
||||||
r0start = equilibrium bond distance at start of run (distance units)
|
r0start = equilibrium bond distance at start of run (distance units)
|
||||||
@ -46,7 +46,7 @@ Examples
|
|||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
|
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
|
||||||
fix holdem all restrain lbond 45 48 2000.0 2000.0 2.75
|
fix holdem all restrain lbound 45 48 2000.0 2000.0 2.75
|
||||||
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
|
fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
|
||||||
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
|
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
|
||||||
fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
|
fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
|
||||||
@ -150,7 +150,7 @@ is included in :math:`K`.
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The *lbond* keyword applies a lower bound bond restraint to the specified atoms
|
The *lbound* keyword applies a lower bound bond restraint to the specified atoms
|
||||||
using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command if the distance between
|
using the same functional form used by the :doc:`bond_style harmonic <bond_harmonic>` command if the distance between
|
||||||
the atoms is smaller than the equilibrium bond distance and 0 otherwise. The potential associated with
|
the atoms is smaller than the equilibrium bond distance and 0 otherwise. The potential associated with
|
||||||
the restraint is
|
the restraint is
|
||||||
|
|||||||
@ -110,8 +110,8 @@ location specified. E.g. if the file is specified as "niu3.eam", it
|
|||||||
is looked for in the current working directory. If it is specified as
|
is looked for in the current working directory. If it is specified as
|
||||||
"../potentials/niu3.eam", then it is looked for in the potentials
|
"../potentials/niu3.eam", then it is looked for in the potentials
|
||||||
directory, assuming it is a sister directory of the current working
|
directory, assuming it is a sister directory of the current working
|
||||||
directory. If the file is not found, it is then looked for in the
|
directory. If the file is not found, it is then looked for in one of
|
||||||
directory specified by the LAMMPS_POTENTIALS environment variable.
|
the directories specified by the ``LAMMPS_POTENTIALS`` environment variable.
|
||||||
Thus if this is set to the potentials directory in the LAMMPS distribution,
|
Thus if this is set to the potentials directory in the LAMMPS distribution,
|
||||||
then you can use those files from anywhere on your system, without
|
then you can use those files from anywhere on your system, without
|
||||||
copying them into your working directory. Environment variables are
|
copying them into your working directory. Environment variables are
|
||||||
@ -136,6 +136,11 @@ Windows:
|
|||||||
|
|
||||||
% set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials"
|
% set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials"
|
||||||
|
|
||||||
|
The ``LAMMPS_POTENTIALS`` environment variable may contain paths
|
||||||
|
to multiple folders, if they are separated by ";" on Windows and
|
||||||
|
":" on all other operating systems, just like the ``PATH`` and
|
||||||
|
similar environment variables.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The alphabetic list of pair styles defined in LAMMPS is given on the
|
The alphabetic list of pair styles defined in LAMMPS is given on the
|
||||||
|
|||||||
@ -129,10 +129,10 @@ For style *comb3*\ , in addition to ffield.comb3, a special parameter
|
|||||||
file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be
|
file, *lib.comb3*\ , that is exclusively used for C/O/H systems, will be
|
||||||
automatically loaded if carbon atom is detected in LAMMPS input
|
automatically loaded if carbon atom is detected in LAMMPS input
|
||||||
structure. This file must be in your working directory or in the
|
structure. This file must be in your working directory or in the
|
||||||
directory pointed to by the environment variable LAMMPS_POTENTIALS, as
|
directories listed in the environment variable ``LAMMPS_POTENTIALS``, as
|
||||||
described on the :doc:`pair_coeff <pair_coeff>` command doc page.
|
described on the :doc:`pair_coeff <pair_coeff>` command doc page.
|
||||||
|
|
||||||
Keyword *polar* indicates whether the force field includes
|
The keyword *polar* indicates whether the force field includes
|
||||||
the atomic polarization. Since the equilibration of the polarization
|
the atomic polarization. Since the equilibration of the polarization
|
||||||
has not yet been implemented, it can only set polar_off at present.
|
has not yet been implemented, it can only set polar_off at present.
|
||||||
|
|
||||||
|
|||||||
@ -107,7 +107,7 @@ These pair styles can only be used via the *pair* keyword of the
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
The *cosine/squared* style is part of the "USER-MISC" package. It is only
|
The *cosine/squared* style is part of the USER-MISC package. It is only
|
||||||
enabled if LAMMPS is build with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
enabled if LAMMPS is build with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
|
|||||||
@ -95,7 +95,7 @@ This pair style can only be used via the *pair* keyword of the
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
This style is part of the "USER-MISC" package. It is only enabled if
|
This style is part of the USER-MISC package. It is only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
|
|||||||
@ -95,7 +95,7 @@ Restrictions
|
|||||||
|
|
||||||
The *coul/slater/long* style requires the long-range solvers included in the KSPACE package.
|
The *coul/slater/long* style requires the long-range solvers included in the KSPACE package.
|
||||||
|
|
||||||
These styles are part of the "USER-MISC" package. They are only enabled if
|
These styles are part of the USER-MISC package. They are only enabled if
|
||||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
|
|||||||
@ -164,8 +164,18 @@ heading) the following commands could be included in an input script:
|
|||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
The *gauss/cut* style is part of the "user-misc" package. It is only
|
The *gauss/cut* style is part of the USER-MISC package. It is only
|
||||||
enabled if LAMMPS is build with that package. See the :doc:`Build package <Build_package>` doc page for more info.
|
enabled if LAMMPS is build with that package. See the :doc:`Build
|
||||||
|
package <Build_package>` doc page for more info.
|
||||||
|
|
||||||
|
The *gauss* style does not apply :doc:`special_bonds <special_bonds>`
|
||||||
|
factors. When using this pair style on a system that has bonds, the
|
||||||
|
special_bonds factors, if using the default setting of 0.0, may need to
|
||||||
|
be adjusted to some very small number (e.g. 1.0e-100), so that those
|
||||||
|
special pairs are not completely excluded from the neighbor lists, but
|
||||||
|
won't contribute forces or energies from styles (e.g. when used in
|
||||||
|
combination with a :doc:`hybrid pair style <pair_hybrid>`) that do
|
||||||
|
apply those factors.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -93,7 +93,7 @@ on particle *i* due to contact with particle *j* is given by:
|
|||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{F}_{ne, Hooke} = k_N \delta_{ij} \mathbf{n}
|
\mathbf{F}_{ne, Hooke} = k_n \delta_{ij} \mathbf{n}
|
||||||
|
|
||||||
Where :math:`\delta_{ij} = R_i + R_j - \|\mathbf{r}_{ij}\|` is the particle
|
Where :math:`\delta_{ij} = R_i + R_j - \|\mathbf{r}_{ij}\|` is the particle
|
||||||
overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = \mathbf{r}_i - \mathbf{r}_j` is the vector separating the two
|
overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = \mathbf{r}_i - \mathbf{r}_j` is the vector separating the two
|
||||||
@ -106,7 +106,7 @@ For the *hertz* model, the normal component of force is given by:
|
|||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{F}_{ne, Hertz} = k_N R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}
|
\mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}
|
||||||
|
|
||||||
Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective
|
Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective
|
||||||
radius, denoted for simplicity as *R* from here on. For *hertz*\ , the
|
radius, denoted for simplicity as *R* from here on. For *hertz*\ , the
|
||||||
@ -123,7 +123,7 @@ Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\r
|
|||||||
modulus, with :math:`\nu_i, \nu_j` the Poisson ratios of the particles of
|
modulus, with :math:`\nu_i, \nu_j` the Poisson ratios of the particles of
|
||||||
types *i* and *j*\ . Note that if the elastic modulus and the shear
|
types *i* and *j*\ . Note that if the elastic modulus and the shear
|
||||||
modulus of the two particles are the same, the *hertz/material* model
|
modulus of the two particles are the same, the *hertz/material* model
|
||||||
is equivalent to the *hertz* model with :math:`k_N = 4/3 E_{eff}`
|
is equivalent to the *hertz* model with :math:`k_n = 4/3 E_{eff}`
|
||||||
|
|
||||||
The *dmt* model corresponds to the
|
The *dmt* model corresponds to the
|
||||||
:ref:`(Derjaguin-Muller-Toporov) <DMT1975>` cohesive model, where the force
|
:ref:`(Derjaguin-Muller-Toporov) <DMT1975>` cohesive model, where the force
|
||||||
@ -140,7 +140,7 @@ where the force is computed as:
|
|||||||
|
|
||||||
\mathbf{F}_{ne, jkr} = \left(\frac{4Ea^3}{3R} - 2\pi a^2\sqrt{\frac{4\gamma E}{\pi a}}\right)\mathbf{n}
|
\mathbf{F}_{ne, jkr} = \left(\frac{4Ea^3}{3R} - 2\pi a^2\sqrt{\frac{4\gamma E}{\pi a}}\right)\mathbf{n}
|
||||||
|
|
||||||
Here, *a* is the radius of the contact zone, related to the overlap
|
Here, :math:`a` is the radius of the contact zone, related to the overlap
|
||||||
:math:`\delta` according to:
|
:math:`\delta` according to:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
@ -167,7 +167,7 @@ following general form:
|
|||||||
|
|
||||||
\mathbf{F}_{n,damp} = -\eta_n \mathbf{v}_{n,rel}
|
\mathbf{F}_{n,damp} = -\eta_n \mathbf{v}_{n,rel}
|
||||||
|
|
||||||
Here, :math:`\mathbf{v}_{n,rel} = (\mathbf{v}_j - \mathbf{v}_i) \cdot \mathbf{n} \mathbf{n}` is the component of relative velocity along
|
Here, :math:`\mathbf{v}_{n,rel} = (\mathbf{v}_j - \mathbf{v}_i) \cdot \mathbf{n}\ \mathbf{n}` is the component of relative velocity along
|
||||||
:math:`\mathbf{n}`.
|
:math:`\mathbf{n}`.
|
||||||
|
|
||||||
The optional *damping* keyword to the *pair_coeff* command followed by
|
The optional *damping* keyword to the *pair_coeff* command followed by
|
||||||
@ -259,7 +259,9 @@ tangential model choices and their expected parameters are as follows:
|
|||||||
1. *linear_nohistory* : :math:`x_{\gamma,t}`, :math:`\mu_s`
|
1. *linear_nohistory* : :math:`x_{\gamma,t}`, :math:`\mu_s`
|
||||||
2. *linear_history* : :math:`k_t`, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
2. *linear_history* : :math:`k_t`, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
||||||
3. *mindlin* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
3. *mindlin* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
||||||
4. *mindlin_rescale* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
4. *mindlin/force* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
||||||
|
5. *mindlin_rescale* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
||||||
|
6. *mindlin_rescale/force* : :math:`k_t` or NULL, :math:`x_{\gamma,t}`, :math:`\mu_s`
|
||||||
|
|
||||||
Here, :math:`x_{\gamma,t}` is a dimensionless multiplier for the normal
|
Here, :math:`x_{\gamma,t}` is a dimensionless multiplier for the normal
|
||||||
damping :math:`\eta_n` that determines the magnitude of the tangential
|
damping :math:`\eta_n` that determines the magnitude of the tangential
|
||||||
@ -268,11 +270,11 @@ coefficient, and :math:`k_t` is the tangential stiffness coefficient.
|
|||||||
|
|
||||||
For *tangential linear_nohistory*, a simple velocity-dependent Coulomb
|
For *tangential linear_nohistory*, a simple velocity-dependent Coulomb
|
||||||
friction criterion is used, which mimics the behavior of the *pair
|
friction criterion is used, which mimics the behavior of the *pair
|
||||||
gran/hooke* style. The tangential force (\mathbf{F}_t\) is given by:
|
gran/hooke* style. The tangential force :math:`\mathbf{F}_t` is given by:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{F}_t = -min(\mu_t F_{n0}, \|\mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}
|
\mathbf{F}_t = -\min(\mu_t F_{n0}, \|\mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}
|
||||||
|
|
||||||
The tangential damping force :math:`\mathbf{F}_\mathrm{t,damp}` is given by:
|
The tangential damping force :math:`\mathbf{F}_\mathrm{t,damp}` is given by:
|
||||||
|
|
||||||
@ -294,8 +296,8 @@ keyword also affects the tangential damping. The parameter
|
|||||||
literature use :math:`x_{\gamma,t} = 1` (:ref:`Marshall <Marshall2009>`,
|
literature use :math:`x_{\gamma,t} = 1` (:ref:`Marshall <Marshall2009>`,
|
||||||
:ref:`Tsuji et al <Tsuji1992>`, :ref:`Silbert et al <Silbert2001>`). The relative
|
:ref:`Tsuji et al <Tsuji1992>`, :ref:`Silbert et al <Silbert2001>`). The relative
|
||||||
tangential velocity at the point of contact is given by
|
tangential velocity at the point of contact is given by
|
||||||
:math:`\mathbf{v}_{t, rel} = \mathbf{v}_{t} - (R_i\Omega_i + R_j\Omega_j) \times \mathbf{n}`, where :math:`\mathbf{v}_{t} = \mathbf{v}_r - \mathbf{v}_r\cdot\mathbf{n}{n}`,
|
:math:`\mathbf{v}_{t, rel} = \mathbf{v}_{t} - (R_i\mathbf{\Omega}_i + R_j\mathbf{\Omega}_j) \times \mathbf{n}`, where :math:`\mathbf{v}_{t} = \mathbf{v}_r - \mathbf{v}_r\cdot\mathbf{n}\ \mathbf{n}`,
|
||||||
:math:`\mathbf{v}_r = \mathbf{v}_j - \mathbf{v}_i`.
|
:math:`\mathbf{v}_r = \mathbf{v}_j - \mathbf{v}_i` .
|
||||||
The direction of the applied force is :math:`\mathbf{t} = \mathbf{v_{t,rel}}/\|\mathbf{v_{t,rel}}\|` .
|
The direction of the applied force is :math:`\mathbf{t} = \mathbf{v_{t,rel}}/\|\mathbf{v_{t,rel}}\|` .
|
||||||
|
|
||||||
The normal force value :math:`F_{n0}` used to compute the critical force
|
The normal force value :math:`F_{n0}` used to compute the critical force
|
||||||
@ -314,21 +316,24 @@ form:
|
|||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
F_{n0} = \|\mathbf{F}_ne + 2 F_{pulloff}\|
|
F_{n0} = \|\mathbf{F}_{ne} + 2 F_{pulloff}\|
|
||||||
|
|
||||||
Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*\ , and
|
Where :math:`F_{pulloff} = 3\pi \gamma R` for *jkr*\ , and
|
||||||
:math:`F_{pulloff} = 4\pi \gamma R` for *dmt*\ .
|
:math:`F_{pulloff} = 4\pi \gamma R` for *dmt*\ .
|
||||||
|
|
||||||
The remaining tangential options all use accumulated tangential
|
The remaining tangential options all use accumulated tangential
|
||||||
displacement (i.e. contact history). This is discussed below in the
|
displacement (i.e. contact history), except for the options
|
||||||
context of the *linear_history* option, but the same treatment of the
|
*mindlin/force* and *mindlin_rescale/force*, that use accumulated
|
||||||
accumulated displacement applies to the other options as well.
|
tangential force instead, and are discussed further below.
|
||||||
|
The accumulated tangential displacement is discussed in details below
|
||||||
|
in the context of the *linear_history* option. The same treatment of
|
||||||
|
the accumulated displacement applies to the other options as well.
|
||||||
|
|
||||||
For *tangential linear_history*, the tangential force is given by:
|
For *tangential linear_history*, the tangential force is given by:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{F}_t = -min(\mu_t F_{n0}, \|-k_t\mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}
|
\mathbf{F}_t = -\min(\mu_t F_{n0}, \|-k_t\mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}
|
||||||
|
|
||||||
Here, :math:`\mathbf{\xi}` is the tangential displacement accumulated
|
Here, :math:`\mathbf{\xi}` is the tangential displacement accumulated
|
||||||
during the entire duration of the contact:
|
during the entire duration of the contact:
|
||||||
@ -356,7 +361,7 @@ work:
|
|||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{\xi} = \left(\mathbf{\xi'} - (\mathbf{n} \cdot \mathbf{\xi'})\mathbf{n}\right) \frac{\|\mathbf{\xi'}\|}{\|\mathbf{\xi'}\| - \mathbf{n}\cdot\mathbf{\xi'}}
|
\mathbf{\xi} = \left(\mathbf{\xi'} - (\mathbf{n} \cdot \mathbf{\xi'})\mathbf{n}\right) \frac{\|\mathbf{\xi'}\|}{\|\mathbf{\xi'} - (\mathbf{n}\cdot\mathbf{\xi'})\mathbf{n}\|}
|
||||||
|
|
||||||
Here, :math:`\mathbf{\xi'}` is the accumulated displacement prior to the
|
Here, :math:`\mathbf{\xi'}` is the accumulated displacement prior to the
|
||||||
current time step and :math:`\mathbf{\xi}` is the corrected
|
current time step and :math:`\mathbf{\xi}` is the corrected
|
||||||
@ -372,7 +377,7 @@ discussion):
|
|||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{\xi} = -\frac{1}{k_t}\left(\mu_t F_{n0}\mathbf{t} + \mathbf{F}_{t,damp}\right)
|
\mathbf{\xi} = -\frac{1}{k_t}\left(\mu_t F_{n0}\mathbf{t} - \mathbf{F}_{t,damp}\right)
|
||||||
|
|
||||||
The tangential force is added to the total normal force (elastic plus
|
The tangential force is added to the total normal force (elastic plus
|
||||||
damping) to produce the total force on the particle. The tangential
|
damping) to produce the total force on the particle. The tangential
|
||||||
@ -387,27 +392,68 @@ overlap region) to induce a torque on each particle according to:
|
|||||||
|
|
||||||
\mathbf{\tau}_j = -(R_j - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t
|
\mathbf{\tau}_j = -(R_j - 0.5 \delta) \mathbf{n} \times \mathbf{F}_t
|
||||||
|
|
||||||
For *tangential mindlin*\ , the :ref:`Mindlin <Mindlin1949>` no-slip solution is used, which differs from the *linear_history*
|
For *tangential mindlin*\ , the :ref:`Mindlin <Mindlin1949>` no-slip solution
|
||||||
option by an additional factor of *a*\ , the radius of the contact region. The tangential force is given by:
|
is used which differs from the *linear_history* option by an additional factor
|
||||||
|
of :math:`a`, the radius of the contact region. The tangential force is given by:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{F}_t = -min(\mu_t F_{n0}, \|-k_t a \mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}
|
\mathbf{F}_t = -\min(\mu_t F_{n0}, \|-k_t a \mathbf{\xi} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}
|
||||||
|
|
||||||
Here, *a* is the radius of the contact region, given by :math:`a =\sqrt{R\delta}`
|
|
||||||
|
Here, :math:`a` is the radius of the contact region, given by :math:`a =\sqrt{R\delta}`
|
||||||
for all normal contact models, except for *jkr*\ , where it is given
|
for all normal contact models, except for *jkr*\ , where it is given
|
||||||
implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see
|
implicitly by :math:`\delta = a^2/R - 2\sqrt{\pi \gamma a/E}`, see
|
||||||
discussion above. To match the Mindlin solution, one should set :math:`k_t = 4G/(2-\nu)`, where :math:`G` is the shear modulus, related to Young's modulus
|
discussion above. To match the Mindlin solution, one should set
|
||||||
:math:`E` by :math:`G = E/(2(1+\nu))`, where :math:`\nu` is Poisson's ratio. This
|
:math:`k_t = 8G_{eff}`, where :math:`G_{eff}` is the effective shear modulus given by:
|
||||||
can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
G_{eff} = \left(\frac{2-\nu_i}{G_i} + \frac{2-\nu_j}{G_j}\right)^{-1}
|
||||||
|
|
||||||
|
where :math:`G` is the shear modulus, related to Young's modulus :math:`E`
|
||||||
|
and Poisson's ratio :math:`\nu` by :math:`G = E/(2(1+\nu))`. This can also be
|
||||||
|
achieved by specifying *NULL* for :math:`k_t`, in which case a
|
||||||
normal contact model that specifies material parameters :math:`E` and
|
normal contact model that specifies material parameters :math:`E` and
|
||||||
:math:`\nu` is required (e.g. *hertz/material*\ , *dmt* or *jkr*\ ). In this
|
:math:`\nu` is required (e.g. *hertz/material*\ , *dmt* or *jkr*\ ). In this
|
||||||
case, mixing of the shear modulus for different particle types *i* and
|
case, mixing of the shear modulus for different particle types *i* and
|
||||||
*j* is done according to:
|
*j* is done according to the formula above.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
The radius of the contact region :math:`a` depends on the normal overlap.
|
||||||
|
As a result, the tangential force for *mindlin* can change due to
|
||||||
|
a variation in normal overlap, even with no change in tangential displacement.
|
||||||
|
|
||||||
|
For *tangential mindlin/force*, the accumulated elastic tangential force
|
||||||
|
characterizes the contact history, instead of the accumulated tangential
|
||||||
|
displacement. This prevents the dependence of the tangential force on the
|
||||||
|
normal overlap as noted above. The tangential force is given by:
|
||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
1/G = 2(2-\nu_i)(1+\nu_i)/E_i + 2(2-\nu_j)(1+\nu_j)/E_j
|
\mathbf{F}_t = -\min(\mu_t F_{n0}, \|\mathbf{F}_{te} + \mathbf{F}_\mathrm{t,damp}\|) \mathbf{t}
|
||||||
|
|
||||||
|
The increment of the elastic component of the tangential force
|
||||||
|
:math:`\mathbf{F}_{te}` is given by:
|
||||||
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
\mathrm{d}\mathbf{F}_{te} = -k_t a \mathbf{v}_{t,rel} \mathrm{d}\tau
|
||||||
|
|
||||||
|
The changes in frame of reference of the contacting pair of particles during
|
||||||
|
contact are accounted for by the same formula as above, replacing the
|
||||||
|
accumulated tangential displacement :math:`\xi`, by the accumulated tangential
|
||||||
|
elastic force :math:`F_{te}`. When the tangential force exceeds the critical
|
||||||
|
force, the tangential force is directly re-scaled to match the value for
|
||||||
|
the critical force:
|
||||||
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
\mathbf{F}_{te} = - \mu_t F_{n0}\mathbf{t} + \mathbf{F}_{t,damp}
|
||||||
|
|
||||||
|
The same rules as those described for *mindlin* apply regarding the tangential
|
||||||
|
stiffness and mixing of the shear modulus for different particle types.
|
||||||
|
|
||||||
The *mindlin_rescale* option uses the same form as *mindlin*\ , but the
|
The *mindlin_rescale* option uses the same form as *mindlin*\ , but the
|
||||||
magnitude of the tangential displacement is re-scaled as the contact
|
magnitude of the tangential displacement is re-scaled as the contact
|
||||||
@ -421,9 +467,32 @@ Here, :math:`t_{n-1}` indicates the value at the previous time
|
|||||||
step. This rescaling accounts for the fact that a decrease in the
|
step. This rescaling accounts for the fact that a decrease in the
|
||||||
contact area upon unloading leads to the contact being unable to
|
contact area upon unloading leads to the contact being unable to
|
||||||
support the previous tangential loading, and spurious energy is
|
support the previous tangential loading, and spurious energy is
|
||||||
created without the rescaling above (:ref:`Walton <WaltonPC>` ). See also
|
created without the rescaling above (:ref:`Walton <WaltonPC>` ).
|
||||||
discussion in :ref:`Thornton et al, 2013 <Thornton2013>` , particularly
|
|
||||||
equation 18(b) of that work and associated discussion.
|
.. note::
|
||||||
|
|
||||||
|
For *mindlin*, a decrease in the tangential force already occurs as the
|
||||||
|
contact unloads, due to the dependence of the tangential force on the normal
|
||||||
|
force described above. By re-scaling :math:`\xi`, *mindlin_rescale*
|
||||||
|
effectively re-scales the tangential force twice, i.e., proportionally to
|
||||||
|
:math:`a^2`. This peculiar behavior results from use of the accumulated
|
||||||
|
tangential displacement to characterize the contact history. Although
|
||||||
|
*mindlin_rescale* remains available for historic reasons and backward
|
||||||
|
compatibility purposes, it should be avoided in favor of *mindlin_rescale/force*.
|
||||||
|
|
||||||
|
The *mindlin_rescale/force* option uses the same form as *mindlin/force*,
|
||||||
|
but the magnitude of the tangential elastic force is re-scaled as the contact
|
||||||
|
unloads, i.e. if :math:`a < a_{t_{n-1}}`:
|
||||||
|
|
||||||
|
.. math::
|
||||||
|
|
||||||
|
\mathbf{F}_{te} = \mathbf{F}_{te, t_{n-1}} \frac{a}{a_{t_{n-1}}}
|
||||||
|
|
||||||
|
This approach provides a better approximation of the :ref:`Mindlin-Deresiewicz <Mindlin1953>`
|
||||||
|
laws and is more consistent than *mindlin_rescale*. See discussions in
|
||||||
|
:ref:`Thornton et al, 2013 <Thornton2013>`, particularly equation 18(b) of that
|
||||||
|
work and associated discussion, and :ref:`Agnolin and Roux, 2007 <AgnolinRoux2007>`,
|
||||||
|
particularly Appendix A.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -460,7 +529,7 @@ exceeds a critical value:
|
|||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\mathbf{F}_{roll} = min(\mu_{roll} F_{n,0}, \|\mathbf{F}_{roll,0}\|)\mathbf{k}
|
\mathbf{F}_{roll} = \min(\mu_{roll} F_{n,0}, \|\mathbf{F}_{roll,0}\|)\mathbf{k}
|
||||||
|
|
||||||
Here, :math:`\mathbf{k} = \mathbf{v}_{roll}/\|\mathbf{v}_{roll}\|` is the direction of
|
Here, :math:`\mathbf{k} = \mathbf{v}_{roll}/\|\mathbf{v}_{roll}\|` is the direction of
|
||||||
the pseudo-force. As with tangential displacement, the rolling
|
the pseudo-force. As with tangential displacement, the rolling
|
||||||
@ -512,7 +581,7 @@ is then truncated according to:
|
|||||||
|
|
||||||
.. math::
|
.. math::
|
||||||
|
|
||||||
\tau_{twist} = min(\mu_{twist} F_{n,0}, \tau_{twist,0})
|
\tau_{twist} = \min(\mu_{twist} F_{n,0}, \tau_{twist,0})
|
||||||
|
|
||||||
Similar to the sliding and rolling displacement, the angular
|
Similar to the sliding and rolling displacement, the angular
|
||||||
displacement is rescaled so that it corresponds to the critical value
|
displacement is rescaled so that it corresponds to the critical value
|
||||||
@ -763,3 +832,15 @@ Technology, 233, 30-46.
|
|||||||
.. _WaltonPC:
|
.. _WaltonPC:
|
||||||
|
|
||||||
**(Otis R. Walton)** Walton, O.R., Personal Communication
|
**(Otis R. Walton)** Walton, O.R., Personal Communication
|
||||||
|
|
||||||
|
.. _Mindlin1953:
|
||||||
|
|
||||||
|
**(Mindlin and Deresiewicz, 1953)** Mindlin, R.D., & Deresiewicz, H (1953).
|
||||||
|
Elastic Spheres in Contact under Varying Oblique Force.
|
||||||
|
J. Appl. Mech., ASME 20, 327-344.
|
||||||
|
|
||||||
|
.. _AgnolinRoux2007:
|
||||||
|
|
||||||
|
**(Agnolin and Roux 2007)** Agnolin, I. & Roux, J-N. (2007).
|
||||||
|
Internal states of model isotropic granular packings.
|
||||||
|
I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
|
||||||
|
|||||||
@ -250,8 +250,12 @@ from :ref:`(Li2013_POF) <Li2013_POF>`. The short mDPD run (about 2 minutes
|
|||||||
on a single core) generates a particle trajectory which can
|
on a single core) generates a particle trajectory which can
|
||||||
be visualized as follows.
|
be visualized as follows.
|
||||||
|
|
||||||
|
.. only:: html
|
||||||
|
|
||||||
|
.. image:: JPG/examples_mdpd.gif
|
||||||
|
:align: center
|
||||||
|
|
||||||
.. image:: JPG/examples_mdpd_first.jpg
|
.. image:: JPG/examples_mdpd_first.jpg
|
||||||
:target: JPG/examples_mdpd.gif
|
|
||||||
:align: center
|
:align: center
|
||||||
|
|
||||||
.. image:: JPG/examples_mdpd_last.jpg
|
.. image:: JPG/examples_mdpd_last.jpg
|
||||||
|
|||||||
@ -128,7 +128,7 @@ viscoelastic relaxation parameter and time constant,
|
|||||||
respectively. m_lambdai varies within zero to one. For very small
|
respectively. m_lambdai varies within zero to one. For very small
|
||||||
values of m_lambdai the viscoelastic model responds very similar to a
|
values of m_lambdai the viscoelastic model responds very similar to a
|
||||||
linear elastic model. For details please see the description in
|
linear elastic model. For details please see the description in
|
||||||
"(Mtchell2011)".
|
"(Mitchell2011)".
|
||||||
|
|
||||||
For the *peri/eps* style:
|
For the *peri/eps* style:
|
||||||
|
|
||||||
@ -142,7 +142,7 @@ For the *peri/eps* style:
|
|||||||
K is the bulk modulus and G is the shear modulus. The horizon is a
|
K is the bulk modulus and G is the shear modulus. The horizon is a
|
||||||
cutoff distance and s00 and :math:`\alpha` are used as a bond breaking
|
cutoff distance and s00 and :math:`\alpha` are used as a bond breaking
|
||||||
criteria. m_yield_stress is the yield stress of the material. For
|
criteria. m_yield_stress is the yield stress of the material. For
|
||||||
details please see the description in "(Mtchell2011a)".
|
details please see the description in "(Mitchell2011a)".
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
|||||||
@ -38,12 +38,12 @@ corresponding compiled code. This penalty can be significantly reduced
|
|||||||
through generating tabulations from the python code through the
|
through generating tabulations from the python code through the
|
||||||
:doc:`pair_write <pair_write>` command, which is supported by this style.
|
:doc:`pair_write <pair_write>` command, which is supported by this style.
|
||||||
|
|
||||||
Only a single pair_coeff command is used with the *python* pair style
|
Only a single :doc:`pair_coeff <pair_coeff>` command is used with the
|
||||||
which specifies a python class inside a python module or file that
|
*python* pair style which specifies a python class inside a python module
|
||||||
LAMMPS will look up in the current directory, the folder pointed to by
|
or a file that LAMMPS will look up in the current directory, a folder
|
||||||
the LAMMPS_POTENTIALS environment variable or somewhere in your python
|
pointed to by the ``LAMMPS_POTENTIALS`` environment variable or somewhere
|
||||||
path. A single python module can hold multiple python pair class
|
in your python path. A single python module can hold multiple python pair
|
||||||
definitions. The class definitions itself have to follow specific
|
class definitions. The class definitions itself have to follow specific
|
||||||
rules that are explained below.
|
rules that are explained below.
|
||||||
|
|
||||||
Atom types in the python class are specified through symbolic
|
Atom types in the python class are specified through symbolic
|
||||||
|
|||||||
91
doc/src/pg_cplusplus.rst
Normal file
91
doc/src/pg_cplusplus.rst
Normal file
@ -0,0 +1,91 @@
|
|||||||
|
Using the C++ API directly
|
||||||
|
**************************
|
||||||
|
|
||||||
|
Using the C++ classes of the LAMMPS library is lacking some of the
|
||||||
|
convenience of the C library API, but it allows a more direct access to
|
||||||
|
simulation data and thus more low-level manipulations and tighter
|
||||||
|
integration of LAMMPS into another code. While for the complete C
|
||||||
|
library API is provided in the ``library.h`` header file, for using
|
||||||
|
the C++ API it is required to include the individual header files
|
||||||
|
defining the individual classes in use. Typically the name of the
|
||||||
|
class and the name of the header follow some simple rule. Examples
|
||||||
|
are given below.
|
||||||
|
|
||||||
|
|
||||||
|
Creating or deleting a LAMMPS object
|
||||||
|
*************************************
|
||||||
|
|
||||||
|
When using the LAMMPS library interfaces, the core task is to create an
|
||||||
|
instance of the :cpp:class:`LAMMPS_NS::LAMMPS` class. In C++ this can
|
||||||
|
be done directly through the ``new`` operator. All further operations
|
||||||
|
are then initiated through calling member functions of some of the
|
||||||
|
components of the LAMMPS class or accessing their data members. The
|
||||||
|
destruction of the LAMMPS instance is correspondingly initiated by using
|
||||||
|
the ``delete`` operator. Here is a simple example:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
#include "lammps.h"
|
||||||
|
#include "universe.h"
|
||||||
|
|
||||||
|
#include <mpi.h>
|
||||||
|
#include <iostream>
|
||||||
|
|
||||||
|
int main(int argc, char **argv)
|
||||||
|
{
|
||||||
|
LAMMPS_NS::LAMMPS *lmp;
|
||||||
|
// custom argument vector for LAMMPS library
|
||||||
|
const char *lmpargv[] {"liblammps", "-log", "none"};
|
||||||
|
int lmpargc = sizeof(lmpargv)/sizeof(const char *);
|
||||||
|
|
||||||
|
// explicitly initialize MPI
|
||||||
|
MPI_Init(&argc, &argv);
|
||||||
|
|
||||||
|
// create LAMMPS instance
|
||||||
|
lmp = new LAMMPS_NS::LAMMPS(lmpargc, (char **)lmpargv, MPI_COMM_WORLD);
|
||||||
|
// output numerical version string
|
||||||
|
std::cout << "LAMMPS version: " << lmp->universe->num_ver << std::endl;
|
||||||
|
// delete LAMMPS instance
|
||||||
|
delete lmp;
|
||||||
|
|
||||||
|
// stop MPI environment
|
||||||
|
MPI_Finalize();
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
Please note that this requires to include the ``lammps.h`` header for accessing
|
||||||
|
the members of the LAMMPS class and then the ``universe.h`` header for accessing the ``num_ver`` member of the :cpp:class:`Universe` class.
|
||||||
|
|
||||||
|
|
||||||
|
Executing LAMMPS commands
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Once a LAMMPS instance is created by your C++ code, you need to set up a
|
||||||
|
simulation and that is most conveniently done by "driving" it through
|
||||||
|
issuing commands like you would do when running a LAMMPS simulation from
|
||||||
|
an input script. Processing of input in LAMMPS is handled by the
|
||||||
|
:cpp:class:`Input <LAMMPS_NS::Input>` class an instance of which is a
|
||||||
|
member of the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class. You have
|
||||||
|
two options: reading commands from a file, or executing a single
|
||||||
|
command from a string. See below for a small example:
|
||||||
|
|
||||||
|
.. code-block:: c++
|
||||||
|
|
||||||
|
#include "lammps.h"
|
||||||
|
#include "input.h"
|
||||||
|
#include <mpi.h>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
int main(int argc, char **argv)
|
||||||
|
{
|
||||||
|
const char *lmpargv[] {"liblammps", "-log", "none"};
|
||||||
|
int lmpargc = sizeof(lmpargv)/sizeof(const char *);
|
||||||
|
|
||||||
|
MPI_Init(&argc, &argv);
|
||||||
|
LAMMPS *lmp = new LAMMPS(lmpargc, (char **)lmpargv, MPI_COMM_WORLD);
|
||||||
|
lmp->input->file("in.melt");
|
||||||
|
lmp->input->one("run 100 post no");
|
||||||
|
delete lmp;
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
1088
doc/src/pg_developer.rst
Normal file
1088
doc/src/pg_developer.rst
Normal file
File diff suppressed because it is too large
Load Diff
202
doc/src/pg_fortran.rst
Normal file
202
doc/src/pg_fortran.rst
Normal file
@ -0,0 +1,202 @@
|
|||||||
|
The ``LIBLAMMPS`` Fortran Module
|
||||||
|
********************************
|
||||||
|
|
||||||
|
The ``LIBLAMMPS`` module provides an interface to call LAMMPS from a
|
||||||
|
Fortran code. It is based on the LAMMPS C-library interface and
|
||||||
|
requires a Fortran 2003 compatible compiler to be compiled.
|
||||||
|
|
||||||
|
While C libraries have a defined binary interface (ABI) and can thus be
|
||||||
|
used from multiple compiler versions from different vendors for as long
|
||||||
|
as they are compatible with the hosting operating system, the same is
|
||||||
|
not true for Fortran codes. Thus the LAMMPS Fortran module needs to be
|
||||||
|
compiled alongside the code using it from the source code in
|
||||||
|
``fortran/lammps.f90``. When linking, you also need to
|
||||||
|
:doc:`link to the LAMMPS library <Build_link>`. A typical command line
|
||||||
|
for a simple program using the Fortran interface would be:
|
||||||
|
|
||||||
|
.. code-block:: bash
|
||||||
|
|
||||||
|
mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
|
||||||
|
|
||||||
|
Please note, that the MPI compiler wrapper is only required when the
|
||||||
|
calling the library from an MPI parallel code. Please also note the order
|
||||||
|
of the source files: the lammps.f90 file needs to be compiled first,
|
||||||
|
since it provides the ``LIBLAMMPS`` module that is imported by the
|
||||||
|
Fortran code using the interface.
|
||||||
|
|
||||||
|
.. versionadded:: 30Sep2020
|
||||||
|
|
||||||
|
.. admonition:: Work in Progress
|
||||||
|
|
||||||
|
This Fortran module is work in progress and only the documented
|
||||||
|
functionality is currently available. The final implementation should
|
||||||
|
cover the entire range of functionality available in the C and
|
||||||
|
Python library interfaces.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Creating or deleting a LAMMPS object
|
||||||
|
************************************
|
||||||
|
|
||||||
|
With the Fortran interface the creation of a :cpp:class:`LAMMPS
|
||||||
|
<LAMMPS_NS::LAMMPS>` instance is included in the constructor for
|
||||||
|
creating the :f:func:`lammps` derived type. To import the definition of
|
||||||
|
that type and its type bound procedures you need to add a ``USE
|
||||||
|
LIBLAMMPS`` statement. Internally it will call either
|
||||||
|
:cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
|
||||||
|
the C library API to create the class instance. All arguments are
|
||||||
|
optional and :cpp:func:`lammps_mpi_init` will be called automatically,
|
||||||
|
if it is needed. Similarly, a possible call to :cpp:func:`lammps_finalize`
|
||||||
|
is integrated into the :f:func:`close` function and triggered with
|
||||||
|
the optional logical argument set to ``.true.``. Here is a simple example:
|
||||||
|
|
||||||
|
.. code-block:: fortran
|
||||||
|
|
||||||
|
PROGRAM testlib
|
||||||
|
USE LIBLAMMPS ! include the LAMMPS library interface
|
||||||
|
TYPE(lammps) :: lmp ! derived type to hold LAMMPS instance
|
||||||
|
CHARACTER(len=*), DIMENSION(*), PARAMETER :: args = &
|
||||||
|
[ CHARACTER(len=12) :: 'liblammps', '-log', 'none' ]
|
||||||
|
|
||||||
|
! create a LAMMPS instance (and initialize MPI)
|
||||||
|
lmp = lammps(args)
|
||||||
|
! get and print numerical version code
|
||||||
|
PRINT*, 'LAMMPS Version: ', lmp%version()
|
||||||
|
! delete LAMMPS instance (and shuts down MPI)
|
||||||
|
CALL lmp%close(.true.)
|
||||||
|
|
||||||
|
END PROGRAM testlib
|
||||||
|
|
||||||
|
--------------------
|
||||||
|
|
||||||
|
Executing LAMMPS commands
|
||||||
|
=========================
|
||||||
|
|
||||||
|
Once a LAMMPS instance is created, it is possible to "drive" the LAMMPS
|
||||||
|
simulation by telling LAMMPS to read commands from a file, or pass
|
||||||
|
individual or multiple commands from strings or lists of strings. This
|
||||||
|
is done similar to how it is implemented in the `C-library
|
||||||
|
<pg_lib_execute>` interface. Before handing off the calls to the
|
||||||
|
C-library interface, the corresponding Fortran versions of the calls
|
||||||
|
(:f:func:`file`, :f:func:`command`, :f:func:`commands_list`, and
|
||||||
|
:f:func:`commands_string`) have to make a copy of the strings passed as
|
||||||
|
arguments so that they can be modified to be compatible with the
|
||||||
|
requirements of strings in C without affecting the original strings.
|
||||||
|
Those copies are automatically deleted after the functions return.
|
||||||
|
Below is a small demonstration of the uses of the different functions:
|
||||||
|
|
||||||
|
.. code-block:: fortran
|
||||||
|
|
||||||
|
PROGRAM testcmd
|
||||||
|
USE LIBLAMMPS
|
||||||
|
TYPE(lammps) :: lmp
|
||||||
|
CHARACTER(len=512) :: cmds
|
||||||
|
CHARACTER(len=40),ALLOCATABLE :: cmdlist(:)
|
||||||
|
CHARACTER(len=10) :: trimmed
|
||||||
|
INTEGER :: i
|
||||||
|
|
||||||
|
lmp = lammps()
|
||||||
|
CALL lmp%file('in.melt')
|
||||||
|
CALL lmp%command('variable zpos index 1.0')
|
||||||
|
! define 10 groups of 10 atoms each
|
||||||
|
ALLOCATE(cmdlist(10))
|
||||||
|
DO i=1,10
|
||||||
|
WRITE(trimmed,'(I10)') 10*i
|
||||||
|
WRITE(cmdlist(i),'(A,I1,A,I10,A,A)') &
|
||||||
|
'group g',i-1,' id ',10*(i-1)+1,':',ADJUSTL(trimmed)
|
||||||
|
END DO
|
||||||
|
CALL lmp%commands_list(cmdlist)
|
||||||
|
! run multiple commands from multi-line string
|
||||||
|
cmds = 'clear' // NEW_LINE('A') // &
|
||||||
|
'region box block 0 2 0 2 0 2' // NEW_LINE('A') // &
|
||||||
|
'create_box 1 box' // NEW_LINE('A') // &
|
||||||
|
'create_atoms 1 single 1.0 1.0 ${zpos}'
|
||||||
|
CALL lmp%commands_string(cmds)
|
||||||
|
CALL lmp%close()
|
||||||
|
|
||||||
|
END PROGRAM testcmd
|
||||||
|
|
||||||
|
---------------
|
||||||
|
|
||||||
|
The ``LIBLAMMPS`` module API
|
||||||
|
****************************
|
||||||
|
|
||||||
|
Below are the detailed descriptions of definitions and interfaces
|
||||||
|
of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
|
||||||
|
|
||||||
|
.. f:type:: lammps
|
||||||
|
|
||||||
|
Derived type that is the general class of the Fortran interface.
|
||||||
|
It holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance
|
||||||
|
that any of the included calls are forwarded to.
|
||||||
|
|
||||||
|
:f c_ptr handle: reference to the LAMMPS class
|
||||||
|
:f close: :f:func:`close`
|
||||||
|
:f version: :f:func:`version`
|
||||||
|
:f file: :f:func:`file`
|
||||||
|
:f command: :f:func:`command`
|
||||||
|
:f commands_list: :f:func:`commands_list`
|
||||||
|
:f commands_string: :f:func:`commands_string`
|
||||||
|
|
||||||
|
.. f:function:: lammps(args[,comm])
|
||||||
|
|
||||||
|
This is the constructor for the Fortran class and will forward
|
||||||
|
the arguments to a call to either :cpp:func:`lammps_open_fortran`
|
||||||
|
or :cpp:func:`lammps_open_no_mpi`. If the LAMMPS library has been
|
||||||
|
compiled with MPI support, it will also initialize MPI, if it has
|
||||||
|
not already been initialized before.
|
||||||
|
|
||||||
|
The *args* argument with the list of command line parameters is
|
||||||
|
optional and so it the *comm* argument with the MPI communicator.
|
||||||
|
If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For
|
||||||
|
more details please see the documentation of :cpp:func:`lammps_open`.
|
||||||
|
|
||||||
|
:p character(len=*) args(*) [optional]: arguments as list of strings
|
||||||
|
:o integer comm [optional]: MPI communicator
|
||||||
|
:r lammps: an instance of the :f:type:`lammps` derived type
|
||||||
|
|
||||||
|
.. f:subroutine:: close([finalize])
|
||||||
|
|
||||||
|
This method will close down the LAMMPS instance through calling
|
||||||
|
:cpp:func:`lammps_close`. If the *finalize* argument is present and
|
||||||
|
has a value of ``.true.``, then this subroutine also calls
|
||||||
|
:cpp:func:`lammps_mpi_finalize`.
|
||||||
|
|
||||||
|
:o logical finalize [optional]: shut down the MPI environment of the LAMMPS library if true.
|
||||||
|
|
||||||
|
.. f:function:: version()
|
||||||
|
|
||||||
|
This method returns the numeric LAMMPS version like :cpp:func:`lammps_version`
|
||||||
|
|
||||||
|
:r integer: LAMMPS version
|
||||||
|
|
||||||
|
--------
|
||||||
|
|
||||||
|
.. f:subroutine:: file(filename)
|
||||||
|
|
||||||
|
This method will call :cpp:func:`lammps_file` to have LAMMPS read
|
||||||
|
and process commands from a file.
|
||||||
|
|
||||||
|
:p character(len=*) filename: name of file with LAMMPS commands
|
||||||
|
|
||||||
|
.. f:subroutine:: command(cmd)
|
||||||
|
|
||||||
|
This method will call :cpp:func:`lammps_command` to have LAMMPS
|
||||||
|
execute a single command.
|
||||||
|
|
||||||
|
:p character(len=*) cmd: single LAMMPS command
|
||||||
|
|
||||||
|
.. f:subroutine:: commands_list(cmds)
|
||||||
|
|
||||||
|
This method will call :cpp:func:`lammps_commands_list` to have LAMMPS
|
||||||
|
execute a list of input lines.
|
||||||
|
|
||||||
|
:p character(len=*) cmd(*): list of LAMMPS input lines
|
||||||
|
|
||||||
|
.. f:subroutine:: commands_string(str)
|
||||||
|
|
||||||
|
This method will call :cpp:func:`lammps_commands_string` to have LAMMPS
|
||||||
|
execute a block of commands from a string.
|
||||||
|
|
||||||
|
:p character(len=*) str: LAMMPS input in string
|
||||||
|
|
||||||
33
doc/src/pg_lib_add.rst
Normal file
33
doc/src/pg_lib_add.rst
Normal file
@ -0,0 +1,33 @@
|
|||||||
|
Adding code to the Library interface
|
||||||
|
====================================
|
||||||
|
|
||||||
|
The functionality of the LAMMPS library interface has historically
|
||||||
|
always been motivated by the needs of its users and functions were
|
||||||
|
added or expanded as they were needed and used. Contributions to
|
||||||
|
the interface are always welcome. However with a refactoring of
|
||||||
|
the library interface and its documentation that started in 2020,
|
||||||
|
there are now a few requirements for inclusion of changes.
|
||||||
|
|
||||||
|
- New functions should be orthogonal to existing ones and not
|
||||||
|
implement functionality that can already be achieved with the
|
||||||
|
existing APIs.
|
||||||
|
- All changes and additions should be documented with
|
||||||
|
`Doxygen <https://doxgygen.org>`_ style comments and references
|
||||||
|
to those functions added to the corresponding files in the
|
||||||
|
``doc/src`` folder.
|
||||||
|
- If possible, new unit tests to test those new features should
|
||||||
|
be added.
|
||||||
|
- The new feature should also be implemented and documented for
|
||||||
|
the Python and Fortran modules.
|
||||||
|
- All additions should work and be compatible with ``-DLAMMPS_BIGBIG``,
|
||||||
|
``-DLAMMPS_SMALLBIG``, ``-DLAMMPS_SMALLSMALL`` and compiling
|
||||||
|
with and without MPI support.
|
||||||
|
- The ``library.h`` file should be kept compatible to C code at
|
||||||
|
a level similar to C89. Its interfaces may not reference any
|
||||||
|
custom data types (e.g. ``bigint``, ``tagint``, and so on) only
|
||||||
|
known inside of LAMMPS.
|
||||||
|
- only C style comments, not C++ style
|
||||||
|
|
||||||
|
Please note, that these are *not* *strict* requirements, but the
|
||||||
|
LAMMPS developers appreciate if they are followed closely and will
|
||||||
|
assist with implementing what is missing.
|
||||||
67
doc/src/pg_lib_config.rst
Normal file
67
doc/src/pg_lib_config.rst
Normal file
@ -0,0 +1,67 @@
|
|||||||
|
Retrieving LAMMPS configuration information
|
||||||
|
===========================================
|
||||||
|
|
||||||
|
The following library functions can be used to query the
|
||||||
|
LAMMPS library about compile time settings and included
|
||||||
|
packages and styles.
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_has_mpi_support
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_has_gzip_support
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_has_png_support
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_has_jpeg_support
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_has_ffmpeg_support
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_has_exceptions
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_has_package
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_package_count
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_config_package_name
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_has_style
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_style_count
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_style_name
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
104
doc/src/pg_lib_create.rst
Normal file
104
doc/src/pg_lib_create.rst
Normal file
@ -0,0 +1,104 @@
|
|||||||
|
Creating or deleting a LAMMPS object
|
||||||
|
====================================
|
||||||
|
|
||||||
|
The :cpp:func:`lammps_open` and :cpp:func:`lammps_open_no_mpi`
|
||||||
|
functions are used to create and initialize a
|
||||||
|
:cpp:func:`LAMMPS` instance. The calling program has to
|
||||||
|
provide a handle where a reference to this instance can be stored and
|
||||||
|
which has to be used in all subsequent function calls until that
|
||||||
|
instance is destroyed by calling :cpp:func:`lammps_close`.
|
||||||
|
Here is a simple example demonstrating its use:
|
||||||
|
|
||||||
|
.. code-block:: C
|
||||||
|
|
||||||
|
#include "library.h"
|
||||||
|
#include <stdio.h>
|
||||||
|
|
||||||
|
int main(int argc, char **argv)
|
||||||
|
{
|
||||||
|
void *handle;
|
||||||
|
int version;
|
||||||
|
const char *lmpargv[] = { "liblammps", "-log", "none"};
|
||||||
|
int lmpargc = sizeof(lmpargv)/sizeof(const char *);
|
||||||
|
|
||||||
|
/* create LAMMPS instance */
|
||||||
|
handle = lammps_open_no_mpi(lmpargc, lmpargv, NULL);
|
||||||
|
if (handle == NULL) {
|
||||||
|
printf("LAMMPS initialization failed");
|
||||||
|
lammps_mpi_finalize();
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* get and print numerical version code */
|
||||||
|
version = lammps_version(handle);
|
||||||
|
printf("LAMMPS Version: %d\n",version);
|
||||||
|
|
||||||
|
/* delete LAMMPS instance and shut down MPI */
|
||||||
|
lammps_close(handle);
|
||||||
|
lammps_mpi_finalize();
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
The LAMMPS library will be using the MPI library it was compiled with
|
||||||
|
and will either run on all processors in the ``MPI_COMM_WORLD``
|
||||||
|
communicator or on the set of processors in the communicator given in
|
||||||
|
the ``comm`` argument of :cpp:func:`lammps_open`. This means
|
||||||
|
the calling code can run LAMMPS on all or a subset of processors. For
|
||||||
|
example, a wrapper code might decide to alternate between LAMMPS and
|
||||||
|
another code, allowing them both to run on all the processors. Or it
|
||||||
|
might allocate part of the processors to LAMMPS and the rest to the
|
||||||
|
other code by creating a custom communicator with ``MPI_Comm_split()``
|
||||||
|
and running both codes concurrently before syncing them up periodically.
|
||||||
|
Or it might instantiate multiple instances of LAMMPS to perform
|
||||||
|
different calculations and either alternate between them, run them
|
||||||
|
concurrently on split communicators, or run them one after the other.
|
||||||
|
The :cpp:func:`lammps_open` function may be called multiple
|
||||||
|
times for this latter purpose.
|
||||||
|
|
||||||
|
The :cpp:func:`lammps_close` function is used to shut down
|
||||||
|
the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class pointed to by the handle
|
||||||
|
passed as an argument and free all its memory. This has to be called for
|
||||||
|
every instance created with any of the :cpp:func:`lammps_open` functions. It will, however, **not** call
|
||||||
|
``MPI_Finalize()``, since that may only be called once. See
|
||||||
|
:cpp:func:`lammps_mpi_finalize` for an alternative to calling
|
||||||
|
``MPI_Finalize()`` explicitly in the calling program.
|
||||||
|
|
||||||
|
The :cpp:func:`lammps_free` function is a clean-up
|
||||||
|
function to free memory that the library allocated previously
|
||||||
|
via other function calls. See below for notes in the descriptions
|
||||||
|
of the individual commands where such memory buffers were allocated.
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_open
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_open_no_mpi
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_open_fortran
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_close
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_mpi_init
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_mpi_finalize
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_free
|
||||||
|
:project: progguide
|
||||||
69
doc/src/pg_lib_execute.rst
Normal file
69
doc/src/pg_lib_execute.rst
Normal file
@ -0,0 +1,69 @@
|
|||||||
|
Executing LAMMPS commands
|
||||||
|
=========================
|
||||||
|
|
||||||
|
Once a LAMMPS instance is created, there are multiple ways to "drive" a
|
||||||
|
simulation. In most cases it is easiest to process single or multiple
|
||||||
|
LAMMPS commands like in an input file. This can be done through reading
|
||||||
|
a file or passing single commands or lists of commands or blocks of
|
||||||
|
commands with the following functions.
|
||||||
|
|
||||||
|
Via these functions, the calling code can have the LAMMPS instance act
|
||||||
|
on a series of :doc:`input file commands <Commands_all>` that are either
|
||||||
|
read from a file or passed as strings. This for, for example, allows to
|
||||||
|
setup a problem from a template file and then run it in stages while
|
||||||
|
performing other operations in between or concurrently. The caller can
|
||||||
|
interleave the LAMMPS function calls with operations it performs, calls
|
||||||
|
to extract information from or set information within LAMMPS, or calls
|
||||||
|
to another code's library.
|
||||||
|
|
||||||
|
Also equivalent to regular :doc:`input script parsing <Commands_parse>`
|
||||||
|
is the handling of comments and expansion of variables with ``${name}``
|
||||||
|
or ``$(expression)`` syntax before the commands are parsed and
|
||||||
|
executed. Below is a short example using some of these functions.
|
||||||
|
|
||||||
|
.. code-block:: C
|
||||||
|
|
||||||
|
#include "library.h"
|
||||||
|
#include <mpi.h>
|
||||||
|
#include <stdio.h>
|
||||||
|
|
||||||
|
int main(int argc, char **argv)
|
||||||
|
{
|
||||||
|
void *handle;
|
||||||
|
int i;
|
||||||
|
|
||||||
|
MPI_Init(&argc, &argv);
|
||||||
|
handle = lammps_open(0, NULL, MPI_COMM_WORLD, NULL);
|
||||||
|
lammps_file(handle,"in.sysinit");
|
||||||
|
lammps_command(handle,"run 1000 post no");
|
||||||
|
|
||||||
|
for (i=0; i < 100; ++i) {
|
||||||
|
lammps_commands_string(handle,"run 100 pre no post no\n"
|
||||||
|
"print 'PE = $(pe)'\n"
|
||||||
|
"print 'KE = $(ke)'\n");
|
||||||
|
}
|
||||||
|
lammps_close(handle);
|
||||||
|
MPI_Finalize();
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_file
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_command
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_commands_list
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_commands_string
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
30
doc/src/pg_lib_neighbor.rst
Normal file
30
doc/src/pg_lib_neighbor.rst
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
Accessing LAMMPS Neighbor lists
|
||||||
|
===============================
|
||||||
|
|
||||||
|
The following functions allow to access neighbor lists
|
||||||
|
generated by LAMMPS or query their properties.
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_find_compute_neighlist
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_find_fix_neighlist
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_find_pair_neighlist
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_neighlist_num_elements
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_neighlist_element_neighbors
|
||||||
|
:project: progguide
|
||||||
31
doc/src/pg_lib_objects.rst
Normal file
31
doc/src/pg_lib_objects.rst
Normal file
@ -0,0 +1,31 @@
|
|||||||
|
Retrieving or setting properties of LAMMPS objects
|
||||||
|
==================================================
|
||||||
|
|
||||||
|
This section documents accessing or modifying data from objects like
|
||||||
|
computes, fixes, or variables in LAMMPS.
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_extract_compute
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_extract_fix
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_extract_variable
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_set_variable
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenenum:: _LMP_STYLE_CONST
|
||||||
|
|
||||||
|
.. doxygenenum:: _LMP_TYPE_CONST
|
||||||
62
doc/src/pg_lib_properties.rst
Normal file
62
doc/src/pg_lib_properties.rst
Normal file
@ -0,0 +1,62 @@
|
|||||||
|
Retrieving or setting LAMMPS system properties
|
||||||
|
==============================================
|
||||||
|
|
||||||
|
The library interface allows to extract different kinds of information
|
||||||
|
about the active simulation instance and also to modify some of them.
|
||||||
|
This allows to combine MD simulation steps with other processing and
|
||||||
|
simulation methods computed in the calling code or another code that is
|
||||||
|
coupled to LAMMPS via the library interface. In some cases the data
|
||||||
|
returned is direct reference to the original data inside LAMMPS cast
|
||||||
|
to a void pointer. In that case the data needs to be cast to a suitable
|
||||||
|
pointer to be able to access it, and you need to know the correct dimensions
|
||||||
|
and lengths. When accessing per-atom data, please note that this data
|
||||||
|
is the per-processor **local** data and indexed accordingly. These arrays
|
||||||
|
can change sizes and order at every neighbor list rebuild and atom sort
|
||||||
|
event as atoms are migrating between sub-domains.
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_version
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_get_natoms
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_get_thermo
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_extract_box
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_reset_box
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_extract_setting
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_extract_global
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_extract_atom
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_create_atoms(void *handle, int n, int *id, int *type, double *x, double *v, int *image, int bexpand)
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
|
||||||
29
doc/src/pg_lib_scatter.rst
Normal file
29
doc/src/pg_lib_scatter.rst
Normal file
@ -0,0 +1,29 @@
|
|||||||
|
Library functions for scatter/gather operations
|
||||||
|
================================================
|
||||||
|
|
||||||
|
.. TODO add description
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_gather_atoms
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_gather_atoms_concat
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_gather_atoms_subset
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_scatter_atoms
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_scatter_atoms_subset
|
||||||
|
:project: progguide
|
||||||
30
doc/src/pg_lib_utility.rst
Normal file
30
doc/src/pg_lib_utility.rst
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
Library interface utility functions
|
||||||
|
===================================
|
||||||
|
|
||||||
|
To simplify some of the tasks, the library interface contains
|
||||||
|
some utility functions that are not directly calling LAMMPS.
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_encode_image_flags
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_decode_image_flags(int image, int *flags)
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_set_fix_external_callback(void *, char *, FixExternalFnPtr, void*)
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_has_error
|
||||||
|
:project: progguide
|
||||||
|
|
||||||
|
-----------------------
|
||||||
|
|
||||||
|
.. doxygenfunction:: lammps_get_last_error_message
|
||||||
|
:project: progguide
|
||||||
158
doc/src/pg_library.rst
Normal file
158
doc/src/pg_library.rst
Normal file
@ -0,0 +1,158 @@
|
|||||||
|
LAMMPS Library Interfaces
|
||||||
|
*************************
|
||||||
|
|
||||||
|
As described on the :doc:`library interface to LAMMPS <Howto_library>`
|
||||||
|
doc page, LAMMPS can be built as a library (static or shared), so that
|
||||||
|
it can be called by another code, used in a :doc:`coupled manner
|
||||||
|
<Howto_couple>` with other codes, or driven through a :doc:`Python
|
||||||
|
script <Python_head>`. Even the LAMMPS standalone executable is
|
||||||
|
essentially a thin wrapper on top of the LAMMPS library, creating a
|
||||||
|
LAMMPS instance, processing input and then existing.
|
||||||
|
|
||||||
|
Several of these approaches are based on C language wrapper functions
|
||||||
|
in the files ``src/library.h`` and ``src/library.cpp``, but it is also
|
||||||
|
possible to use C++ directly. The basic procedure is always the same:
|
||||||
|
you create one or more instances of the
|
||||||
|
:cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` and then pass commands as
|
||||||
|
strings or from files to that LAMMPS instance to execute calculations,
|
||||||
|
or read, manipulate, and update data from the active class instances
|
||||||
|
inside the LAMMPS to do analysis or perform operations that are not
|
||||||
|
possible with existing commands.
|
||||||
|
|
||||||
|
.. _thread-safety:
|
||||||
|
|
||||||
|
.. admonition:: Thread-safety
|
||||||
|
:class: note
|
||||||
|
|
||||||
|
LAMMPS was initially not conceived as a thread-safe program, but over
|
||||||
|
the years changes have been applied to replace operations that
|
||||||
|
collide with creating multiple LAMMPS instances from multiple-threads
|
||||||
|
of the same process with thread-safe alternatives. This primarily
|
||||||
|
applies to the core LAMMPS code and less so on add-on packages,
|
||||||
|
especially when those packages require additional code in the *lib*
|
||||||
|
folder, interface LAMMPS to Fortran libraries, or the code uses
|
||||||
|
static variables (like the USER-COLVARS package).
|
||||||
|
|
||||||
|
Another major issue to deal with is to correctly handle MPI.
|
||||||
|
Creating a LAMMPS instance requires passing an MPI communicator, or
|
||||||
|
it assumes the ``MPI_COMM_WORLD`` communicator, which spans all MPI
|
||||||
|
processor ranks. When creating multiple LAMMPS object instances from
|
||||||
|
different threads, this communicator has to be different for each
|
||||||
|
thread or else collisions can happen. or it has to be guaranteed,
|
||||||
|
that only one thread at a time is active. MPI communicators,
|
||||||
|
however, are not a problem, if LAMMPS is compiled with the MPI STUBS
|
||||||
|
library, which implies that there is no MPI communication and only 1
|
||||||
|
MPI rank.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
.. _lammps_c_api:
|
||||||
|
|
||||||
|
LAMMPS C Library API
|
||||||
|
====================
|
||||||
|
|
||||||
|
The C library interface is most commonly used path to manage LAMMPS
|
||||||
|
instances from a compiled code and it is the basis for the :doc:`Python
|
||||||
|
<pg_python>` and :doc:`Fortran <pg_fortran>` modules. Almost all
|
||||||
|
functions of the C language API require an argument containing a
|
||||||
|
"handle" in the form of a ``void *`` type variable, which points to the
|
||||||
|
location of a LAMMPS class instance.
|
||||||
|
|
||||||
|
The ``library.h`` header file by default includes the ``mpi.h`` header
|
||||||
|
for an MPI library, so it must be present when compiling code using the
|
||||||
|
library interface. This usually must be the header from the same MPI
|
||||||
|
library as the LAMMPS library was compiled with. The exception is when
|
||||||
|
LAMMPS was compiled in serial mode using the ``STUBS`` MPI library. In
|
||||||
|
that case the calling code may be compiled with a different MPI library
|
||||||
|
for as long as :cpp:func:`lammps_open_no_mpi` is called to create a
|
||||||
|
LAMMPS instance. Then you may set the define ``-DLAMMPS_LIB_NO_MPI``
|
||||||
|
when compiling your code and the inclusion of ``mpi.h`` will be skipped
|
||||||
|
and consequently the function :cpp:func:`lammps_open` may not be used.
|
||||||
|
|
||||||
|
.. admonition:: Errors versus exceptions
|
||||||
|
:class: note
|
||||||
|
|
||||||
|
If any of the function calls in the LAMMPS library API will trigger
|
||||||
|
an error inside LAMMPS, this will result in an abort of the entire
|
||||||
|
program. This is not always desirable. Instead, LAMMPS can be
|
||||||
|
compiled to instead :ref:`throw a C++ exception <exceptions>`.
|
||||||
|
|
||||||
|
.. warning::
|
||||||
|
|
||||||
|
No checks are made on the arguments of the function calls of the C
|
||||||
|
library interface. *All* function arguments must be non-NULL unless
|
||||||
|
*explicitly* allowed and point to consistent and valid data. Buffers
|
||||||
|
for storing returned data must be allocated to a suitable size.
|
||||||
|
Passing invalid or unsuitable information will likely cause crashes
|
||||||
|
or corrupt data.
|
||||||
|
|
||||||
|
------------------------------
|
||||||
|
|
||||||
|
.. toctree::
|
||||||
|
:maxdepth: 1
|
||||||
|
|
||||||
|
pg_lib_create
|
||||||
|
pg_lib_execute
|
||||||
|
pg_lib_properties
|
||||||
|
pg_lib_objects
|
||||||
|
pg_lib_scatter
|
||||||
|
pg_lib_neighbor
|
||||||
|
pg_lib_config
|
||||||
|
pg_lib_utility
|
||||||
|
pg_lib_add
|
||||||
|
|
||||||
|
--------------------
|
||||||
|
|
||||||
|
.. _lammps_python_api:
|
||||||
|
|
||||||
|
LAMMPS Python APIs
|
||||||
|
==================
|
||||||
|
|
||||||
|
The LAMMPS Python module enables calling the LAMMPS C library API from
|
||||||
|
Python by dynamically loading functions in the LAMMPS shared library through
|
||||||
|
the `Python ctypes module <https://docs.python.org/3/library/ctypes.html>`_.
|
||||||
|
Because of the dynamic loading, it is **required** that LAMMPS is compiled
|
||||||
|
in :ref:`"shared" mode <exe>`. The Python interface is object oriented, but
|
||||||
|
otherwise trying to be very similar to the C library API. Three different
|
||||||
|
Python classes to run LAMMPS are available and they build on each other.
|
||||||
|
|
||||||
|
.. toctree::
|
||||||
|
:maxdepth: 1
|
||||||
|
|
||||||
|
pg_python
|
||||||
|
|
||||||
|
-------------------
|
||||||
|
|
||||||
|
.. _lammps_fortran_api:
|
||||||
|
|
||||||
|
LAMMPS Fortran API
|
||||||
|
==================
|
||||||
|
|
||||||
|
The LAMMPS Fortran module is a wrapper around calling functions from the
|
||||||
|
LAMMPS C library API from Fortran through the ISO_C_BINDING feature in
|
||||||
|
Fortran 2003. The interface is object oriented but otherwise trying to
|
||||||
|
be very similar to the C library API and the basic Python module.
|
||||||
|
|
||||||
|
.. toctree::
|
||||||
|
:maxdepth: 1
|
||||||
|
|
||||||
|
pg_fortran
|
||||||
|
|
||||||
|
-------------------
|
||||||
|
|
||||||
|
.. _lammps_cplusplus_api:
|
||||||
|
|
||||||
|
LAMMPS C++ API
|
||||||
|
==============
|
||||||
|
|
||||||
|
It is also possible to invoke the LAMMPS C++ API directly in your code.
|
||||||
|
It is lacking some of the convenience of the C library API, but it allows
|
||||||
|
a more direct access to simulation data and thus more low-level manipulations.
|
||||||
|
The following links provide some examples and references to the C++ API.
|
||||||
|
|
||||||
|
.. toctree::
|
||||||
|
:maxdepth: 1
|
||||||
|
|
||||||
|
pg_cplusplus
|
||||||
|
|
||||||
|
|
||||||
188
doc/src/pg_python.rst
Normal file
188
doc/src/pg_python.rst
Normal file
@ -0,0 +1,188 @@
|
|||||||
|
The ``lammps`` Python module
|
||||||
|
****************************
|
||||||
|
|
||||||
|
.. py:module:: lammps
|
||||||
|
|
||||||
|
The LAMMPS Python interface is implemented as a module called
|
||||||
|
:py:mod:`lammps` in the ``lammps.py`` file in the ``python`` folder of
|
||||||
|
the LAMMPS source code distribution. After compilation of LAMMPS, the
|
||||||
|
module can be installed into a Python system folder or a user folder
|
||||||
|
with ``make install-python``. Components of the module can then loaded
|
||||||
|
into a Python session with the ``import`` command.
|
||||||
|
|
||||||
|
There are multiple Python interface classes in the :py:mod:`lammps` module:
|
||||||
|
|
||||||
|
- the :py:class:`lammps <lammps.lammps>` class. This is a wrapper around
|
||||||
|
the C-library interface and its member functions try to replicate the
|
||||||
|
:doc:`C-library API <pg_library>` closely. This is the most
|
||||||
|
feature-complete Python API.
|
||||||
|
- the :py:class:`PyLammps <lammps.PyLammps>` class. This is a more high-level
|
||||||
|
and more Python style class implemented on top of the
|
||||||
|
:py:class:`lammps <lammps.lammps>` class.
|
||||||
|
- the :py:class:`IPyLammps <lammps.IPyLammps>` class is derived from
|
||||||
|
:py:class:`PyLammps <lammps.PyLammps>` and adds embedded graphics
|
||||||
|
features to conveniently include LAMMPS into `Jupyter
|
||||||
|
<https://jupyter.org/>`_ notebooks.
|
||||||
|
|
||||||
|
.. _mpi4py_url: https://mpi4py.readthedocs.io
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Creating or deleting a LAMMPS object
|
||||||
|
************************************
|
||||||
|
|
||||||
|
With the Python interface the creation of a :cpp:class:`LAMMPS
|
||||||
|
<LAMMPS_NS::LAMMPS>` instance is included in the constructor for the
|
||||||
|
:py:func:`lammps <lammps.lammps>` class. Internally it will call either
|
||||||
|
:cpp:func:`lammps_open` or :cpp:func:`lammps_open_no_mpi` from the C
|
||||||
|
library API to create the class instance.
|
||||||
|
|
||||||
|
All arguments are optional. The *name* argument is to allow loading a
|
||||||
|
LAMMPS shared library that is named ``liblammps_machine.so`` instead of
|
||||||
|
the default name of ``liblammps.so``. In most cases the latter will be
|
||||||
|
installed or used. The *ptr* argument is for use of the
|
||||||
|
:py:mod:`lammps` module from inside a LAMMPS instance, e.g. with the
|
||||||
|
:doc:`python <python>` command, where a pointer to the already existing
|
||||||
|
:cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance can be passed
|
||||||
|
to the Python class and used instead of creating a new instance. The
|
||||||
|
*comm* argument may be used in combination with the `mpi4py <mpi4py_url_>`_
|
||||||
|
module to pass an MPI communicator to LAMMPS and thus it is possible
|
||||||
|
to run the Python module like the library interface on a subset of the
|
||||||
|
MPI ranks after splitting the communicator. Here is a simple example:
|
||||||
|
|
||||||
|
.. code-block:: python
|
||||||
|
|
||||||
|
from lammps import lammps
|
||||||
|
|
||||||
|
# NOTE: argv[0] is set by the Python module
|
||||||
|
args = ["-log", "none"]
|
||||||
|
# create LAMMPS instance
|
||||||
|
lmp = lammps(cmdargs=args)
|
||||||
|
# get and print numerical version code
|
||||||
|
print("LAMMPS Version: ", lmp.version())
|
||||||
|
# explicitly close and delete LAMMPS instance (optional)
|
||||||
|
lmp.close()
|
||||||
|
|
||||||
|
Same as with the :doc:`C library API <pg_lib_create>` this will use the
|
||||||
|
``MPI_COMM_WORLD`` communicator for the MPI library that LAMMPS was
|
||||||
|
compiled with. The :py:func:`lmp.close() <lammps.lammps.close>` call is
|
||||||
|
optional since the LAMMPS class instance will also be deleted
|
||||||
|
automatically during the :py:class:`lammps <lammps.lammps>` class
|
||||||
|
destructor.
|
||||||
|
|
||||||
|
Executing LAMMPS commands
|
||||||
|
*************************
|
||||||
|
|
||||||
|
Once an instance of the :py:class:`lammps <lammps.lammps>` class is
|
||||||
|
created, there are multiple ways to "feed" it commands. In a way that is
|
||||||
|
not very different from running a LAMMPS input script, except that
|
||||||
|
Python has many more facilities for structured programming than the
|
||||||
|
LAMMPS input script syntax. Furthermore it is possible to "compute"
|
||||||
|
what the next LAMMPS command should be. Same as in the equivalent `C
|
||||||
|
library functions <pg_lib_execute>`, commands can be read from a file, a
|
||||||
|
single string, a list of strings and a block of commands in a single
|
||||||
|
multi-line string. They are processed under the same boundary conditions
|
||||||
|
as the C library counterparts. The example below demonstrates the use
|
||||||
|
of :py:func:`lammps.file`, :py:func:`lammps.command`,
|
||||||
|
:py:func:`lammps.commands_list`, and :py:func:`lammps.commands_string`:
|
||||||
|
|
||||||
|
.. code-block:: python
|
||||||
|
|
||||||
|
from lammps import lammps
|
||||||
|
|
||||||
|
lmp = lammps()
|
||||||
|
# read commands from file 'in.melt'
|
||||||
|
lmp.file('in.melt')
|
||||||
|
# issue a single command
|
||||||
|
lmp.command('variable zpos index 1.0')
|
||||||
|
# create 10 groups with 10 atoms each
|
||||||
|
cmds = ["group g{} id {}:{}".format(i,10*i+1,10*(i+1)) for i in range(10)]
|
||||||
|
lmp.commands_list(cmds)
|
||||||
|
# run commands from a multi-line string
|
||||||
|
block = """
|
||||||
|
clear
|
||||||
|
region box block 0 2 0 2 0 2
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 single 1.0 1.0 ${zpos}
|
||||||
|
"""
|
||||||
|
lmp.commands_string(block)
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The ``lammps`` class API
|
||||||
|
************************
|
||||||
|
|
||||||
|
The :py:class:`lammps <lammps.lammps>` class is the core of the LAMMPS
|
||||||
|
Python interfaces. It is a wrapper around the :doc:`LAMMPS C library
|
||||||
|
API <pg_library>` using the `Python ctypes module
|
||||||
|
<https://docs.python.org/3/library/ctypes.html>`_ and a shared library
|
||||||
|
compiled from the LAMMPS sources code. The individual methods in this
|
||||||
|
class try to closely follow the corresponding C functions. The handle
|
||||||
|
argument that needs to be passed to the C functions is stored internally
|
||||||
|
in the class and automatically added when calling the C library
|
||||||
|
functions. Below is a detailed documentation of the API.
|
||||||
|
|
||||||
|
.. autoclass:: lammps.lammps
|
||||||
|
:members:
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The ``PyLammps`` class API
|
||||||
|
**************************
|
||||||
|
|
||||||
|
.. autoclass:: lammps.PyLammps
|
||||||
|
:members:
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The ``IPyLammps`` class API
|
||||||
|
***************************
|
||||||
|
|
||||||
|
.. autoclass:: lammps.IPyLammps
|
||||||
|
:members:
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Additional components of the ``lammps`` module
|
||||||
|
**********************************************
|
||||||
|
|
||||||
|
The :py:mod:`lammps` module additionally contains several constants
|
||||||
|
and the :py:class:`NeighList <lammps.NeighList>` class:
|
||||||
|
|
||||||
|
.. _py_data_constants:
|
||||||
|
.. py:data:: LAMMPS_INT, LAMMPS_DOUBLE, LAMMPS_BIGINT, LAMMPS_TAGINT, LAMMPS_STRING
|
||||||
|
:type: int
|
||||||
|
|
||||||
|
Constants in the :py:mod:`lammps` module to indicate how to
|
||||||
|
cast data when the C library function returns a void pointer.
|
||||||
|
Used in :py:func:`lammps.extract_global`.
|
||||||
|
|
||||||
|
.. _py_style_constants:
|
||||||
|
.. py:data:: LMP_STYLE_GLOBAL, LMP_STYLE_ATOM, LMP_STYLE_LOCAL
|
||||||
|
:type: int
|
||||||
|
|
||||||
|
Constants in the :py:mod:`lammps` module to select what style of data
|
||||||
|
to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST`
|
||||||
|
for the equivalent constants in the C library interface. Used in
|
||||||
|
:py:func:`lammps.extract_compute` and :py:func:`lammps.extract_fix`.
|
||||||
|
|
||||||
|
.. _py_type_constants:
|
||||||
|
.. py:data:: LMP_TYPE_SCALAR, LMP_TYLE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
|
||||||
|
:type: int
|
||||||
|
|
||||||
|
Constants in the :py:mod:`lammps` module to select what type of data
|
||||||
|
to request from computes or fixes. See :cpp:enum:`_LMP_TYPE_CONST`
|
||||||
|
for the equivalent constants in the C library interface. Used in
|
||||||
|
:py:func:`lammps.extract_compute` and :py:func:`lammps.extract_fix`.
|
||||||
|
|
||||||
|
.. _py_var_constants:
|
||||||
|
.. py:data:: LMP_VAR_EQUAL, LMP_VAR_ATOM
|
||||||
|
:type: int
|
||||||
|
|
||||||
|
Constants in the :py:mod:`lammps` module to select what style of
|
||||||
|
variable to query when calling :py:func:`lammps.extract_variable`.
|
||||||
|
|
||||||
|
.. autoclass:: lammps.NeighList
|
||||||
|
:members:
|
||||||
|
:no-undoc-members:
|
||||||
|
|
||||||
@ -1 +1,5 @@
|
|||||||
Sphinx
|
Sphinx
|
||||||
|
sphinxcontrib-spelling
|
||||||
|
sphinx-fortran
|
||||||
|
breathe
|
||||||
|
Pygments
|
||||||
|
|||||||
@ -7,3 +7,10 @@
|
|||||||
display: block;
|
display: block;
|
||||||
margin-bottom: 0.809em;
|
margin-bottom: 0.809em;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.lammps_release {
|
||||||
|
text-align: center;
|
||||||
|
font-size: 11px;
|
||||||
|
display: block;
|
||||||
|
margin-bottom: 0.405em;
|
||||||
|
}
|
||||||
|
|||||||
|
Before Width: | Height: | Size: 16 KiB After Width: | Height: | Size: 16 KiB |
@ -103,6 +103,12 @@
|
|||||||
{%- endif %}
|
{%- endif %}
|
||||||
{%- endblock %}
|
{%- endblock %}
|
||||||
{%- block extrahead %} {% endblock %}
|
{%- block extrahead %} {% endblock %}
|
||||||
|
|
||||||
|
{# Keep modernizr in head - http://modernizr.com/docs/#installing #}
|
||||||
|
<script src="{{ pathto('_static/js/modernizr.min.js', 1) }}"></script>
|
||||||
|
|
||||||
|
{# for improved browser compatibility #}
|
||||||
|
<script src="{{ pathto('_static/polyfill.js', 1) }}"></script>
|
||||||
</head>
|
</head>
|
||||||
|
|
||||||
<body class="wy-body-for-nav">
|
<body class="wy-body-for-nav">
|
||||||
@ -135,9 +141,8 @@
|
|||||||
{%- set nav_version = current_version %}
|
{%- set nav_version = current_version %}
|
||||||
{% endif %}
|
{% endif %}
|
||||||
{% if nav_version %}
|
{% if nav_version %}
|
||||||
<div class="version">
|
<div class="lammps_version">Version: <b>{{ nav_version }}</b></div>
|
||||||
{{ nav_version }}
|
<div class="lammps_release">git info: {{ release }}</div>
|
||||||
</div>
|
|
||||||
{% endif %}
|
{% endif %}
|
||||||
{% endif %}
|
{% endif %}
|
||||||
|
|
||||||
|
|||||||
@ -23,11 +23,16 @@ try:
|
|||||||
except:
|
except:
|
||||||
pass
|
pass
|
||||||
|
|
||||||
|
LAMMPS_DOC_DIR = '@LAMMPS_DOC_DIR@'
|
||||||
|
LAMMPS_SOURCE_DIR = '@LAMMPS_SOURCE_DIR@'
|
||||||
|
LAMMPS_PYTHON_DIR = '@LAMMPS_PYTHON_DIR@'
|
||||||
|
LAMMPS_DOXYGEN_XML_DIR = '@DOXYGEN_XML_DIR@'
|
||||||
|
|
||||||
# If extensions (or modules to document with autodoc) are in another directory,
|
# If extensions (or modules to document with autodoc) are in another directory,
|
||||||
# add these directories to sys.path here. If the directory is relative to the
|
# add these directories to sys.path here. If the directory is relative to the
|
||||||
# documentation root, use os.path.abspath to make it absolute, like shown here.
|
# documentation root, use os.path.abspath to make it absolute, like shown here.
|
||||||
#sys.path.insert(0, os.path.abspath('.'))
|
#sys.path.insert(0, os.path.abspath('.'))
|
||||||
sys.path.append(os.path.join(os.path.dirname(__file__), '../../src/_ext'))
|
sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'src', '_ext'))
|
||||||
|
|
||||||
# -- General configuration ------------------------------------------------
|
# -- General configuration ------------------------------------------------
|
||||||
|
|
||||||
@ -41,7 +46,9 @@ extensions = [
|
|||||||
'sphinx.ext.mathjax',
|
'sphinx.ext.mathjax',
|
||||||
'sphinx.ext.imgmath',
|
'sphinx.ext.imgmath',
|
||||||
'sphinx.ext.autodoc',
|
'sphinx.ext.autodoc',
|
||||||
|
'sphinxfortran.fortran_domain',
|
||||||
'table_from_list',
|
'table_from_list',
|
||||||
|
'breathe',
|
||||||
]
|
]
|
||||||
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
|
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
|
||||||
# yet we can no longer use Sphinx 15.x, since that breaks with
|
# yet we can no longer use Sphinx 15.x, since that breaks with
|
||||||
@ -72,12 +79,24 @@ copyright = '2003-2020 Sandia Corporation'
|
|||||||
def get_lammps_version():
|
def get_lammps_version():
|
||||||
import os
|
import os
|
||||||
script_dir = os.path.dirname(os.path.realpath(__file__))
|
script_dir = os.path.dirname(os.path.realpath(__file__))
|
||||||
with open(os.path.join(script_dir, '../../../src/version.h'), 'r') as f:
|
with open(os.path.join(LAMMPS_SOURCE_DIR, 'version.h'), 'r') as f:
|
||||||
line = f.readline()
|
line = f.readline()
|
||||||
start_pos = line.find('"')+1
|
start_pos = line.find('"')+1
|
||||||
end_pos = line.find('"', start_pos)
|
end_pos = line.find('"', start_pos)
|
||||||
return line[start_pos:end_pos]
|
return line[start_pos:end_pos]
|
||||||
|
|
||||||
|
def get_git_info():
|
||||||
|
import subprocess,time
|
||||||
|
|
||||||
|
git_n_date = ''
|
||||||
|
try:
|
||||||
|
gitinfo = subprocess.run(['git','describe'],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
|
||||||
|
if gitinfo.returncode == 0:
|
||||||
|
git_n_date = gitinfo.stdout.decode().replace('_',' ')
|
||||||
|
except:
|
||||||
|
pass
|
||||||
|
return git_n_date
|
||||||
|
|
||||||
# The version info for the project you're documenting, acts as replacement for
|
# The version info for the project you're documenting, acts as replacement for
|
||||||
# |version| and |release|, also used in various other places throughout the
|
# |version| and |release|, also used in various other places throughout the
|
||||||
# built documents.
|
# built documents.
|
||||||
@ -85,7 +104,7 @@ def get_lammps_version():
|
|||||||
# The short X.Y version.
|
# The short X.Y version.
|
||||||
version = get_lammps_version()
|
version = get_lammps_version()
|
||||||
# The full version, including alpha/beta/rc tags.
|
# The full version, including alpha/beta/rc tags.
|
||||||
release = ''
|
release = get_git_info()
|
||||||
|
|
||||||
# The language for content autogenerated by Sphinx. Refer to documentation
|
# The language for content autogenerated by Sphinx. Refer to documentation
|
||||||
# for a list of supported languages.
|
# for a list of supported languages.
|
||||||
@ -153,7 +172,7 @@ html_title = "LAMMPS documentation"
|
|||||||
|
|
||||||
# The name of an image file (relative to this directory) to place at the top
|
# The name of an image file (relative to this directory) to place at the top
|
||||||
# of the sidebar.
|
# of the sidebar.
|
||||||
html_logo = 'lammps-logo.png'
|
html_logo = '_static/lammps-logo.png'
|
||||||
|
|
||||||
# The name of an image file (within the static path) to use as favicon of the
|
# The name of an image file (within the static path) to use as favicon of the
|
||||||
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
|
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
|
||||||
@ -314,7 +333,7 @@ texinfo_documents = [
|
|||||||
|
|
||||||
epub_title = 'LAMMPS Documentation - ' + get_lammps_version()
|
epub_title = 'LAMMPS Documentation - ' + get_lammps_version()
|
||||||
|
|
||||||
epub_cover = ('lammps-logo.png', '')
|
epub_cover = ('_static/lammps-logo.png', '')
|
||||||
|
|
||||||
epub_description = """
|
epub_description = """
|
||||||
This is the Manual for the LAMMPS software package.
|
This is the Manual for the LAMMPS software package.
|
||||||
@ -342,13 +361,29 @@ if spelling_spec and has_enchant:
|
|||||||
spelling_lang='en_US'
|
spelling_lang='en_US'
|
||||||
spelling_word_list_filename='false_positives.txt'
|
spelling_word_list_filename='false_positives.txt'
|
||||||
|
|
||||||
sys.path.append(os.path.join(os.path.dirname(__file__), '.'))
|
conf_script_dir = os.path.dirname(os.path.realpath(__file__))
|
||||||
|
sys.path.append(os.path.join(conf_script_dir, '.'))
|
||||||
import LAMMPSLexer
|
import LAMMPSLexer
|
||||||
from sphinx.highlighting import lexers
|
from sphinx.highlighting import lexers
|
||||||
|
|
||||||
lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
|
lexers['LAMMPS'] = LAMMPSLexer.LAMMPSLexer(startinline=True)
|
||||||
|
|
||||||
sys.path.append(os.path.join(os.path.dirname(__file__), '../../../python'))
|
sys.path.append(LAMMPS_PYTHON_DIR)
|
||||||
|
|
||||||
# avoid syntax highlighting in blocks that don't specify language
|
# avoid syntax highlighting in blocks that don't specify language
|
||||||
highlight_language = 'none'
|
highlight_language = 'none'
|
||||||
|
|
||||||
|
# autodoc configuration
|
||||||
|
|
||||||
|
autodoc_member_order = 'bysource'
|
||||||
|
#autoclass_content = 'both'
|
||||||
|
|
||||||
|
# breathe configuration
|
||||||
|
|
||||||
|
breathe_projects = { 'progguide' : LAMMPS_DOXYGEN_XML_DIR }
|
||||||
|
breathe_default_project = 'progguide'
|
||||||
|
breathe_show_define_initializer = True
|
||||||
|
breathe_domain_by_extension = { 'h' : 'cpp',
|
||||||
|
'cpp' : 'cpp',
|
||||||
|
'c' : 'c',
|
||||||
|
}
|
||||||
@ -43,6 +43,7 @@ Afshar
|
|||||||
agilio
|
agilio
|
||||||
Agilio
|
Agilio
|
||||||
agni
|
agni
|
||||||
|
Agnolin
|
||||||
Ai
|
Ai
|
||||||
Aidan
|
Aidan
|
||||||
aij
|
aij
|
||||||
@ -114,6 +115,7 @@ Archlinux
|
|||||||
arcsin
|
arcsin
|
||||||
arg
|
arg
|
||||||
args
|
args
|
||||||
|
argv
|
||||||
arrhenius
|
arrhenius
|
||||||
Arun
|
Arun
|
||||||
arXiv
|
arXiv
|
||||||
@ -137,6 +139,8 @@ atc
|
|||||||
AtC
|
AtC
|
||||||
ATC
|
ATC
|
||||||
athermal
|
athermal
|
||||||
|
atime
|
||||||
|
atimestep
|
||||||
athomps
|
athomps
|
||||||
atm
|
atm
|
||||||
atomeye
|
atomeye
|
||||||
@ -206,7 +210,6 @@ bcolor
|
|||||||
bdiam
|
bdiam
|
||||||
bdw
|
bdw
|
||||||
Beckman
|
Beckman
|
||||||
behaviour
|
|
||||||
Belak
|
Belak
|
||||||
Bellott
|
Bellott
|
||||||
benchmarking
|
benchmarking
|
||||||
@ -247,6 +250,7 @@ bispectrum
|
|||||||
Bispectrum
|
Bispectrum
|
||||||
bitbucket
|
bitbucket
|
||||||
bitmapped
|
bitmapped
|
||||||
|
bitmask
|
||||||
bitrate
|
bitrate
|
||||||
bitrates
|
bitrates
|
||||||
Bitzek
|
Bitzek
|
||||||
@ -265,6 +269,7 @@ bodystyle
|
|||||||
Bogaerts
|
Bogaerts
|
||||||
Bogusz
|
Bogusz
|
||||||
Bohrs
|
Bohrs
|
||||||
|
boltz
|
||||||
Boltzman
|
Boltzman
|
||||||
BondAngle
|
BondAngle
|
||||||
BondBond
|
BondBond
|
||||||
@ -283,6 +288,14 @@ Botu
|
|||||||
Bouguet
|
Bouguet
|
||||||
Bourne
|
Bourne
|
||||||
boxcolor
|
boxcolor
|
||||||
|
boxlo
|
||||||
|
boxhi
|
||||||
|
boxxlo
|
||||||
|
boxxhi
|
||||||
|
boxylo
|
||||||
|
boxyhi
|
||||||
|
boxzlo
|
||||||
|
boxzhi
|
||||||
bp
|
bp
|
||||||
bpclermont
|
bpclermont
|
||||||
bpls
|
bpls
|
||||||
@ -301,6 +314,7 @@ Bryantsev
|
|||||||
Btarget
|
Btarget
|
||||||
btype
|
btype
|
||||||
buckPlusAttr
|
buckPlusAttr
|
||||||
|
buf
|
||||||
builtin
|
builtin
|
||||||
Bulatov
|
Bulatov
|
||||||
Bureekaew
|
Bureekaew
|
||||||
@ -369,6 +383,7 @@ charmm
|
|||||||
CHARMM
|
CHARMM
|
||||||
charmmfsh
|
charmmfsh
|
||||||
charmmfsw
|
charmmfsw
|
||||||
|
charptr
|
||||||
Chaudhuri
|
Chaudhuri
|
||||||
checkbox
|
checkbox
|
||||||
checkmark
|
checkmark
|
||||||
@ -407,6 +422,7 @@ cmap
|
|||||||
Cmax
|
Cmax
|
||||||
cmd
|
cmd
|
||||||
cmdlist
|
cmdlist
|
||||||
|
cmds
|
||||||
Cmin
|
Cmin
|
||||||
cmm
|
cmm
|
||||||
CMM
|
CMM
|
||||||
@ -436,6 +452,7 @@ Colvars
|
|||||||
COLVARS
|
COLVARS
|
||||||
comID
|
comID
|
||||||
Commun
|
Commun
|
||||||
|
compositing
|
||||||
compressibility
|
compressibility
|
||||||
compressive
|
compressive
|
||||||
Comput
|
Comput
|
||||||
@ -584,6 +601,7 @@ del
|
|||||||
delaystep
|
delaystep
|
||||||
DeleteIDs
|
DeleteIDs
|
||||||
deleteIDs
|
deleteIDs
|
||||||
|
delflag
|
||||||
Dellago
|
Dellago
|
||||||
delocalization
|
delocalization
|
||||||
delocalized
|
delocalized
|
||||||
@ -599,6 +617,7 @@ Dequidt
|
|||||||
der
|
der
|
||||||
dereference
|
dereference
|
||||||
derekt
|
derekt
|
||||||
|
Deresiewicz
|
||||||
Derjagin
|
Derjagin
|
||||||
Derjaguin
|
Derjaguin
|
||||||
Derlet
|
Derlet
|
||||||
@ -668,6 +687,8 @@ Donadio
|
|||||||
dotc
|
dotc
|
||||||
Doty
|
Doty
|
||||||
doxygen
|
doxygen
|
||||||
|
doxygenclass
|
||||||
|
doxygenfunction
|
||||||
downarrow
|
downarrow
|
||||||
Doye
|
Doye
|
||||||
dpd
|
dpd
|
||||||
@ -721,6 +742,7 @@ Eaat
|
|||||||
Eacn
|
Eacn
|
||||||
eam
|
eam
|
||||||
eangle
|
eangle
|
||||||
|
earg
|
||||||
eatom
|
eatom
|
||||||
Eb
|
Eb
|
||||||
Eba
|
Eba
|
||||||
@ -841,6 +863,7 @@ Erhart
|
|||||||
erorate
|
erorate
|
||||||
erose
|
erose
|
||||||
erotate
|
erotate
|
||||||
|
errno
|
||||||
Ertas
|
Ertas
|
||||||
ervel
|
ervel
|
||||||
Espanol
|
Espanol
|
||||||
@ -899,6 +922,7 @@ Fc
|
|||||||
fcc
|
fcc
|
||||||
fcm
|
fcm
|
||||||
Fd
|
Fd
|
||||||
|
fd
|
||||||
fdotr
|
fdotr
|
||||||
fdt
|
fdt
|
||||||
Fehlberg
|
Fehlberg
|
||||||
@ -923,6 +947,7 @@ ffplay
|
|||||||
fft
|
fft
|
||||||
fftbench
|
fftbench
|
||||||
fftw
|
fftw
|
||||||
|
fgets
|
||||||
fhg
|
fhg
|
||||||
Fi
|
Fi
|
||||||
Fichthorn
|
Fichthorn
|
||||||
@ -958,6 +983,7 @@ fmackay
|
|||||||
fmag
|
fmag
|
||||||
fmass
|
fmass
|
||||||
fmm
|
fmm
|
||||||
|
fmt
|
||||||
fmx
|
fmx
|
||||||
fmy
|
fmy
|
||||||
fmz
|
fmz
|
||||||
@ -971,6 +997,7 @@ Fock
|
|||||||
Fogarty
|
Fogarty
|
||||||
Foiles
|
Foiles
|
||||||
fopenmp
|
fopenmp
|
||||||
|
forceclear
|
||||||
forestgreen
|
forestgreen
|
||||||
formatarg
|
formatarg
|
||||||
formulae
|
formulae
|
||||||
@ -987,6 +1014,7 @@ Fraige
|
|||||||
framerate
|
framerate
|
||||||
Frauenheim
|
Frauenheim
|
||||||
Fraunhofer
|
Fraunhofer
|
||||||
|
fread
|
||||||
Freitas
|
Freitas
|
||||||
Frenkel
|
Frenkel
|
||||||
Friedrichs
|
Friedrichs
|
||||||
@ -994,6 +1022,7 @@ fs
|
|||||||
fsh
|
fsh
|
||||||
fstyle
|
fstyle
|
||||||
fsw
|
fsw
|
||||||
|
ftm
|
||||||
ftol
|
ftol
|
||||||
fugacity
|
fugacity
|
||||||
Fumi
|
Fumi
|
||||||
@ -1101,6 +1130,7 @@ gromos
|
|||||||
Gronbech
|
Gronbech
|
||||||
Groot
|
Groot
|
||||||
groupbig
|
groupbig
|
||||||
|
groupbit
|
||||||
grp
|
grp
|
||||||
Grueneisen
|
Grueneisen
|
||||||
gsmooth
|
gsmooth
|
||||||
@ -1163,6 +1193,7 @@ hexorder
|
|||||||
Heyes
|
Heyes
|
||||||
HfO
|
HfO
|
||||||
hgrid
|
hgrid
|
||||||
|
hhmrr
|
||||||
Hibbs
|
Hibbs
|
||||||
Higdon
|
Higdon
|
||||||
Hijazi
|
Hijazi
|
||||||
@ -1172,6 +1203,7 @@ histogrammed
|
|||||||
histogramming
|
histogramming
|
||||||
hma
|
hma
|
||||||
hmaktulga
|
hmaktulga
|
||||||
|
hplanck
|
||||||
hoc
|
hoc
|
||||||
Hochbruck
|
Hochbruck
|
||||||
Hofling
|
Hofling
|
||||||
@ -1214,6 +1246,7 @@ hyperspherical
|
|||||||
hysteretic
|
hysteretic
|
||||||
hz
|
hz
|
||||||
Ibanez
|
Ibanez
|
||||||
|
iatom
|
||||||
ibar
|
ibar
|
||||||
ibm
|
ibm
|
||||||
icc
|
icc
|
||||||
@ -1256,6 +1289,7 @@ indices
|
|||||||
inertiax
|
inertiax
|
||||||
inertiay
|
inertiay
|
||||||
inertiaz
|
inertiaz
|
||||||
|
infile
|
||||||
infty
|
infty
|
||||||
inhomogeneities
|
inhomogeneities
|
||||||
inhomogeneous
|
inhomogeneous
|
||||||
@ -1296,6 +1330,7 @@ ipp
|
|||||||
Ippolito
|
Ippolito
|
||||||
IPv
|
IPv
|
||||||
IPython
|
IPython
|
||||||
|
ipython
|
||||||
Isele
|
Isele
|
||||||
isenthalpic
|
isenthalpic
|
||||||
ish
|
ish
|
||||||
@ -1444,6 +1479,7 @@ Kloza
|
|||||||
kmax
|
kmax
|
||||||
Kmax
|
Kmax
|
||||||
KMP
|
KMP
|
||||||
|
kmu
|
||||||
Knizhnik
|
Knizhnik
|
||||||
knl
|
knl
|
||||||
Kofke
|
Kofke
|
||||||
@ -1931,6 +1967,7 @@ muz
|
|||||||
mv
|
mv
|
||||||
mV
|
mV
|
||||||
Mvapich
|
Mvapich
|
||||||
|
mvh
|
||||||
mvv
|
mvv
|
||||||
MxN
|
MxN
|
||||||
myCompute
|
myCompute
|
||||||
@ -1943,11 +1980,13 @@ na
|
|||||||
nabla
|
nabla
|
||||||
Nagaosa
|
Nagaosa
|
||||||
Nakano
|
Nakano
|
||||||
|
nall
|
||||||
namespace
|
namespace
|
||||||
namespaces
|
namespaces
|
||||||
nan
|
nan
|
||||||
NaN
|
NaN
|
||||||
Nandor
|
Nandor
|
||||||
|
nangles
|
||||||
Nangletype
|
Nangletype
|
||||||
nangletypes
|
nangletypes
|
||||||
Nangletypes
|
Nangletypes
|
||||||
@ -1976,6 +2015,7 @@ Nbin
|
|||||||
Nbins
|
Nbins
|
||||||
nbody
|
nbody
|
||||||
Nbody
|
Nbody
|
||||||
|
nbonds
|
||||||
nbondtype
|
nbondtype
|
||||||
Nbondtype
|
Nbondtype
|
||||||
nbondtypes
|
nbondtypes
|
||||||
@ -1988,9 +2028,11 @@ Nc
|
|||||||
nchunk
|
nchunk
|
||||||
Nchunk
|
Nchunk
|
||||||
ncoeff
|
ncoeff
|
||||||
|
ncol
|
||||||
ncorr
|
ncorr
|
||||||
ncount
|
ncount
|
||||||
nd
|
nd
|
||||||
|
ndihedrals
|
||||||
Ndihedraltype
|
Ndihedraltype
|
||||||
Ndirango
|
Ndirango
|
||||||
ndof
|
ndof
|
||||||
@ -2032,10 +2074,12 @@ Ngyuen
|
|||||||
nh
|
nh
|
||||||
nharmonic
|
nharmonic
|
||||||
nhc
|
nhc
|
||||||
|
nhi
|
||||||
NiAlH
|
NiAlH
|
||||||
Nicklas
|
Nicklas
|
||||||
Niklasson
|
Niklasson
|
||||||
Nikolskiy
|
Nikolskiy
|
||||||
|
nimpropers
|
||||||
Nimpropertype
|
Nimpropertype
|
||||||
Ninteger
|
Ninteger
|
||||||
Nissila
|
Nissila
|
||||||
@ -2044,9 +2088,11 @@ nitride
|
|||||||
nitrides
|
nitrides
|
||||||
niu
|
niu
|
||||||
Nk
|
Nk
|
||||||
|
nktv
|
||||||
nl
|
nl
|
||||||
nlen
|
nlen
|
||||||
Nlines
|
Nlines
|
||||||
|
nlo
|
||||||
nlocal
|
nlocal
|
||||||
Nlocal
|
Nlocal
|
||||||
Nlog
|
Nlog
|
||||||
@ -2054,7 +2100,9 @@ nlp
|
|||||||
nm
|
nm
|
||||||
Nm
|
Nm
|
||||||
Nmax
|
Nmax
|
||||||
|
nmax
|
||||||
Nmin
|
Nmin
|
||||||
|
nmin
|
||||||
Nmols
|
Nmols
|
||||||
nn
|
nn
|
||||||
Nocedal
|
Nocedal
|
||||||
@ -2107,6 +2155,7 @@ Nrepeat
|
|||||||
nreset
|
nreset
|
||||||
Nrho
|
Nrho
|
||||||
Nroff
|
Nroff
|
||||||
|
nrow
|
||||||
nrun
|
nrun
|
||||||
Ns
|
Ns
|
||||||
Nsample
|
Nsample
|
||||||
@ -2125,6 +2174,7 @@ Nt
|
|||||||
Ntable
|
Ntable
|
||||||
ntheta
|
ntheta
|
||||||
nthreads
|
nthreads
|
||||||
|
ntimestep
|
||||||
Ntptask
|
Ntptask
|
||||||
Ntriples
|
Ntriples
|
||||||
Ntype
|
Ntype
|
||||||
@ -2220,6 +2270,7 @@ oxdna
|
|||||||
oxrna
|
oxrna
|
||||||
oxDNA
|
oxDNA
|
||||||
oxRNA
|
oxRNA
|
||||||
|
packings
|
||||||
padua
|
padua
|
||||||
Padua
|
Padua
|
||||||
pafi
|
pafi
|
||||||
@ -2252,6 +2303,8 @@ Particuology
|
|||||||
pastewka
|
pastewka
|
||||||
Pastewka
|
Pastewka
|
||||||
pathangle
|
pathangle
|
||||||
|
pathname
|
||||||
|
pathnames
|
||||||
Patomtrans
|
Patomtrans
|
||||||
Pattnaik
|
Pattnaik
|
||||||
Pavese
|
Pavese
|
||||||
@ -2352,6 +2405,7 @@ polydisperse
|
|||||||
polydispersity
|
polydispersity
|
||||||
polyelectrolyte
|
polyelectrolyte
|
||||||
polyhedra
|
polyhedra
|
||||||
|
polymorphism
|
||||||
popen
|
popen
|
||||||
Popov
|
Popov
|
||||||
popstore
|
popstore
|
||||||
@ -2385,6 +2439,7 @@ proc
|
|||||||
Proc
|
Proc
|
||||||
procs
|
procs
|
||||||
Prony
|
Prony
|
||||||
|
progguide
|
||||||
ps
|
ps
|
||||||
Ps
|
Ps
|
||||||
pscreen
|
pscreen
|
||||||
@ -2431,7 +2486,9 @@ qbmsst
|
|||||||
qcore
|
qcore
|
||||||
qdist
|
qdist
|
||||||
qE
|
qE
|
||||||
|
qe
|
||||||
qeff
|
qeff
|
||||||
|
qelectron
|
||||||
qeq
|
qeq
|
||||||
QeQ
|
QeQ
|
||||||
QEq
|
QEq
|
||||||
@ -2449,6 +2506,8 @@ qmol
|
|||||||
qoffload
|
qoffload
|
||||||
qopenmp
|
qopenmp
|
||||||
qoverride
|
qoverride
|
||||||
|
qqr
|
||||||
|
qqrd
|
||||||
qtb
|
qtb
|
||||||
quadratically
|
quadratically
|
||||||
quadrupolar
|
quadrupolar
|
||||||
@ -2504,6 +2563,7 @@ rebo
|
|||||||
recursing
|
recursing
|
||||||
Ree
|
Ree
|
||||||
refactored
|
refactored
|
||||||
|
refactoring
|
||||||
reflectionstyle
|
reflectionstyle
|
||||||
regoin
|
regoin
|
||||||
Reinders
|
Reinders
|
||||||
@ -2589,6 +2649,7 @@ Rkouter
|
|||||||
RkouterN
|
RkouterN
|
||||||
rmask
|
rmask
|
||||||
Rmask
|
Rmask
|
||||||
|
rmass
|
||||||
rmax
|
rmax
|
||||||
Rmax
|
Rmax
|
||||||
rmdir
|
rmdir
|
||||||
@ -2723,6 +2784,7 @@ shlib
|
|||||||
SHM
|
SHM
|
||||||
shm
|
shm
|
||||||
shockvel
|
shockvel
|
||||||
|
shrinkexceed
|
||||||
Shugaev
|
Shugaev
|
||||||
si
|
si
|
||||||
SiC
|
SiC
|
||||||
@ -2851,11 +2913,16 @@ strcmp
|
|||||||
streitz
|
streitz
|
||||||
Streitz
|
Streitz
|
||||||
Streiz
|
Streiz
|
||||||
|
strerror
|
||||||
strided
|
strided
|
||||||
strietz
|
strietz
|
||||||
|
strmatch
|
||||||
|
strncmp
|
||||||
|
strstr
|
||||||
Stukowski
|
Stukowski
|
||||||
Su
|
Su
|
||||||
subbox
|
subbox
|
||||||
|
Subclassed
|
||||||
subcutoff
|
subcutoff
|
||||||
subcycle
|
subcycle
|
||||||
subcycling
|
subcycling
|
||||||
@ -2996,6 +3063,7 @@ Tmin
|
|||||||
tmp
|
tmp
|
||||||
tN
|
tN
|
||||||
Tobias
|
Tobias
|
||||||
|
tokenizer
|
||||||
tokyo
|
tokyo
|
||||||
tol
|
tol
|
||||||
toolchain
|
toolchain
|
||||||
@ -3226,6 +3294,7 @@ vv
|
|||||||
vx
|
vx
|
||||||
Vx
|
Vx
|
||||||
vxcm
|
vxcm
|
||||||
|
vxmu
|
||||||
vy
|
vy
|
||||||
Vy
|
Vy
|
||||||
vycm
|
vycm
|
||||||
@ -3258,8 +3327,9 @@ Widom
|
|||||||
widom
|
widom
|
||||||
Wijk
|
Wijk
|
||||||
Wikipedia
|
Wikipedia
|
||||||
wildcard
|
|
||||||
Wildcard
|
Wildcard
|
||||||
|
wildcard
|
||||||
|
wildcards
|
||||||
Wirnsberger
|
Wirnsberger
|
||||||
wirtes
|
wirtes
|
||||||
witin
|
witin
|
||||||
@ -3301,6 +3371,7 @@ Xmax
|
|||||||
xmgrace
|
xmgrace
|
||||||
xMIC
|
xMIC
|
||||||
xmin
|
xmin
|
||||||
|
xml
|
||||||
xmovie
|
xmovie
|
||||||
Xmovie
|
Xmovie
|
||||||
xmu
|
xmu
|
||||||
@ -3315,6 +3386,7 @@ xsu
|
|||||||
xtc
|
xtc
|
||||||
xu
|
xu
|
||||||
Xu
|
Xu
|
||||||
|
xxt
|
||||||
xxxxx
|
xxxxx
|
||||||
xy
|
xy
|
||||||
xyz
|
xyz
|
||||||
|
|||||||
@ -1 +0,0 @@
|
|||||||
../../src/JPG/lammps-logo.png
|
|
||||||
11
fortran/README
Normal file
11
fortran/README
Normal file
@ -0,0 +1,11 @@
|
|||||||
|
This directory contains Fortran code which interface LAMMPS as a library
|
||||||
|
and allows the LAMMPS library interface to be invoked from Fortran codes.
|
||||||
|
It requires a Fortran compiler that supports the Fortran 2003 standard.
|
||||||
|
|
||||||
|
This interface is based on and supersedes the previous Fortran interfaces
|
||||||
|
in the examples/COUPLE/fortran* folders. But is fully supported by the
|
||||||
|
LAMMPS developers and included in the documentation and unit testing.
|
||||||
|
|
||||||
|
Details on this Fortran interface and how to build programs using it
|
||||||
|
are in the manual in the doc/html/pg_fortran.html file.
|
||||||
|
|
||||||
281
fortran/lammps.f90
Normal file
281
fortran/lammps.f90
Normal file
@ -0,0 +1,281 @@
|
|||||||
|
! -------------------------------------------------------------------------
|
||||||
|
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
! http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
! Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
!
|
||||||
|
! 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.
|
||||||
|
! -------------------------------------------------------------------------
|
||||||
|
!
|
||||||
|
! Fortran interface to the LAMMPS library implemented as a Fortran 2003
|
||||||
|
! style module that wraps the C-style library interface in library.cpp
|
||||||
|
! and library.h using the ISO_C_BINDING module of the Fortran compiler.
|
||||||
|
!
|
||||||
|
! Based on the LAMMPS Fortran 2003 module contributed by:
|
||||||
|
! Karl D. Hammond <karlh@ugcs.caltech.edu>
|
||||||
|
! University of Tennessee, Knoxville (USA), 2012
|
||||||
|
!
|
||||||
|
! The Fortran module tries to follow the API of the C-library interface
|
||||||
|
! closely, but like the Python wrapper it employs an object oriented
|
||||||
|
! approach. To accommodate the object oriented approach, all exported
|
||||||
|
! subroutine and functions have to be implemented in Fortran to then
|
||||||
|
! call the interfaced C style functions with adapted calling conventions
|
||||||
|
! as needed. The C-library interfaced functions retain their names
|
||||||
|
! starting with "lammps_" while the Fortran versions start with "lmp_".
|
||||||
|
!
|
||||||
|
MODULE LIBLAMMPS
|
||||||
|
|
||||||
|
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_ptr, c_null_ptr, c_loc, &
|
||||||
|
c_int, c_char, c_null_char, c_double
|
||||||
|
|
||||||
|
IMPLICIT NONE
|
||||||
|
PRIVATE
|
||||||
|
PUBLIC :: lammps
|
||||||
|
|
||||||
|
TYPE lammps
|
||||||
|
TYPE(c_ptr) :: handle
|
||||||
|
CONTAINS
|
||||||
|
PROCEDURE :: close => lmp_close
|
||||||
|
PROCEDURE :: file => lmp_file
|
||||||
|
PROCEDURE :: command => lmp_command
|
||||||
|
PROCEDURE :: commands_list => lmp_commands_list
|
||||||
|
PROCEDURE :: commands_string => lmp_commands_string
|
||||||
|
PROCEDURE :: version => lmp_version
|
||||||
|
PROCEDURE :: get_natoms => lmp_get_natoms
|
||||||
|
END TYPE lammps
|
||||||
|
|
||||||
|
INTERFACE lammps
|
||||||
|
MODULE PROCEDURE lmp_open
|
||||||
|
END INTERFACE lammps
|
||||||
|
|
||||||
|
! interface definitions for calling functions in library.cpp
|
||||||
|
INTERFACE
|
||||||
|
FUNCTION lammps_open(argc,argv,comm,handle) &
|
||||||
|
BIND(C, name='lammps_open_fortran')
|
||||||
|
IMPORT :: c_ptr, c_int
|
||||||
|
INTEGER(c_int), VALUE, INTENT(in) :: argc, comm
|
||||||
|
TYPE(c_ptr), DIMENSION(*), INTENT(in) :: argv
|
||||||
|
TYPE(c_ptr), INTENT(out) :: handle
|
||||||
|
TYPE(c_ptr) :: lammps_open
|
||||||
|
END FUNCTION lammps_open
|
||||||
|
|
||||||
|
FUNCTION lammps_open_no_mpi(argc,argv,handle) &
|
||||||
|
BIND(C, name='lammps_open_no_mpi')
|
||||||
|
IMPORT :: c_ptr, c_int
|
||||||
|
INTEGER(c_int), VALUE, INTENT(in) :: argc
|
||||||
|
TYPE(c_ptr), DIMENSION(*), INTENT(in) :: argv
|
||||||
|
TYPE(c_ptr), INTENT(out) :: handle
|
||||||
|
TYPE(c_ptr) :: lammps_open_no_mpi
|
||||||
|
END FUNCTION lammps_open_no_mpi
|
||||||
|
|
||||||
|
SUBROUTINE lammps_close(handle) BIND(C, name='lammps_close')
|
||||||
|
IMPORT :: c_ptr
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
END SUBROUTINE lammps_close
|
||||||
|
|
||||||
|
SUBROUTINE lammps_mpi_init(handle) BIND(C, name='lammps_mpi_init')
|
||||||
|
IMPORT :: c_ptr
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
END SUBROUTINE lammps_mpi_init
|
||||||
|
|
||||||
|
SUBROUTINE lammps_mpi_finalize(handle) &
|
||||||
|
BIND(C, name='lammps_mpi_finalize')
|
||||||
|
IMPORT :: c_ptr
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
END SUBROUTINE lammps_mpi_finalize
|
||||||
|
|
||||||
|
SUBROUTINE lammps_file(handle,filename) BIND(C, name='lammps_file')
|
||||||
|
IMPORT :: c_ptr
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
TYPE(c_ptr), VALUE :: filename
|
||||||
|
END SUBROUTINE lammps_file
|
||||||
|
|
||||||
|
SUBROUTINE lammps_command(handle,cmd) BIND(C, name='lammps_command')
|
||||||
|
IMPORT :: c_ptr
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
TYPE(c_ptr), VALUE :: cmd
|
||||||
|
END SUBROUTINE lammps_command
|
||||||
|
|
||||||
|
SUBROUTINE lammps_commands_list(handle,ncmd,cmds) &
|
||||||
|
BIND(C, name='lammps_commands_list')
|
||||||
|
IMPORT :: c_ptr, c_int
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
INTEGER(c_int), VALUE, INTENT(in) :: ncmd
|
||||||
|
TYPE(c_ptr), DIMENSION(*), INTENT(in) :: cmds
|
||||||
|
END SUBROUTINE lammps_commands_list
|
||||||
|
|
||||||
|
SUBROUTINE lammps_commands_string(handle,str) &
|
||||||
|
BIND(C, name='lammps_commands_string')
|
||||||
|
IMPORT :: c_ptr
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
TYPE(c_ptr), VALUE :: str
|
||||||
|
END SUBROUTINE lammps_commands_string
|
||||||
|
|
||||||
|
SUBROUTINE lammps_free(ptr) BIND(C, name='lammps_free')
|
||||||
|
IMPORT :: c_ptr
|
||||||
|
TYPE(c_ptr), VALUE :: ptr
|
||||||
|
END SUBROUTINE lammps_free
|
||||||
|
|
||||||
|
FUNCTION lammps_version(handle) BIND(C, name='lammps_version')
|
||||||
|
IMPORT :: c_ptr, c_int
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
INTEGER(c_int) :: lammps_version
|
||||||
|
END FUNCTION lammps_version
|
||||||
|
|
||||||
|
FUNCTION lammps_get_natoms(handle) BIND(C, name='lammps_get_natoms')
|
||||||
|
IMPORT :: c_ptr, c_double
|
||||||
|
TYPE(c_ptr), VALUE :: handle
|
||||||
|
REAL(c_double) :: lammps_get_natoms
|
||||||
|
END FUNCTION lammps_get_natoms
|
||||||
|
END INTERFACE
|
||||||
|
|
||||||
|
CONTAINS
|
||||||
|
|
||||||
|
! Fortran wrappers and helper functions.
|
||||||
|
|
||||||
|
! Constructor for the LAMMPS class.
|
||||||
|
! Combined wrapper around lammps_open_fortran() and lammps_open_no_mpi()
|
||||||
|
TYPE(lammps) FUNCTION lmp_open(args,comm)
|
||||||
|
IMPLICIT NONE
|
||||||
|
INTEGER,INTENT(in), OPTIONAL :: comm
|
||||||
|
CHARACTER(len=*), INTENT(in), OPTIONAL :: args(:)
|
||||||
|
TYPE(c_ptr), ALLOCATABLE :: argv(:)
|
||||||
|
TYPE(c_ptr) :: dummy=c_null_ptr
|
||||||
|
INTEGER :: i,argc
|
||||||
|
|
||||||
|
IF (PRESENT(args)) THEN
|
||||||
|
! convert argument list to c style
|
||||||
|
argc = SIZE(args)
|
||||||
|
ALLOCATE(argv(argc))
|
||||||
|
DO i=1,argc
|
||||||
|
argv(i) = f2c_string(args(i))
|
||||||
|
END DO
|
||||||
|
ELSE
|
||||||
|
argc = 1
|
||||||
|
ALLOCATE(argv(1))
|
||||||
|
argv(1) = f2c_string("liblammps")
|
||||||
|
ENDIF
|
||||||
|
|
||||||
|
IF (PRESENT(comm)) THEN
|
||||||
|
lmp_open%handle = lammps_open(argc,argv,comm,dummy)
|
||||||
|
ELSE
|
||||||
|
lmp_open%handle = lammps_open_no_mpi(argc,argv,dummy)
|
||||||
|
END IF
|
||||||
|
|
||||||
|
! Clean up allocated memory
|
||||||
|
DO i=1,argc
|
||||||
|
CALL lammps_free(argv(i))
|
||||||
|
END DO
|
||||||
|
DEALLOCATE(argv)
|
||||||
|
END FUNCTION lmp_open
|
||||||
|
|
||||||
|
! Combined Fortran wrapper around lammps_close() and lammps_mpi_finalize()
|
||||||
|
SUBROUTINE lmp_close(self,finalize)
|
||||||
|
IMPLICIT NONE
|
||||||
|
CLASS(lammps) :: self
|
||||||
|
LOGICAL,INTENT(in),OPTIONAL :: finalize
|
||||||
|
|
||||||
|
CALL lammps_close(self%handle)
|
||||||
|
|
||||||
|
IF (PRESENT(finalize)) THEN
|
||||||
|
IF (finalize) THEN
|
||||||
|
CALL lammps_mpi_finalize(self%handle)
|
||||||
|
END IF
|
||||||
|
END IF
|
||||||
|
END SUBROUTINE lmp_close
|
||||||
|
|
||||||
|
INTEGER FUNCTION lmp_version(self)
|
||||||
|
IMPLICIT NONE
|
||||||
|
CLASS(lammps) :: self
|
||||||
|
|
||||||
|
lmp_version = lammps_version(self%handle)
|
||||||
|
END FUNCTION lmp_version
|
||||||
|
|
||||||
|
DOUBLE PRECISION FUNCTION lmp_get_natoms(self)
|
||||||
|
IMPLICIT NONE
|
||||||
|
CLASS(lammps) :: self
|
||||||
|
|
||||||
|
lmp_get_natoms = lammps_get_natoms(self%handle)
|
||||||
|
END FUNCTION lmp_get_natoms
|
||||||
|
|
||||||
|
SUBROUTINE lmp_file(self,filename)
|
||||||
|
IMPLICIT NONE
|
||||||
|
CLASS(lammps) :: self
|
||||||
|
CHARACTER(len=*) :: filename
|
||||||
|
TYPE(c_ptr) :: str
|
||||||
|
|
||||||
|
str = f2c_string(filename)
|
||||||
|
CALL lammps_file(self%handle,str)
|
||||||
|
CALL lammps_free(str)
|
||||||
|
END SUBROUTINE lmp_file
|
||||||
|
|
||||||
|
! equivalent function to lammps_command()
|
||||||
|
SUBROUTINE lmp_command(self,cmd)
|
||||||
|
IMPLICIT NONE
|
||||||
|
CLASS(lammps) :: self
|
||||||
|
CHARACTER(len=*) :: cmd
|
||||||
|
TYPE(c_ptr) :: str
|
||||||
|
|
||||||
|
str = f2c_string(cmd)
|
||||||
|
CALL lammps_command(self%handle,str)
|
||||||
|
CALL lammps_free(str)
|
||||||
|
END SUBROUTINE lmp_command
|
||||||
|
|
||||||
|
! equivalent function to lammps_commands_list()
|
||||||
|
SUBROUTINE lmp_commands_list(self,cmds)
|
||||||
|
IMPLICIT NONE
|
||||||
|
CLASS(lammps) :: self
|
||||||
|
CHARACTER(len=*), INTENT(in), OPTIONAL :: cmds(:)
|
||||||
|
TYPE(c_ptr), ALLOCATABLE :: cmdv(:)
|
||||||
|
INTEGER :: i,ncmd
|
||||||
|
|
||||||
|
! convert command list to c style
|
||||||
|
ncmd = SIZE(cmds)
|
||||||
|
ALLOCATE(cmdv(ncmd))
|
||||||
|
DO i=1,ncmd
|
||||||
|
cmdv(i) = f2c_string(cmds(i))
|
||||||
|
END DO
|
||||||
|
|
||||||
|
CALL lammps_commands_list(self%handle,ncmd,cmdv)
|
||||||
|
|
||||||
|
! Clean up allocated memory
|
||||||
|
DO i=1,ncmd
|
||||||
|
CALL lammps_free(cmdv(i))
|
||||||
|
END DO
|
||||||
|
DEALLOCATE(cmdv)
|
||||||
|
END SUBROUTINE lmp_commands_list
|
||||||
|
|
||||||
|
! equivalent function to lammps_commands_string()
|
||||||
|
SUBROUTINE lmp_commands_string(self,str)
|
||||||
|
IMPLICIT NONE
|
||||||
|
CLASS(lammps) :: self
|
||||||
|
CHARACTER(len=*) :: str
|
||||||
|
TYPE(c_ptr) :: tmp
|
||||||
|
|
||||||
|
tmp = f2c_string(str)
|
||||||
|
CALL lammps_commands_string(self%handle,tmp)
|
||||||
|
CALL lammps_free(tmp)
|
||||||
|
END SUBROUTINE lmp_commands_string
|
||||||
|
|
||||||
|
! ----------------------------------------------------------------------
|
||||||
|
! local helper functions
|
||||||
|
! copy fortran string to zero terminated c string
|
||||||
|
FUNCTION f2c_string(f_string) RESULT(ptr)
|
||||||
|
CHARACTER (len=*), INTENT(in) :: f_string
|
||||||
|
CHARACTER (len=1, kind=c_char), POINTER :: c_string(:)
|
||||||
|
TYPE(c_ptr) :: ptr
|
||||||
|
INTEGER :: i, n
|
||||||
|
|
||||||
|
n = LEN_TRIM(f_string)
|
||||||
|
ALLOCATE(c_string(n+1))
|
||||||
|
DO i=1,n
|
||||||
|
c_string(i) = f_string(i:i)
|
||||||
|
END DO
|
||||||
|
c_string(n+1) = c_null_char
|
||||||
|
ptr = c_loc(c_string(1))
|
||||||
|
END FUNCTION f2c_string
|
||||||
|
END MODULE LIBLAMMPS
|
||||||
@ -22,13 +22,13 @@ NVCC = nvcc
|
|||||||
#CUDA_ARCH = -arch=sm_21
|
#CUDA_ARCH = -arch=sm_21
|
||||||
|
|
||||||
# Kepler hardware
|
# Kepler hardware
|
||||||
CUDA_ARCH = -arch=sm_30
|
#CUDA_ARCH = -arch=sm_30
|
||||||
#CUDA_ARCH = -arch=sm_32
|
#CUDA_ARCH = -arch=sm_32
|
||||||
#CUDA_ARCH = -arch=sm_35
|
#CUDA_ARCH = -arch=sm_35
|
||||||
#CUDA_ARCH = -arch=sm_37
|
#CUDA_ARCH = -arch=sm_37
|
||||||
|
|
||||||
# Maxwell hardware
|
# Maxwell hardware
|
||||||
#CUDA_ARCH = -arch=sm_50
|
CUDA_ARCH = -arch=sm_50
|
||||||
#CUDA_ARCH = -arch=sm_52
|
#CUDA_ARCH = -arch=sm_52
|
||||||
|
|
||||||
# Pascal hardware
|
# Pascal hardware
|
||||||
|
|||||||
@ -7,18 +7,40 @@
|
|||||||
|
|
||||||
EXTRAMAKE = Makefile.lammps.standard
|
EXTRAMAKE = Makefile.lammps.standard
|
||||||
|
|
||||||
|
ifeq ($(CUDA_HOME),)
|
||||||
CUDA_HOME = /usr/local/cuda
|
CUDA_HOME = /usr/local/cuda
|
||||||
|
endif
|
||||||
|
|
||||||
NVCC = nvcc
|
NVCC = nvcc
|
||||||
|
|
||||||
# Kepler CUDA
|
# obsolete hardware. not supported by current drivers anymore.
|
||||||
#CUDA_ARCH = -arch=sm_35
|
|
||||||
# Tesla CUDA
|
|
||||||
CUDA_ARCH = -arch=sm_21
|
|
||||||
# newer CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_13
|
#CUDA_ARCH = -arch=sm_13
|
||||||
# older CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||||
|
|
||||||
|
# Fermi hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_20
|
||||||
|
#CUDA_ARCH = -arch=sm_21
|
||||||
|
|
||||||
|
# Kepler hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_30
|
||||||
|
#CUDA_ARCH = -arch=sm_32
|
||||||
|
#CUDA_ARCH = -arch=sm_35
|
||||||
|
#CUDA_ARCH = -arch=sm_37
|
||||||
|
|
||||||
|
# Maxwell hardware
|
||||||
|
CUDA_ARCH = -arch=sm_50
|
||||||
|
#CUDA_ARCH = -arch=sm_52
|
||||||
|
|
||||||
|
# Pascal hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_60
|
||||||
|
#CUDA_ARCH = -arch=sm_61
|
||||||
|
|
||||||
|
# Volta hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_70
|
||||||
|
|
||||||
|
# Turing hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_75
|
||||||
|
|
||||||
# this setting should match LAMMPS Makefile
|
# this setting should match LAMMPS Makefile
|
||||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||||
|
|
||||||
@ -33,7 +55,7 @@ CUDA_PRECISION = -D_DOUBLE_DOUBLE
|
|||||||
|
|
||||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math
|
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||||
|
|
||||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||||
|
|||||||
@ -7,18 +7,41 @@
|
|||||||
|
|
||||||
EXTRAMAKE = Makefile.lammps.standard
|
EXTRAMAKE = Makefile.lammps.standard
|
||||||
|
|
||||||
|
ifeq ($(CUDA_HOME),)
|
||||||
CUDA_HOME = /usr/local/cuda
|
CUDA_HOME = /usr/local/cuda
|
||||||
|
endif
|
||||||
|
|
||||||
NVCC = nvcc
|
NVCC = nvcc
|
||||||
|
|
||||||
# Kepler CUDA
|
# obsolete hardware. not supported by current drivers anymore.
|
||||||
#CUDA_ARCH = -arch=sm_35
|
|
||||||
# Tesla CUDA
|
|
||||||
CUDA_ARCH = -arch=sm_21
|
|
||||||
# newer CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_13
|
#CUDA_ARCH = -arch=sm_13
|
||||||
# older CUDA
|
# older CUDA
|
||||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||||
|
|
||||||
|
# Fermi hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_20
|
||||||
|
#CUDA_ARCH = -arch=sm_21
|
||||||
|
|
||||||
|
# Kepler hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_30
|
||||||
|
#CUDA_ARCH = -arch=sm_32
|
||||||
|
#CUDA_ARCH = -arch=sm_35
|
||||||
|
#CUDA_ARCH = -arch=sm_37
|
||||||
|
|
||||||
|
# Maxwell hardware
|
||||||
|
CUDA_ARCH = -arch=sm_50
|
||||||
|
#CUDA_ARCH = -arch=sm_52
|
||||||
|
|
||||||
|
# Pascal hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_60
|
||||||
|
#CUDA_ARCH = -arch=sm_61
|
||||||
|
|
||||||
|
# Volta hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_70
|
||||||
|
|
||||||
|
# Turing hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_75
|
||||||
|
|
||||||
# this setting should match LAMMPS Makefile
|
# this setting should match LAMMPS Makefile
|
||||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||||
|
|
||||||
@ -33,7 +56,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
|
|||||||
|
|
||||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math
|
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||||
|
|
||||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||||
|
|||||||
@ -7,18 +7,40 @@
|
|||||||
|
|
||||||
EXTRAMAKE = Makefile.lammps.standard
|
EXTRAMAKE = Makefile.lammps.standard
|
||||||
|
|
||||||
|
ifeq ($(CUDA_HOME),)
|
||||||
CUDA_HOME = /usr/local/cuda
|
CUDA_HOME = /usr/local/cuda
|
||||||
|
endif
|
||||||
|
|
||||||
NVCC = nvcc
|
NVCC = nvcc
|
||||||
|
|
||||||
# Kepler CUDA
|
# obsolete hardware. not supported by current drivers anymore.
|
||||||
#CUDA_ARCH = -arch=sm_35
|
|
||||||
# Tesla CUDA
|
|
||||||
CUDA_ARCH = -arch=sm_21
|
|
||||||
# newer CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_13
|
#CUDA_ARCH = -arch=sm_13
|
||||||
# older CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||||
|
|
||||||
|
# Fermi hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_20
|
||||||
|
#CUDA_ARCH = -arch=sm_21
|
||||||
|
|
||||||
|
# Kepler hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_30
|
||||||
|
#CUDA_ARCH = -arch=sm_32
|
||||||
|
#CUDA_ARCH = -arch=sm_35
|
||||||
|
#CUDA_ARCH = -arch=sm_37
|
||||||
|
|
||||||
|
# Maxwell hardware
|
||||||
|
CUDA_ARCH = -arch=sm_50
|
||||||
|
#CUDA_ARCH = -arch=sm_52
|
||||||
|
|
||||||
|
# Pascal hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_60
|
||||||
|
#CUDA_ARCH = -arch=sm_61
|
||||||
|
|
||||||
|
# Volta hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_70
|
||||||
|
|
||||||
|
# Turing hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_75
|
||||||
|
|
||||||
# this setting should match LAMMPS Makefile
|
# this setting should match LAMMPS Makefile
|
||||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||||
|
|
||||||
@ -33,7 +55,7 @@ CUDA_PRECISION = -D_SINGLE_SINGLE
|
|||||||
|
|
||||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs
|
||||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math
|
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||||
|
|
||||||
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK
|
||||||
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias
|
||||||
|
|||||||
@ -13,17 +13,27 @@ endif
|
|||||||
|
|
||||||
NVCC = nvcc
|
NVCC = nvcc
|
||||||
|
|
||||||
# Kepler CUDA
|
# obsolete hardware. not supported by current drivers anymore.
|
||||||
#CUDA_ARCH = -arch=sm_35
|
|
||||||
# newer CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_13
|
#CUDA_ARCH = -arch=sm_13
|
||||||
# older CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||||
CUDA_ARCH = -arch=sm_30
|
|
||||||
|
|
||||||
CUDA_CODE = -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] \
|
# Fermi hardware
|
||||||
-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] \
|
#CUDA_ARCH = -arch=sm_20
|
||||||
-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]
|
#CUDA_ARCH = -arch=sm_21
|
||||||
|
|
||||||
|
# Kepler hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_30
|
||||||
|
#CUDA_ARCH = -arch=sm_32
|
||||||
|
#CUDA_ARCH = -arch=sm_35
|
||||||
|
#CUDA_ARCH = -arch=sm_37
|
||||||
|
|
||||||
|
# Maxwell hardware
|
||||||
|
CUDA_ARCH = -arch=sm_50
|
||||||
|
#CUDA_ARCH = -arch=sm_52
|
||||||
|
|
||||||
|
CUDA_CODE = -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] \
|
||||||
|
-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] \
|
||||||
|
-gencode arch=compute_70,code=[sm_70,compute_70] -gencode arch=compute_75,code=[sm_75,compute_75]
|
||||||
|
|
||||||
CUDA_ARCH += $(CUDA_CODE)
|
CUDA_ARCH += $(CUDA_CODE)
|
||||||
|
|
||||||
|
|||||||
@ -13,13 +13,33 @@ endif
|
|||||||
|
|
||||||
NVCC = nvcc
|
NVCC = nvcc
|
||||||
|
|
||||||
# Tesla CUDA
|
# obsolete hardware. not supported by current drivers anymore.
|
||||||
CUDA_ARCH = -arch=sm_21
|
|
||||||
# newer CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_13
|
#CUDA_ARCH = -arch=sm_13
|
||||||
# older CUDA
|
|
||||||
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
|
||||||
CUDA_ARCH = -arch=sm_35
|
|
||||||
|
# Fermi hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_20
|
||||||
|
#CUDA_ARCH = -arch=sm_21
|
||||||
|
|
||||||
|
# Kepler hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_30
|
||||||
|
#CUDA_ARCH = -arch=sm_32
|
||||||
|
#CUDA_ARCH = -arch=sm_35
|
||||||
|
#CUDA_ARCH = -arch=sm_37
|
||||||
|
|
||||||
|
# Maxwell hardware
|
||||||
|
CUDA_ARCH = -arch=sm_50
|
||||||
|
#CUDA_ARCH = -arch=sm_52
|
||||||
|
|
||||||
|
# Pascal hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_60
|
||||||
|
#CUDA_ARCH = -arch=sm_61
|
||||||
|
|
||||||
|
# Volta hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_70
|
||||||
|
|
||||||
|
# Turing hardware
|
||||||
|
#CUDA_ARCH = -arch=sm_75
|
||||||
|
|
||||||
# this setting should match LAMMPS Makefile
|
# this setting should match LAMMPS Makefile
|
||||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||||
@ -35,7 +55,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
|
|||||||
|
|
||||||
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
CUDA_INCLUDE = -I$(CUDA_HOME)/include
|
||||||
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs -L../../src/STUBS -lmpi_stubs
|
CUDA_LIB = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs -L../../src/STUBS -lmpi_stubs
|
||||||
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC)
|
CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC
|
||||||
|
|
||||||
CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS
|
CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS
|
||||||
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
|
CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
|
||||||
|
|||||||
@ -81,7 +81,7 @@ __kernel void k_gauss(const __global numtyp4 *restrict x_,
|
|||||||
numtyp r2inv = ucl_recip(rsq);
|
numtyp r2inv = ucl_recip(rsq);
|
||||||
numtyp r = ucl_sqrt(rsq);
|
numtyp r = ucl_sqrt(rsq);
|
||||||
numtyp force = (numtyp)-2.0*gauss1[mtype].x*gauss1[mtype].y*rsq*
|
numtyp force = (numtyp)-2.0*gauss1[mtype].x*gauss1[mtype].y*rsq*
|
||||||
ucl_exp(-gauss1[mtype].y*rsq)*r2inv*factor_lj;
|
ucl_exp(-gauss1[mtype].y*rsq)*r2inv; //*factor_lj;
|
||||||
|
|
||||||
f.x+=delx*force;
|
f.x+=delx*force;
|
||||||
f.y+=dely*force;
|
f.y+=dely*force;
|
||||||
@ -90,7 +90,7 @@ __kernel void k_gauss(const __global numtyp4 *restrict x_,
|
|||||||
if (eflag>0) {
|
if (eflag>0) {
|
||||||
numtyp e=-(gauss1[mtype].x*ucl_exp(-gauss1[mtype].y*rsq) -
|
numtyp e=-(gauss1[mtype].x*ucl_exp(-gauss1[mtype].y*rsq) -
|
||||||
gauss1[mtype].w);
|
gauss1[mtype].w);
|
||||||
energy+=factor_lj*e;
|
energy+=e; //factor_lj*e;
|
||||||
}
|
}
|
||||||
if (vflag>0) {
|
if (vflag>0) {
|
||||||
virial[0] += delx*delx*force;
|
virial[0] += delx*delx*force;
|
||||||
@ -168,7 +168,7 @@ __kernel void k_gauss_fast(const __global numtyp4 *restrict x_,
|
|||||||
numtyp r2inv = ucl_recip(rsq);
|
numtyp r2inv = ucl_recip(rsq);
|
||||||
numtyp r = ucl_sqrt(rsq);
|
numtyp r = ucl_sqrt(rsq);
|
||||||
numtyp force = (numtyp)-2.0*gauss1[mtype].x*gauss1[mtype].y*rsq*
|
numtyp force = (numtyp)-2.0*gauss1[mtype].x*gauss1[mtype].y*rsq*
|
||||||
ucl_exp(-gauss1[mtype].y*rsq)*r2inv*factor_lj;
|
ucl_exp(-gauss1[mtype].y*rsq)*r2inv; //*factor_lj;
|
||||||
|
|
||||||
f.x+=delx*force;
|
f.x+=delx*force;
|
||||||
f.y+=dely*force;
|
f.y+=dely*force;
|
||||||
@ -177,7 +177,7 @@ __kernel void k_gauss_fast(const __global numtyp4 *restrict x_,
|
|||||||
if (eflag>0) {
|
if (eflag>0) {
|
||||||
numtyp e=-(gauss1[mtype].x*ucl_exp(-gauss1[mtype].y*rsq) -
|
numtyp e=-(gauss1[mtype].x*ucl_exp(-gauss1[mtype].y*rsq) -
|
||||||
gauss1[mtype].w);
|
gauss1[mtype].w);
|
||||||
energy+=factor_lj*e;
|
energy+=e; //factor_lj*e;
|
||||||
}
|
}
|
||||||
if (vflag>0) {
|
if (vflag>0) {
|
||||||
virial[0] += delx*delx*force;
|
virial[0] += delx*delx*force;
|
||||||
|
|||||||
@ -709,7 +709,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
|
|||||||
for (int i=0; i<6; i++)
|
for (int i=0; i<6; i++)
|
||||||
virial[i]=(acctyp)0;
|
virial[i]=(acctyp)0;
|
||||||
|
|
||||||
__local int red_acc[BLOCK_PAIR];
|
__local int ijnum_shared[BLOCK_PAIR];
|
||||||
|
|
||||||
__syncthreads();
|
__syncthreads();
|
||||||
|
|
||||||
@ -789,14 +789,14 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
|
|||||||
k &= NEIGHMASK;
|
k &= NEIGHMASK;
|
||||||
if (k == i) {
|
if (k == i) {
|
||||||
ijnum = nbor_k;
|
ijnum = nbor_k;
|
||||||
red_acc[m] = ijnum;
|
ijnum_shared[m] = ijnum;
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
numtyp r1 = ucl_sqrt(rsq1);
|
numtyp r1 = ucl_sqrt(rsq1);
|
||||||
numtyp r1inv = ucl_rsqrt(rsq1);
|
numtyp r1inv = ucl_rsqrt(rsq1);
|
||||||
if (ijnum < 0) ijnum = red_acc[m];
|
if (ijnum < 0) ijnum = ijnum_shared[m];
|
||||||
|
|
||||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||||
int idx = ijnum;
|
int idx = ijnum;
|
||||||
|
|||||||
@ -719,7 +719,7 @@ __kernel void k_tersoff_mod_three_end(const __global numtyp4 *restrict x_,
|
|||||||
for (int i=0; i<6; i++)
|
for (int i=0; i<6; i++)
|
||||||
virial[i]=(acctyp)0;
|
virial[i]=(acctyp)0;
|
||||||
|
|
||||||
__local int red_acc[BLOCK_PAIR];
|
__local int ijnum_shared[BLOCK_PAIR];
|
||||||
|
|
||||||
__syncthreads();
|
__syncthreads();
|
||||||
|
|
||||||
@ -799,14 +799,14 @@ __kernel void k_tersoff_mod_three_end(const __global numtyp4 *restrict x_,
|
|||||||
k &= NEIGHMASK;
|
k &= NEIGHMASK;
|
||||||
if (k == i) {
|
if (k == i) {
|
||||||
ijnum = nbor_k;
|
ijnum = nbor_k;
|
||||||
red_acc[m] = ijnum;
|
ijnum_shared[m] = ijnum;
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
numtyp r1 = ucl_sqrt(rsq1);
|
numtyp r1 = ucl_sqrt(rsq1);
|
||||||
numtyp r1inv = ucl_rsqrt(rsq1);
|
numtyp r1inv = ucl_rsqrt(rsq1);
|
||||||
if (ijnum < 0) ijnum = red_acc[m];
|
if (ijnum < 0) ijnum = ijnum_shared[m];
|
||||||
|
|
||||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||||
int idx = ijnum;
|
int idx = ijnum;
|
||||||
@ -957,7 +957,7 @@ __kernel void k_tersoff_mod_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||||||
for (int i=0; i<6; i++)
|
for (int i=0; i<6; i++)
|
||||||
virial[i]=(acctyp)0;
|
virial[i]=(acctyp)0;
|
||||||
|
|
||||||
__local int red_acc[BLOCK_PAIR];
|
__local int ijnum_shared[BLOCK_PAIR];
|
||||||
|
|
||||||
__syncthreads();
|
__syncthreads();
|
||||||
|
|
||||||
@ -1037,14 +1037,14 @@ __kernel void k_tersoff_mod_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||||||
k &= NEIGHMASK;
|
k &= NEIGHMASK;
|
||||||
if (k == i) {
|
if (k == i) {
|
||||||
ijnum = nbor_k;
|
ijnum = nbor_k;
|
||||||
red_acc[m] = ijnum;
|
ijnum_shared[m] = ijnum;
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
numtyp r1 = ucl_sqrt(rsq1);
|
numtyp r1 = ucl_sqrt(rsq1);
|
||||||
numtyp r1inv = ucl_rsqrt(rsq1);
|
numtyp r1inv = ucl_rsqrt(rsq1);
|
||||||
if (ijnum < 0) ijnum = red_acc[m];
|
if (ijnum < 0) ijnum = ijnum_shared[m];
|
||||||
|
|
||||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||||
int idx = ijnum;
|
int idx = ijnum;
|
||||||
|
|||||||
@ -729,7 +729,7 @@ __kernel void k_tersoff_zbl_three_end(const __global numtyp4 *restrict x_,
|
|||||||
for (int i=0; i<6; i++)
|
for (int i=0; i<6; i++)
|
||||||
virial[i]=(acctyp)0;
|
virial[i]=(acctyp)0;
|
||||||
|
|
||||||
__local int red_acc[BLOCK_PAIR];
|
__local int ijnum_shared[BLOCK_PAIR];
|
||||||
|
|
||||||
__syncthreads();
|
__syncthreads();
|
||||||
|
|
||||||
@ -809,14 +809,14 @@ __kernel void k_tersoff_zbl_three_end(const __global numtyp4 *restrict x_,
|
|||||||
k &= NEIGHMASK;
|
k &= NEIGHMASK;
|
||||||
if (k == i) {
|
if (k == i) {
|
||||||
ijnum = nbor_k;
|
ijnum = nbor_k;
|
||||||
red_acc[m] = ijnum;
|
ijnum_shared[m] = ijnum;
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
numtyp r1 = ucl_sqrt(rsq1);
|
numtyp r1 = ucl_sqrt(rsq1);
|
||||||
numtyp r1inv = ucl_rsqrt(rsq1);
|
numtyp r1inv = ucl_rsqrt(rsq1);
|
||||||
if (ijnum < 0) ijnum = red_acc[m];
|
if (ijnum < 0) ijnum = ijnum_shared[m];
|
||||||
|
|
||||||
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
// idx to zetaij is shifted by n_stride relative to ijnum in dev_short_nbor
|
||||||
int idx = ijnum;
|
int idx = ijnum;
|
||||||
|
|||||||
@ -10,33 +10,45 @@ for C++. Applications heavily leveraging Kokkos are strongly encouraged to use
|
|||||||
You can either use Kokkos as an installed package (encouraged) or use Kokkos in-tree in your project.
|
You can either use Kokkos as an installed package (encouraged) or use Kokkos in-tree in your project.
|
||||||
Modern CMake is exceedingly simple at a high-level (with the devil in the details).
|
Modern CMake is exceedingly simple at a high-level (with the devil in the details).
|
||||||
Once Kokkos is installed In your `CMakeLists.txt` simply use:
|
Once Kokkos is installed In your `CMakeLists.txt` simply use:
|
||||||
````
|
````cmake
|
||||||
find_package(Kokkos REQUIRED)
|
find_package(Kokkos REQUIRED)
|
||||||
````
|
````
|
||||||
Then for every executable or library in your project:
|
Then for every executable or library in your project:
|
||||||
````
|
````cmake
|
||||||
target_link_libraries(myTarget Kokkos::kokkos)
|
target_link_libraries(myTarget Kokkos::kokkos)
|
||||||
````
|
````
|
||||||
That's it! There is no checking Kokkos preprocessor, compiler, or linker flags.
|
That's it! There is no checking Kokkos preprocessor, compiler, or linker flags.
|
||||||
Kokkos propagates all the necessary flags to your project.
|
Kokkos propagates all the necessary flags to your project.
|
||||||
This means not only is linking to Kokkos easy, but Kokkos itself can actually configure compiler and linker flags for *your*
|
This means not only is linking to Kokkos easy, but Kokkos itself can actually configure compiler and linker flags for *your*
|
||||||
project. If building in-tree, there is no `find_package` and you link with `target_link_libraries(kokkos)`.
|
project.
|
||||||
|
When configuring your project just set:
|
||||||
|
````bash
|
||||||
|
> cmake ${srcdir} \
|
||||||
|
-DKokkos_ROOT=${kokkos_install_prefix} \
|
||||||
|
-DCMAKE_CXX_COMPILER=${compiler_used_to_build_kokkos}
|
||||||
|
````
|
||||||
|
Note: You may need the following if using some versions of CMake (e.g. 3.12):
|
||||||
|
````cmake
|
||||||
|
cmake_policy(SET CMP0074 NEW)
|
||||||
|
````
|
||||||
|
If building in-tree, there is no `find_package`. You can use `add_subdirectory(kokkos)` with the Kokkos source and again just link with `target_link_libraries(Kokkos::kokkos)`.
|
||||||
|
The examples in `examples/cmake_build_installed` and `examples/cmake_build_in_tree` can help get you started.
|
||||||
|
|
||||||
|
|
||||||
## Configuring CMake
|
## Configuring CMake
|
||||||
A very basic installation is done with:
|
A very basic installation of Kokkos is done with:
|
||||||
````
|
````bash
|
||||||
cmake ${srcdir} \
|
> cmake ${srcdir} \
|
||||||
-DCMAKE_CXX_COMPILER=g++ \
|
-DCMAKE_CXX_COMPILER=g++ \
|
||||||
-DCMAKE_INSTALL_PREFIX=${my_install_folder}
|
-DCMAKE_INSTALL_PREFIX=${kokkos_install_folder}
|
||||||
````
|
````
|
||||||
which builds and installed a default Kokkos when you run `make install`.
|
which builds and installed a default Kokkos when you run `make install`.
|
||||||
There are numerous device backends, options, and architecture-specific optimizations that can be configured, e.g.
|
There are numerous device backends, options, and architecture-specific optimizations that can be configured, e.g.
|
||||||
````
|
````bash
|
||||||
cmake ${srcdir} \
|
> cmake ${srcdir} \
|
||||||
-DCMAKE_CXX_COMPILER=g++ \
|
-DCMAKE_CXX_COMPILER=g++ \
|
||||||
-DCMAKE_INSTALL_PREFIX=${my_install_folder} \
|
-DCMAKE_INSTALL_PREFIX=${kokkos_install_folder} \
|
||||||
-DKokkos_ENABLE_OPENMP=On
|
-DKokkos_ENABLE_OPENMP=ON
|
||||||
````
|
````
|
||||||
which activates the OpenMP backend. All of the options controlling device backends, options, architectures, and third-party libraries (TPLs) are given below.
|
which activates the OpenMP backend. All of the options controlling device backends, options, architectures, and third-party libraries (TPLs) are given below.
|
||||||
|
|
||||||
@ -50,16 +62,16 @@ which activates the OpenMP backend. All of the options controlling device backen
|
|||||||
## Spack
|
## Spack
|
||||||
An alternative to manually building with the CMake is to use the Spack package manager.
|
An alternative to manually building with the CMake is to use the Spack package manager.
|
||||||
To do so, download the `kokkos-spack` git repo and add to the package list:
|
To do so, download the `kokkos-spack` git repo and add to the package list:
|
||||||
````
|
````bash
|
||||||
spack repo add $path-to-kokkos-spack
|
> spack repo add $path-to-kokkos-spack
|
||||||
````
|
````
|
||||||
A basic installation would be done as:
|
A basic installation would be done as:
|
||||||
````
|
````bash
|
||||||
spack install kokkos
|
> spack install kokkos
|
||||||
````
|
````
|
||||||
Spack allows options and and compilers to be tuned in the install command.
|
Spack allows options and and compilers to be tuned in the install command.
|
||||||
````
|
````bash
|
||||||
spack install kokkos@3.0 %gcc@7.3.0 +openmp
|
> spack install kokkos@3.0 %gcc@7.3.0 +openmp
|
||||||
````
|
````
|
||||||
This example illustrates the three most common parameters to Spack:
|
This example illustrates the three most common parameters to Spack:
|
||||||
* Variants: specified with, e.g. `+openmp`, this activates (or deactivates with, e.g. `~openmp`) certain options.
|
* Variants: specified with, e.g. `+openmp`, this activates (or deactivates with, e.g. `~openmp`) certain options.
|
||||||
@ -67,17 +79,17 @@ This example illustrates the three most common parameters to Spack:
|
|||||||
* Compiler: a default compiler will be chosen if not specified, but an exact compiler version can be given with the `%`option.
|
* Compiler: a default compiler will be chosen if not specified, but an exact compiler version can be given with the `%`option.
|
||||||
|
|
||||||
For a complete list of Kokkos options, run:
|
For a complete list of Kokkos options, run:
|
||||||
|
````bash
|
||||||
|
> spack info kokkos
|
||||||
````
|
````
|
||||||
spack info kokkos
|
More details can be found in the [Spack README](Spack.md)
|
||||||
````
|
|
||||||
More details can be found in the kokkos-spack repository [README](https://github.com/kokkos/kokkos-spack/blob/master/README.md).
|
|
||||||
|
|
||||||
#### Spack Development
|
#### Spack Development
|
||||||
Spack currently installs packages to a location determined by a unique hash. This hash name is not really "human readable".
|
Spack currently installs packages to a location determined by a unique hash. This hash name is not really "human readable".
|
||||||
Generally, Spack usage should never really require you to reference the computer-generated unique install folder.
|
Generally, Spack usage should never really require you to reference the computer-generated unique install folder.
|
||||||
If you must know, you can locate Spack Kokkos installations with:
|
If you must know, you can locate Spack Kokkos installations with:
|
||||||
````
|
````bash
|
||||||
spack find -p kokkos ...
|
> spack find -p kokkos ...
|
||||||
````
|
````
|
||||||
where `...` is the unique spec identifying the particular Kokkos configuration and version.
|
where `...` is the unique spec identifying the particular Kokkos configuration and version.
|
||||||
|
|
||||||
@ -104,6 +116,12 @@ Device backends can be enabled by specifying `-DKokkos_ENABLE_X`.
|
|||||||
* Kokkos_ENABLE_SERIAL
|
* Kokkos_ENABLE_SERIAL
|
||||||
* Whether to build serial backend
|
* Whether to build serial backend
|
||||||
* BOOL Default: ON
|
* BOOL Default: ON
|
||||||
|
* Kokkos_ENABLE_HIP (Experimental)
|
||||||
|
* Whether to build HIP backend
|
||||||
|
* BOOL Default: OFF
|
||||||
|
* Kokkos_ENABLE_OPENMPTARGET (Experimental)
|
||||||
|
* Whether to build the OpenMP target backend
|
||||||
|
* BOOL Default: OFF
|
||||||
|
|
||||||
## Enable Options
|
## Enable Options
|
||||||
Options can be enabled by specifying `-DKokkos_ENABLE_X`.
|
Options can be enabled by specifying `-DKokkos_ENABLE_X`.
|
||||||
@ -138,9 +156,6 @@ Options can be enabled by specifying `-DKokkos_ENABLE_X`.
|
|||||||
* Kokkos_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK
|
* Kokkos_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK
|
||||||
* Debug check on dual views
|
* Debug check on dual views
|
||||||
* BOOL Default: OFF
|
* BOOL Default: OFF
|
||||||
* Kokkos_ENABLE_DEPRECATED_CODE
|
|
||||||
* Whether to enable deprecated code
|
|
||||||
* BOOL Default: OFF
|
|
||||||
* Kokkos_ENABLE_EXAMPLES
|
* Kokkos_ENABLE_EXAMPLES
|
||||||
* Whether to enable building examples
|
* Whether to enable building examples
|
||||||
* BOOL Default: OFF
|
* BOOL Default: OFF
|
||||||
@ -150,9 +165,6 @@ Options can be enabled by specifying `-DKokkos_ENABLE_X`.
|
|||||||
* Kokkos_ENABLE_LARGE_MEM_TESTS
|
* Kokkos_ENABLE_LARGE_MEM_TESTS
|
||||||
* Whether to perform extra large memory tests
|
* Whether to perform extra large memory tests
|
||||||
* BOOL_Default: OFF
|
* BOOL_Default: OFF
|
||||||
* Kokkos_ENABLE_PROFILING
|
|
||||||
* Whether to create bindings for profiling tools
|
|
||||||
* BOOL Default: ON
|
|
||||||
* Kokkos_ENABLE_PROFILING_LOAD_PRINT
|
* Kokkos_ENABLE_PROFILING_LOAD_PRINT
|
||||||
* Whether to print information about which profiling tools gotloaded
|
* Whether to print information about which profiling tools gotloaded
|
||||||
* BOOL Default: OFF
|
* BOOL Default: OFF
|
||||||
@ -235,8 +247,11 @@ Architecture-specific optimizations can be enabled by specifying `-DKokkos_ARCH_
|
|||||||
* Kokkos_ARCH_BGQ
|
* Kokkos_ARCH_BGQ
|
||||||
* Whether to optimize for the BGQ architecture
|
* Whether to optimize for the BGQ architecture
|
||||||
* BOOL Default: OFF
|
* BOOL Default: OFF
|
||||||
* Kokkos_ARCH_EPYC
|
* Kokkos_ARCH_ZEN
|
||||||
* Whether to optimize for the EPYC architecture
|
* Whether to optimize for the Zen architecture
|
||||||
|
* BOOL Default: OFF
|
||||||
|
* Kokkos_ARCH_ZEN2
|
||||||
|
* Whether to optimize for the Zen2 architecture
|
||||||
* BOOL Default: OFF
|
* BOOL Default: OFF
|
||||||
* Kokkos_ARCH_HSW
|
* Kokkos_ARCH_HSW
|
||||||
* Whether to optimize for the HSW architecture
|
* Whether to optimize for the HSW architecture
|
||||||
|
|||||||
@ -1,6 +1,113 @@
|
|||||||
# Change Log
|
# Change Log
|
||||||
|
|
||||||
## [3.1.1](https://github.com/kokkos/kokkos/tree/3.1.1) (2020-04-14)
|
## [3.2.00](https://github.com/kokkos/kokkos/tree/3.2.00) (2020-08-19)
|
||||||
|
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.1.01...3.2.00)
|
||||||
|
|
||||||
|
**Implemented enhancements:**
|
||||||
|
|
||||||
|
- HIP:Enable stream in HIP [\#3163](https://github.com/kokkos/kokkos/issues/3163)
|
||||||
|
- HIP:Add support for shuffle reduction for the HIP backend [\#3154](https://github.com/kokkos/kokkos/issues/3154)
|
||||||
|
- HIP:Add implementations of missing HIPHostPinnedSpace methods for LAMMPS [\#3137](https://github.com/kokkos/kokkos/issues/3137)
|
||||||
|
- HIP:Require HIP 3.5.0 or higher [\#3099](https://github.com/kokkos/kokkos/issues/3099)
|
||||||
|
- HIP:WorkGraphPolicy for HIP [\#3096](https://github.com/kokkos/kokkos/issues/3096)
|
||||||
|
- OpenMPTarget: Significant update to the new experimental backend. Requires C++17, works on Intel GPUs, reference counting fixes. [\#3169](https://github.com/kokkos/kokkos/issues/3169)
|
||||||
|
- Windows Cuda support [\#3018](https://github.com/kokkos/kokkos/issues/3018)
|
||||||
|
- Pass `-Wext-lambda-captures-this` to NVCC when support for `__host__ __device__` lambda is enabled from CUDA 11 [\#3241](https://github.com/kokkos/kokkos/issues/3241)
|
||||||
|
- Use explicit staging buffer for constant memory kernel launches and cleanup host/device synchronization [\#3234](https://github.com/kokkos/kokkos/issues/3234)
|
||||||
|
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 1: [\#3202](https://github.com/kokkos/kokkos/issues/3202)
|
||||||
|
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 2: [\#3203](https://github.com/kokkos/kokkos/issues/3203)
|
||||||
|
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 3: [\#3196](https://github.com/kokkos/kokkos/issues/3196)
|
||||||
|
- Annotations for `DefaultExectutionSpace` and `DefaultHostExectutionSpace` to use in static analysis [\#3189](https://github.com/kokkos/kokkos/issues/3189)
|
||||||
|
- Add documentation on using Spack to install Kokkos and developing packages that depend on Kokkos [\#3187](https://github.com/kokkos/kokkos/issues/3187)
|
||||||
|
- Improve support for nvcc\_wrapper with exotic host compiler [\#3186](https://github.com/kokkos/kokkos/issues/3186)
|
||||||
|
- Add OpenMPTarget backend flags for NVC++ compiler [\#3185](https://github.com/kokkos/kokkos/issues/3185)
|
||||||
|
- Move deep\_copy/create\_mirror\_view on Experimental::OffsetView into Kokkos:: namespace [\#3166](https://github.com/kokkos/kokkos/issues/3166)
|
||||||
|
- Allow for larger block size in HIP [\#3165](https://github.com/kokkos/kokkos/issues/3165)
|
||||||
|
- View: Added names of Views to the different View initialize/free kernels [\#3159](https://github.com/kokkos/kokkos/issues/3159)
|
||||||
|
- Cuda: Caching cudaFunctorAttributes and whether L1/Shmem prefer was set [\#3151](https://github.com/kokkos/kokkos/issues/3151)
|
||||||
|
- BuildSystem: Provide an explicit default CMAKE\_BUILD\_TYPE [\#3131](https://github.com/kokkos/kokkos/issues/3131)
|
||||||
|
- Cuda: Update CUDA occupancy calculation [\#3124](https://github.com/kokkos/kokkos/issues/3124)
|
||||||
|
- Vector: Adding data() to Vector [\#3123](https://github.com/kokkos/kokkos/issues/3123)
|
||||||
|
- BuildSystem: Add CUDA Ampere configuration support [\#3122](https://github.com/kokkos/kokkos/issues/3122)
|
||||||
|
- General: Apply [[noreturn]] to Kokkos::abort when applicable [\#3106](https://github.com/kokkos/kokkos/issues/3106)
|
||||||
|
- TeamPolicy: Validate storage level argument passed to TeamPolicy::set\_scratch\_size() [\#3098](https://github.com/kokkos/kokkos/issues/3098)
|
||||||
|
- nvcc\_wrapper: send --cudart to nvcc instead of host compiler [\#3092](https://github.com/kokkos/kokkos/issues/3092)
|
||||||
|
- BuildSystem: Make kokkos\_has\_string() function in Makefile.kokkos case insensitive [\#3091](https://github.com/kokkos/kokkos/issues/3091)
|
||||||
|
- Modify KOKKOS\_FUNCTION macro for clang-tidy analysis [\#3087](https://github.com/kokkos/kokkos/issues/3087)
|
||||||
|
- Move allocation profiling to allocate/deallocate calls [\#3084](https://github.com/kokkos/kokkos/issues/3084)
|
||||||
|
- BuildSystem: FATAL\_ERROR when attempting in-source build [\#3082](https://github.com/kokkos/kokkos/issues/3082)
|
||||||
|
- Change enums in ScatterView to types [\#3076](https://github.com/kokkos/kokkos/issues/3076)
|
||||||
|
- HIP: Changes for new compiler/runtime [\#3067](https://github.com/kokkos/kokkos/issues/3067)
|
||||||
|
- Extract and use get\_gpu [\#3061](https://github.com/kokkos/kokkos/issues/3061)
|
||||||
|
- Extract and use get\_gpu [\#3048](https://github.com/kokkos/kokkos/issues/3048)
|
||||||
|
- Add is\_allocated to View-like containers [\#3059](https://github.com/kokkos/kokkos/issues/3059)
|
||||||
|
- Combined reducers for scalar references [\#3052](https://github.com/kokkos/kokkos/issues/3052)
|
||||||
|
- Add configurable capacity for UniqueToken [\#3051](https://github.com/kokkos/kokkos/issues/3051)
|
||||||
|
- Add installation testing [\#3034](https://github.com/kokkos/kokkos/issues/3034)
|
||||||
|
- BuildSystem: Add -expt-relaxed-constexpr flag to nvcc\_wrapper [\#3021](https://github.com/kokkos/kokkos/issues/3021)
|
||||||
|
- HIP: Add UniqueToken [\#3020](https://github.com/kokkos/kokkos/issues/3020)
|
||||||
|
- Autodetect number of devices [\#3013](https://github.com/kokkos/kokkos/issues/3013)
|
||||||
|
|
||||||
|
|
||||||
|
**Fixed bugs:**
|
||||||
|
|
||||||
|
- Check error code from `cudaStreamSynchronize` in CUDA fences [\#3255](https://github.com/kokkos/kokkos/issues/3255)
|
||||||
|
- Fix issue with C++ standard flags when using `nvcc\_wrapper` with PGI [\#3254](https://github.com/kokkos/kokkos/issues/3254)
|
||||||
|
- Add missing threadfence in lock-based atomics [\#3208](https://github.com/kokkos/kokkos/issues/3208)
|
||||||
|
- Fix dedup of linker flags for shared lib on CMake <=3.12 [\#3176](https://github.com/kokkos/kokkos/issues/3176)
|
||||||
|
- Fix memory leak with CUDA streams [\#3170](https://github.com/kokkos/kokkos/issues/3170)
|
||||||
|
- BuildSystem: Fix OpenMP Target flags for Cray [\#3161](https://github.com/kokkos/kokkos/issues/3161)
|
||||||
|
- ScatterView: fix for OpenmpTarget remove inheritance from reducers [\#3162](https://github.com/kokkos/kokkos/issues/3162)
|
||||||
|
- BuildSystem: Set OpenMP flags according to host compiler [\#3127](https://github.com/kokkos/kokkos/issues/3127)
|
||||||
|
- OpenMP: Fix logic for nested omp in partition\_master bug [\#3101](https://github.com/kokkos/kokkos/issues/3101)
|
||||||
|
- BuildSystem: Fixes for Cuda/11 and c++17 [\#3085](https://github.com/kokkos/kokkos/issues/3085)
|
||||||
|
- HIP: Fix print\_configuration [\#3080](https://github.com/kokkos/kokkos/issues/3080)
|
||||||
|
- Conditionally define get\_gpu [\#3072](https://github.com/kokkos/kokkos/issues/3072)
|
||||||
|
- Fix bounds for ranges in random number generator [\#3069](https://github.com/kokkos/kokkos/issues/3069)
|
||||||
|
- Fix Cuda minor arch check [\#3035](https://github.com/kokkos/kokkos/issues/3035)
|
||||||
|
|
||||||
|
**Incompatibilities:**
|
||||||
|
|
||||||
|
- Remove ETI support [\#3157](https://github.com/kokkos/kokkos/issues/3157)
|
||||||
|
- Remove KOKKOS\_INTERNAL\_ENABLE\_NON\_CUDA\_BACKEND [\#3147](https://github.com/kokkos/kokkos/issues/3147)
|
||||||
|
- Remove core/unit\_test/config [\#3146](https://github.com/kokkos/kokkos/issues/3146)
|
||||||
|
- Removed the preprocessor branch for KOKKOS\_ENABLE\_PROFILING [\#3115](https://github.com/kokkos/kokkos/issues/3115)
|
||||||
|
- Disable profiling with MSVC [\#3066](https://github.com/kokkos/kokkos/issues/3066)
|
||||||
|
|
||||||
|
**Closed issues:**
|
||||||
|
|
||||||
|
- Silent error (Validate storage level arg to set_scratch_size) [\#3097](https://github.com/kokkos/kokkos/issues/3097)
|
||||||
|
- Remove KOKKKOS\_ENABLE\_PROFILING Option [\#3095](https://github.com/kokkos/kokkos/issues/3095)
|
||||||
|
- Cuda 11 -\> allow C++17 [\#3083](https://github.com/kokkos/kokkos/issues/3083)
|
||||||
|
- In source build failure not explained [\#3081](https://github.com/kokkos/kokkos/issues/3081)
|
||||||
|
- Allow naming of Views for initialization kernel [\#3070](https://github.com/kokkos/kokkos/issues/3070)
|
||||||
|
- DefaultInit tests failing when using CTest resource allocation feature [\#3040](https://github.com/kokkos/kokkos/issues/3040)
|
||||||
|
- Add installation testing. [\#3037](https://github.com/kokkos/kokkos/issues/3037)
|
||||||
|
- nvcc\_wrapper needs to handle `-expt-relaxed-constexpr` flag [\#3017](https://github.com/kokkos/kokkos/issues/3017)
|
||||||
|
- CPU core oversubscription warning on macOS with OpenMP backend [\#2996](https://github.com/kokkos/kokkos/issues/2996)
|
||||||
|
- Default behavior of KOKKOS\_NUM\_DEVICES to use all devices available [\#2975](https://github.com/kokkos/kokkos/issues/2975)
|
||||||
|
- Assert blocksize \> 0 [\#2974](https://github.com/kokkos/kokkos/issues/2974)
|
||||||
|
- Add ability to assign kokkos profile function from executable [\#2973](https://github.com/kokkos/kokkos/issues/2973)
|
||||||
|
- ScatterView Support for the pre/post increment operator [\#2967](https://github.com/kokkos/kokkos/issues/2967)
|
||||||
|
|
||||||
|
- Compiler issue: Cuda build with clang 10 has errors with the atomic unit tests [\#3237](https://github.com/kokkos/kokkos/issues/3237)
|
||||||
|
- Incompatibility of flags for C++ standard with PGI v20.4 on Power9/NVIDIA V100 system [\#3252](https://github.com/kokkos/kokkos/issues/3252)
|
||||||
|
- Error configuring as subproject [\#3140](https://github.com/kokkos/kokkos/issues/3140)
|
||||||
|
- CMake fails with Nvidia compilers when the GPU architecture option is not supplied (Fix configure with OMPT and Cuda) [\#3207](https://github.com/kokkos/kokkos/issues/3207)
|
||||||
|
- PGI compiler being passed the gcc -fopenmp flag [\#3125](https://github.com/kokkos/kokkos/issues/3125)
|
||||||
|
- Cuda: Memory leak when using CUDA stream [\#3167](https://github.com/kokkos/kokkos/issues/3167)
|
||||||
|
- RangePolicy has an implicitly deleted assignment operator [\#3192](https://github.com/kokkos/kokkos/issues/3192)
|
||||||
|
- MemorySpace::allocate needs to have memory pool counting. [\#3064](https://github.com/kokkos/kokkos/issues/3064)
|
||||||
|
- Missing write fence for lock based atomics on CUDA [\#3038](https://github.com/kokkos/kokkos/issues/3038)
|
||||||
|
- CUDA compute capability version check problem [\#3026](https://github.com/kokkos/kokkos/issues/3026)
|
||||||
|
- Make DynRankView fencing consistent [\#3014](https://github.com/kokkos/kokkos/issues/3014)
|
||||||
|
- nvcc\_wrapper cant handle -Xcompiler -o out.o [\#2993](https://github.com/kokkos/kokkos/issues/2993)
|
||||||
|
- Reductions of non-trivial types of size 4 fail in CUDA shfl operations [\#2990](https://github.com/kokkos/kokkos/issues/2990)
|
||||||
|
- complex\_double misalignment in reduce, clang+CUDA [\#2989](https://github.com/kokkos/kokkos/issues/2989)
|
||||||
|
- Span of degenerated \(zero-length\) subviews is not zero in some special cases [\#2979](https://github.com/kokkos/kokkos/issues/2979)
|
||||||
|
- Rank 1 custom layouts dont work as expected. [\#2840](https://github.com/kokkos/kokkos/issues/2840)
|
||||||
|
|
||||||
|
## [3.1.01](https://github.com/kokkos/kokkos/tree/3.1.1) (2020-04-14)
|
||||||
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.1.00...3.1.1)
|
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.1.00...3.1.1)
|
||||||
|
|
||||||
**Fixed bugs:**
|
**Fixed bugs:**
|
||||||
|
|||||||
@ -1,4 +1,9 @@
|
|||||||
|
|
||||||
|
# Disable in-source builds to prevent source tree corruption.
|
||||||
|
if( "${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_BINARY_DIR}" )
|
||||||
|
message( FATAL_ERROR "FATAL: In-source builds are not allowed. You should create a separate directory for build files." )
|
||||||
|
endif()
|
||||||
|
|
||||||
# We want to determine if options are given with the wrong case
|
# We want to determine if options are given with the wrong case
|
||||||
# In order to detect which arguments are given to compare against
|
# In order to detect which arguments are given to compare against
|
||||||
# the list of valid arguments, at the beginning here we need to
|
# the list of valid arguments, at the beginning here we need to
|
||||||
@ -34,6 +39,9 @@ IF(COMMAND TRIBITS_PACKAGE_DECL)
|
|||||||
ELSE()
|
ELSE()
|
||||||
SET(KOKKOS_HAS_TRILINOS OFF)
|
SET(KOKKOS_HAS_TRILINOS OFF)
|
||||||
ENDIF()
|
ENDIF()
|
||||||
|
# Is this build a subdirectory of another project
|
||||||
|
GET_DIRECTORY_PROPERTY(HAS_PARENT PARENT_DIRECTORY)
|
||||||
|
|
||||||
|
|
||||||
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_functions.cmake)
|
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_functions.cmake)
|
||||||
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_pick_cxx_std.cmake)
|
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_pick_cxx_std.cmake)
|
||||||
@ -75,16 +83,17 @@ IF(NOT KOKKOS_HAS_TRILINOS)
|
|||||||
SET(CMAKE_CXX_COMPILER ${SPACK_CXX} CACHE STRING "the C++ compiler" FORCE)
|
SET(CMAKE_CXX_COMPILER ${SPACK_CXX} CACHE STRING "the C++ compiler" FORCE)
|
||||||
SET(ENV{CXX} ${SPACK_CXX})
|
SET(ENV{CXX} ${SPACK_CXX})
|
||||||
ENDIF()
|
ENDIF()
|
||||||
ENDif()
|
|
||||||
IF(NOT DEFINED ${PROJECT_NAME})
|
|
||||||
# WORKAROUND FOR HIPCC
|
|
||||||
IF(Kokkos_ENABLE_HIP)
|
|
||||||
SET(KOKKOS_INTERNAL_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
|
|
||||||
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --amdgpu-target=gfx906")
|
|
||||||
ENDIF()
|
ENDIF()
|
||||||
|
# Always call the project command to define Kokkos_ variables
|
||||||
|
# and to make sure that C++ is an enabled language
|
||||||
PROJECT(Kokkos CXX)
|
PROJECT(Kokkos CXX)
|
||||||
IF(Kokkos_ENABLE_HIP)
|
IF(NOT HAS_PARENT)
|
||||||
SET(CMAKE_CXX_FLAGS ${KOKKOS_INTERNAL_CMAKE_CXX_FLAGS})
|
IF (NOT CMAKE_BUILD_TYPE)
|
||||||
|
SET(DEFAULT_BUILD_TYPE "RelWithDebInfo")
|
||||||
|
MESSAGE(STATUS "Setting build type to '${DEFAULT_BUILD_TYPE}' as none was specified.")
|
||||||
|
SET(CMAKE_BUILD_TYPE "${DEFAULT_BUILD_TYPE}" CACHE STRING
|
||||||
|
"Choose the type of build, options are: Debug, Release, RelWithDebInfo and MinSizeRel."
|
||||||
|
FORCE)
|
||||||
ENDIF()
|
ENDIF()
|
||||||
ENDIF()
|
ENDIF()
|
||||||
ENDIF()
|
ENDIF()
|
||||||
@ -102,8 +111,8 @@ ENDIF()
|
|||||||
|
|
||||||
|
|
||||||
set(Kokkos_VERSION_MAJOR 3)
|
set(Kokkos_VERSION_MAJOR 3)
|
||||||
set(Kokkos_VERSION_MINOR 1)
|
set(Kokkos_VERSION_MINOR 2)
|
||||||
set(Kokkos_VERSION_PATCH 1)
|
set(Kokkos_VERSION_PATCH 0)
|
||||||
set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
|
set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
|
||||||
math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}")
|
math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}")
|
||||||
|
|
||||||
@ -147,6 +156,7 @@ INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_tribits.cmake)
|
|||||||
# Check the environment and set certain variables
|
# Check the environment and set certain variables
|
||||||
# to allow platform-specific checks
|
# to allow platform-specific checks
|
||||||
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_check_env.cmake)
|
INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_check_env.cmake)
|
||||||
|
|
||||||
# The build environment setup goes in the following steps
|
# The build environment setup goes in the following steps
|
||||||
# 1) Check all the enable options. This includes checking Kokkos_DEVICES
|
# 1) Check all the enable options. This includes checking Kokkos_DEVICES
|
||||||
# 2) Check the compiler ID (type and version)
|
# 2) Check the compiler ID (type and version)
|
||||||
@ -169,7 +179,6 @@ SET(KOKKOS_EXT_LIBRARIES Kokkos::kokkos Kokkos::kokkoscore Kokkos::kokkoscontain
|
|||||||
SET(KOKKOS_INT_LIBRARIES kokkos kokkoscore kokkoscontainers kokkosalgorithms)
|
SET(KOKKOS_INT_LIBRARIES kokkos kokkoscore kokkoscontainers kokkosalgorithms)
|
||||||
SET_PROPERTY(GLOBAL PROPERTY KOKKOS_INT_LIBRARIES ${KOKKOS_INT_LIBRARIES})
|
SET_PROPERTY(GLOBAL PROPERTY KOKKOS_INT_LIBRARIES ${KOKKOS_INT_LIBRARIES})
|
||||||
|
|
||||||
GET_DIRECTORY_PROPERTY(HAS_PARENT PARENT_DIRECTORY)
|
|
||||||
IF (KOKKOS_HAS_TRILINOS)
|
IF (KOKKOS_HAS_TRILINOS)
|
||||||
SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
|
SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
|
||||||
SET(KOKKOS_HEADER_DIR ${TRILINOS_INCDIR})
|
SET(KOKKOS_HEADER_DIR ${TRILINOS_INCDIR})
|
||||||
@ -203,7 +212,7 @@ IF (KOKKOS_HAS_TRILINOS)
|
|||||||
SET(KOKKOSCORE_XCOMPILER_OPTIONS "${KOKKOSCORE_XCOMPILER_OPTIONS} -Xcompiler ${XCOMP_FLAG}")
|
SET(KOKKOSCORE_XCOMPILER_OPTIONS "${KOKKOSCORE_XCOMPILER_OPTIONS} -Xcompiler ${XCOMP_FLAG}")
|
||||||
LIST(APPEND KOKKOS_ALL_COMPILE_OPTIONS -Xcompiler ${XCOMP_FLAG})
|
LIST(APPEND KOKKOS_ALL_COMPILE_OPTIONS -Xcompiler ${XCOMP_FLAG})
|
||||||
ENDFOREACH()
|
ENDFOREACH()
|
||||||
SET(KOKKOSCORE_CXX_FLAGS "${KOKKOSCORE_COMPILE_OPTIONS} ${CMAKE_CXX${KOKKOS_CXX_STANDARD}_STANDARD_COMPILE_OPTION} ${KOKKOSCORE_XCOMPILER_OPTIONS}")
|
SET(KOKKOSCORE_CXX_FLAGS "${KOKKOSCORE_COMPILE_OPTIONS} ${KOKKOSCORE_XCOMPILER_OPTIONS}")
|
||||||
IF (KOKKOS_ENABLE_CUDA)
|
IF (KOKKOS_ENABLE_CUDA)
|
||||||
STRING(REPLACE ";" " " KOKKOSCORE_CUDA_OPTIONS "${KOKKOS_CUDA_OPTIONS}")
|
STRING(REPLACE ";" " " KOKKOSCORE_CUDA_OPTIONS "${KOKKOS_CUDA_OPTIONS}")
|
||||||
FOREACH(CUDAFE_FLAG ${KOKKOS_CUDAFE_OPTIONS})
|
FOREACH(CUDAFE_FLAG ${KOKKOS_CUDAFE_OPTIONS})
|
||||||
@ -246,7 +255,7 @@ KOKKOS_PACKAGE_POSTPROCESS()
|
|||||||
#We are ready to configure the header
|
#We are ready to configure the header
|
||||||
CONFIGURE_FILE(cmake/KokkosCore_config.h.in KokkosCore_config.h @ONLY)
|
CONFIGURE_FILE(cmake/KokkosCore_config.h.in KokkosCore_config.h @ONLY)
|
||||||
|
|
||||||
IF (NOT KOKKOS_HAS_TRILINOS)
|
IF (NOT KOKKOS_HAS_TRILINOS AND NOT Kokkos_INSTALL_TESTING)
|
||||||
ADD_LIBRARY(kokkos INTERFACE)
|
ADD_LIBRARY(kokkos INTERFACE)
|
||||||
#Make sure in-tree projects can reference this as Kokkos::
|
#Make sure in-tree projects can reference this as Kokkos::
|
||||||
#to match the installed target names
|
#to match the installed target names
|
||||||
@ -262,8 +271,6 @@ INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_install.cmake)
|
|||||||
# If the argument of DESTINATION is a relative path, CMake computes it
|
# If the argument of DESTINATION is a relative path, CMake computes it
|
||||||
# as relative to ${CMAKE_INSTALL_PATH}.
|
# as relative to ${CMAKE_INSTALL_PATH}.
|
||||||
INSTALL(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper DESTINATION ${CMAKE_INSTALL_BINDIR})
|
INSTALL(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||||
INSTALL(FILES "${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_config.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
|
|
||||||
|
|
||||||
|
|
||||||
# Finally - if we are a subproject - make sure the enabled devices are visible
|
# Finally - if we are a subproject - make sure the enabled devices are visible
|
||||||
IF (HAS_PARENT)
|
IF (HAS_PARENT)
|
||||||
|
|||||||
@ -11,8 +11,8 @@ CXXFLAGS += $(SHFLAGS)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
KOKKOS_VERSION_MAJOR = 3
|
KOKKOS_VERSION_MAJOR = 3
|
||||||
KOKKOS_VERSION_MINOR = 1
|
KOKKOS_VERSION_MINOR = 2
|
||||||
KOKKOS_VERSION_PATCH = 1
|
KOKKOS_VERSION_PATCH = 0
|
||||||
KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc)
|
KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc)
|
||||||
|
|
||||||
# Options: Cuda,HIP,ROCm,OpenMP,Pthread,Serial
|
# Options: Cuda,HIP,ROCm,OpenMP,Pthread,Serial
|
||||||
@ -20,11 +20,11 @@ KOKKOS_DEVICES ?= "OpenMP"
|
|||||||
#KOKKOS_DEVICES ?= "Pthread"
|
#KOKKOS_DEVICES ?= "Pthread"
|
||||||
# Options:
|
# Options:
|
||||||
# Intel: KNC,KNL,SNB,HSW,BDW,SKX
|
# Intel: KNC,KNL,SNB,HSW,BDW,SKX
|
||||||
# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75
|
# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80
|
||||||
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2
|
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2
|
||||||
# IBM: BGQ,Power7,Power8,Power9
|
# IBM: BGQ,Power7,Power8,Power9
|
||||||
# AMD-GPUS: Vega900,Vega906
|
# AMD-GPUS: Vega900,Vega906
|
||||||
# AMD-CPUS: AMDAVX,EPYC
|
# AMD-CPUS: AMDAVX,Zen,Zen2
|
||||||
KOKKOS_ARCH ?= ""
|
KOKKOS_ARCH ?= ""
|
||||||
# Options: yes,no
|
# Options: yes,no
|
||||||
KOKKOS_DEBUG ?= "no"
|
KOKKOS_DEBUG ?= "no"
|
||||||
@ -32,10 +32,8 @@ KOKKOS_DEBUG ?= "no"
|
|||||||
KOKKOS_USE_TPLS ?= ""
|
KOKKOS_USE_TPLS ?= ""
|
||||||
# Options: c++11,c++14,c++1y,c++17,c++1z,c++2a
|
# Options: c++11,c++14,c++1y,c++17,c++1z,c++2a
|
||||||
KOKKOS_CXX_STANDARD ?= "c++11"
|
KOKKOS_CXX_STANDARD ?= "c++11"
|
||||||
# Options: aggressive_vectorization,disable_profiling,enable_deprecated_code,disable_deprecated_code,enable_large_mem_tests,disable_complex_align
|
# Options: aggressive_vectorization,disable_profiling,enable_large_mem_tests,disable_complex_align
|
||||||
KOKKOS_OPTIONS ?= ""
|
KOKKOS_OPTIONS ?= ""
|
||||||
# Option for setting ETI path
|
|
||||||
KOKKOS_ETI_PATH ?= ${KOKKOS_PATH}/core/src/eti
|
|
||||||
KOKKOS_CMAKE ?= "no"
|
KOKKOS_CMAKE ?= "no"
|
||||||
KOKKOS_TRIBITS ?= "no"
|
KOKKOS_TRIBITS ?= "no"
|
||||||
KOKKOS_STANDALONE_CMAKE ?= "no"
|
KOKKOS_STANDALONE_CMAKE ?= "no"
|
||||||
@ -74,6 +72,7 @@ KOKKOS_INTERNAL_ENABLE_CXX1Y := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),
|
|||||||
KOKKOS_INTERNAL_ENABLE_CXX17 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++17)
|
KOKKOS_INTERNAL_ENABLE_CXX17 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++17)
|
||||||
KOKKOS_INTERNAL_ENABLE_CXX1Z := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++1z)
|
KOKKOS_INTERNAL_ENABLE_CXX1Z := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++1z)
|
||||||
KOKKOS_INTERNAL_ENABLE_CXX2A := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++2a)
|
KOKKOS_INTERNAL_ENABLE_CXX2A := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++2a)
|
||||||
|
KOKKOS_INTERNAL_ENABLE_CXX20 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++20)
|
||||||
|
|
||||||
# Check for external libraries.
|
# Check for external libraries.
|
||||||
KOKKOS_INTERNAL_USE_HWLOC := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),hwloc)
|
KOKKOS_INTERNAL_USE_HWLOC := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),hwloc)
|
||||||
@ -83,9 +82,7 @@ KOKKOS_INTERNAL_USE_MEMKIND := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),exper
|
|||||||
# Check for advanced settings.
|
# Check for advanced settings.
|
||||||
KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),compiler_warnings)
|
KOKKOS_INTERNAL_ENABLE_COMPILER_WARNINGS := $(call kokkos_has_string,$(KOKKOS_OPTIONS),compiler_warnings)
|
||||||
KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization)
|
KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(call kokkos_has_string,$(KOKKOS_OPTIONS),aggressive_vectorization)
|
||||||
KOKKOS_INTERNAL_DISABLE_PROFILING := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_profiling)
|
KOKKOS_INTERNAL_ENABLE_TUNING := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_tuning)
|
||||||
KOKKOS_INTERNAL_DISABLE_DEPRECATED_CODE := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_deprecated_code)
|
|
||||||
KOKKOS_INTERNAL_ENABLE_DEPRECATED_CODE := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_deprecated_code)
|
|
||||||
KOKKOS_INTERNAL_DISABLE_COMPLEX_ALIGN := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_complex_align)
|
KOKKOS_INTERNAL_DISABLE_COMPLEX_ALIGN := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_complex_align)
|
||||||
KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_dualview_modify_check)
|
KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(call kokkos_has_string,$(KOKKOS_OPTIONS),disable_dualview_modify_check)
|
||||||
KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_profile_load_print)
|
KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_profile_load_print)
|
||||||
@ -96,7 +93,6 @@ KOKKOS_INTERNAL_CUDA_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS
|
|||||||
KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_lambda)
|
KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_lambda)
|
||||||
KOKKOS_INTERNAL_CUDA_USE_CONSTEXPR := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_constexpr)
|
KOKKOS_INTERNAL_CUDA_USE_CONSTEXPR := $(call kokkos_has_string,$(KOKKOS_CUDA_OPTIONS),enable_constexpr)
|
||||||
KOKKOS_INTERNAL_HPX_ENABLE_ASYNC_DISPATCH := $(call kokkos_has_string,$(KOKKOS_HPX_OPTIONS),enable_async_dispatch)
|
KOKKOS_INTERNAL_HPX_ENABLE_ASYNC_DISPATCH := $(call kokkos_has_string,$(KOKKOS_HPX_OPTIONS),enable_async_dispatch)
|
||||||
KOKKOS_INTERNAL_ENABLE_ETI := $(call kokkos_has_string,$(KOKKOS_OPTIONS),enable_eti)
|
|
||||||
|
|
||||||
KOKKOS_INTERNAL_HIP_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_HIP_OPTIONS),rdc)
|
KOKKOS_INTERNAL_HIP_USE_RELOC := $(call kokkos_has_string,$(KOKKOS_HIP_OPTIONS),rdc)
|
||||||
|
|
||||||
@ -140,6 +136,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
|||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
|
||||||
KOKKOS_DEVICELIST += OPENMPTARGET
|
KOKKOS_DEVICELIST += OPENMPTARGET
|
||||||
|
KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER := $(shell expr $(KOKKOS_INTERNAL_ENABLE_CXX17) \
|
||||||
|
+ $(KOKKOS_INTERNAL_ENABLE_CXX20) \
|
||||||
|
+ $(KOKKOS_INTERNAL_ENABLE_CXX2A))
|
||||||
|
ifneq ($(KOKKOS_INTERNAL_HAVE_CXX17_OR_NEWER), 1)
|
||||||
|
$(error OpenMPTarget backend requires C++17 or newer)
|
||||||
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||||
@ -281,7 +283,7 @@ endif
|
|||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
||||||
KOKKOS_INTERNAL_CXX11_FLAG := --c++11
|
KOKKOS_INTERNAL_CXX11_FLAG := --c++11
|
||||||
KOKKOS_INTERNAL_CXX14_FLAG := --c++14
|
KOKKOS_INTERNAL_CXX14_FLAG := --c++14
|
||||||
#KOKKOS_INTERNAL_CXX17_FLAG := --c++17
|
KOKKOS_INTERNAL_CXX17_FLAG := --c++17
|
||||||
else
|
else
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1)
|
||||||
KOKKOS_INTERNAL_CXX11_FLAG := -std=c++11
|
KOKKOS_INTERNAL_CXX11_FLAG := -std=c++11
|
||||||
@ -338,35 +340,27 @@ KOKKOS_INTERNAL_USE_ARCH_PASCAL60 := $(call kokkos_has_string,$(KOKKOS_ARCH),Pas
|
|||||||
KOKKOS_INTERNAL_USE_ARCH_VOLTA70 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta70)
|
KOKKOS_INTERNAL_USE_ARCH_VOLTA70 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta70)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_VOLTA72 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta72)
|
KOKKOS_INTERNAL_USE_ARCH_VOLTA72 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta72)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_TURING75 := $(call kokkos_has_string,$(KOKKOS_ARCH),Turing75)
|
KOKKOS_INTERNAL_USE_ARCH_TURING75 := $(call kokkos_has_string,$(KOKKOS_ARCH),Turing75)
|
||||||
|
KOKKOS_INTERNAL_USE_ARCH_AMPERE80 := $(call kokkos_has_string,$(KOKKOS_ARCH),Ampere80)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30) \
|
KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37) \
|
||||||
|
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
|
||||||
|
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
|
||||||
|
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_AMPERE80))
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53))
|
|
||||||
|
|
||||||
#SEK: This seems like a bug to me
|
#SEK: This seems like a bug to me
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_MAXWELL50 := $(call kokkos_has_string,$(KOKKOS_ARCH),Maxwell)
|
KOKKOS_INTERNAL_USE_ARCH_MAXWELL50 := $(call kokkos_has_string,$(KOKKOS_ARCH),Maxwell)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler)
|
KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(call kokkos_has_string,$(KOKKOS_ARCH),Kepler)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30) \
|
KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32) \
|
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50))
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_KEPLER37) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_PASCAL61) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \
|
|
||||||
+ $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53))
|
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 1)
|
||||||
@ -394,19 +388,20 @@ KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_
|
|||||||
|
|
||||||
# AMD based.
|
# AMD based.
|
||||||
KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX)
|
KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_EPYC := $(call kokkos_has_string,$(KOKKOS_ARCH),EPYC)
|
KOKKOS_INTERNAL_USE_ARCH_ZEN2 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen2)
|
||||||
|
KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900)
|
KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900)
|
||||||
KOKKOS_INTERNAL_USE_ARCH_VEGA906 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega906)
|
KOKKOS_INTERNAL_USE_ARCH_VEGA906 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega906)
|
||||||
|
|
||||||
# Any AVX?
|
# Any AVX?
|
||||||
KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM))
|
KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM))
|
||||||
KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX))
|
KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX))
|
||||||
KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_EPYC))
|
KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2))
|
||||||
KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL))
|
KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL))
|
||||||
KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SKX))
|
KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SKX))
|
||||||
|
|
||||||
# Decide what ISA level we are able to support.
|
# Decide what ISA level we are able to support.
|
||||||
KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_EPYC))
|
KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN) + $(KOKKOS_INTERNAL_USE_ARCH_ZEN2))
|
||||||
KOKKOS_INTERNAL_USE_ISA_KNC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNC))
|
KOKKOS_INTERNAL_USE_ISA_KNC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNC))
|
||||||
KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER8) + $(KOKKOS_INTERNAL_USE_ARCH_POWER9))
|
KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER8) + $(KOKKOS_INTERNAL_USE_ARCH_POWER9))
|
||||||
KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER7))
|
KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER7))
|
||||||
@ -430,7 +425,7 @@ endif
|
|||||||
KOKKOS_CPPFLAGS =
|
KOKKOS_CPPFLAGS =
|
||||||
KOKKOS_LIBDIRS =
|
KOKKOS_LIBDIRS =
|
||||||
ifneq ($(KOKKOS_CMAKE), yes)
|
ifneq ($(KOKKOS_CMAKE), yes)
|
||||||
KOKKOS_CPPFLAGS = -I./ -I$(KOKKOS_PATH)/core/src -I$(KOKKOS_PATH)/containers/src -I$(KOKKOS_PATH)/algorithms/src -I$(KOKKOS_ETI_PATH)
|
KOKKOS_CPPFLAGS = -I./ -I$(KOKKOS_PATH)/core/src -I$(KOKKOS_PATH)/containers/src -I$(KOKKOS_PATH)/algorithms/src
|
||||||
endif
|
endif
|
||||||
KOKKOS_TPL_INCLUDE_DIRS =
|
KOKKOS_TPL_INCLUDE_DIRS =
|
||||||
KOKKOS_TPL_LIBRARY_DIRS =
|
KOKKOS_TPL_LIBRARY_DIRS =
|
||||||
@ -458,88 +453,91 @@ KOKKOS_CONFIG_HEADER=KokkosCore_config.h
|
|||||||
# Functions for generating config header file
|
# Functions for generating config header file
|
||||||
kokkos_append_header = $(shell echo $1 >> $(KOKKOS_INTERNAL_CONFIG_TMP))
|
kokkos_append_header = $(shell echo $1 >> $(KOKKOS_INTERNAL_CONFIG_TMP))
|
||||||
|
|
||||||
|
# assign hash sign to variable for compat. with make 4.3
|
||||||
|
H := \#
|
||||||
|
|
||||||
# Do not append first line
|
# Do not append first line
|
||||||
tmp := $(shell echo "/* ---------------------------------------------" > KokkosCore_config.tmp)
|
tmp := $(shell echo "/* ---------------------------------------------" > KokkosCore_config.tmp)
|
||||||
tmp := $(call kokkos_append_header,"Makefile constructed configuration:")
|
tmp := $(call kokkos_append_header,"Makefile constructed configuration:")
|
||||||
tmp := $(call kokkos_append_header,"$(shell date)")
|
tmp := $(call kokkos_append_header,"$(shell date)")
|
||||||
tmp := $(call kokkos_append_header,"----------------------------------------------*/")
|
tmp := $(call kokkos_append_header,"----------------------------------------------*/")
|
||||||
|
|
||||||
tmp := $(call kokkos_append_header,'\#if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)')
|
tmp := $(call kokkos_append_header,'$H''if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)')
|
||||||
tmp := $(call kokkos_append_header,'\#error "Do not include $(KOKKOS_CONFIG_HEADER) directly; include Kokkos_Macros.hpp instead."')
|
tmp := $(call kokkos_append_header,'$H''error "Do not include $(KOKKOS_CONFIG_HEADER) directly; include Kokkos_Macros.hpp instead."')
|
||||||
tmp := $(call kokkos_append_header,'\#else')
|
tmp := $(call kokkos_append_header,'$H''else')
|
||||||
tmp := $(call kokkos_append_header,'\#define KOKKOS_CORE_CONFIG_H')
|
tmp := $(call kokkos_append_header,'$H''define KOKKOS_CORE_CONFIG_H')
|
||||||
tmp := $(call kokkos_append_header,'\#endif')
|
tmp := $(call kokkos_append_header,'$H''endif')
|
||||||
|
|
||||||
tmp := $(call kokkos_append_header,"")
|
tmp := $(call kokkos_append_header,"")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_VERSION $(KOKKOS_VERSION)")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_VERSION $(KOKKOS_VERSION)")
|
||||||
tmp := $(call kokkos_append_header,"")
|
tmp := $(call kokkos_append_header,"")
|
||||||
|
|
||||||
tmp := $(call kokkos_append_header,"/* Execution Spaces */")
|
tmp := $(call kokkos_append_header,"/* Execution Spaces */")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_COMPILER_CUDA_VERSION $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION)")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_COMPILER_CUDA_VERSION $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION)")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
|
||||||
tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_ROCM')
|
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_ROCM')
|
||||||
tmp := $(call kokkos_append_header,'\#define KOKKOS_IMPL_ROCM_CLANG_WORKAROUND 1')
|
tmp := $(call kokkos_append_header,'$H''define KOKKOS_IMPL_ROCM_CLANG_WORKAROUND 1')
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
||||||
tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_HIP')
|
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_HIP')
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
|
||||||
tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_OPENMPTARGET')
|
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_OPENMPTARGET')
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_GCC), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_WORKAROUND_OPENMPTARGET_GCC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_WORKAROUND_OPENMPTARGET_GCC")
|
||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
|
||||||
tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_OPENMP')
|
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_OPENMP')
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_THREADS")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_THREADS")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_HPX")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_HPX")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_SERIAL")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_SERIAL")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_TM), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_TM), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
|
tmp := $(call kokkos_append_header,"$H""ifndef __CUDA_ARCH__")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_TM")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_TM")
|
||||||
tmp := $(call kokkos_append_header,"\#endif")
|
tmp := $(call kokkos_append_header,"$H""endif")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ISA_X86_64), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ISA_X86_64), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
|
tmp := $(call kokkos_append_header,"$H""ifndef __CUDA_ARCH__")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_X86_64")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_USE_ISA_X86_64")
|
||||||
tmp := $(call kokkos_append_header,"\#endif")
|
tmp := $(call kokkos_append_header,"$H""endif")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ISA_KNC), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ISA_KNC), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
|
tmp := $(call kokkos_append_header,"$H""ifndef __CUDA_ARCH__")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_KNC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_USE_ISA_KNC")
|
||||||
tmp := $(call kokkos_append_header,"\#endif")
|
tmp := $(call kokkos_append_header,"$H""endif")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ISA_POWERPCLE), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ISA_POWERPCLE), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
|
tmp := $(call kokkos_append_header,"$H""ifndef __CUDA_ARCH__")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_POWERPCLE")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_USE_ISA_POWERPCLE")
|
||||||
tmp := $(call kokkos_append_header,"\#endif")
|
tmp := $(call kokkos_append_header,"$H""endif")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ISA_POWERPCBE), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ISA_POWERPCBE), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#ifndef __CUDA_ARCH__")
|
tmp := $(call kokkos_append_header,"$H""ifndef __CUDA_ARCH__")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_ISA_POWERPCBE")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_USE_ISA_POWERPCBE")
|
||||||
tmp := $(call kokkos_append_header,"\#endif")
|
tmp := $(call kokkos_append_header,"$H""endif")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
#only add the c++ standard flags if this is not CMake
|
#only add the c++ standard flags if this is not CMake
|
||||||
@ -548,34 +546,39 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX11), 1)
|
|||||||
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
||||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX11_FLAG)
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX11_FLAG)
|
||||||
endif
|
endif
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX11")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX11")
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX14), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX14), 1)
|
||||||
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
||||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX14_FLAG)
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX14_FLAG)
|
||||||
endif
|
endif
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX14")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX14")
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Y), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Y), 1)
|
||||||
#I cannot make CMake add this in a good way - so add it here
|
#I cannot make CMake add this in a good way - so add it here
|
||||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Y_FLAG)
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Y_FLAG)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX14")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX14")
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX17), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX17), 1)
|
||||||
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
|
||||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX17_FLAG)
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX17_FLAG)
|
||||||
endif
|
endif
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX17")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX17")
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Z), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Z), 1)
|
||||||
#I cannot make CMake add this in a good way - so add it here
|
#I cannot make CMake add this in a good way - so add it here
|
||||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Z_FLAG)
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Z_FLAG)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX17")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX17")
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX2A), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX2A), 1)
|
||||||
#I cannot make CMake add this in a good way - so add it here
|
#I cannot make CMake add this in a good way - so add it here
|
||||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX2A_FLAG)
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX2A_FLAG)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX20")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX20")
|
||||||
|
endif
|
||||||
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX20), 1)
|
||||||
|
#I cannot make CMake add this in a good way - so add it here
|
||||||
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX20_FLAG)
|
||||||
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX20")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1)
|
||||||
@ -585,20 +588,26 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1)
|
|||||||
|
|
||||||
KOKKOS_CXXFLAGS += -g
|
KOKKOS_CXXFLAGS += -g
|
||||||
KOKKOS_LDFLAGS += -g
|
KOKKOS_LDFLAGS += -g
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_DEBUG")
|
||||||
ifeq ($(KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK), 0)
|
ifeq ($(KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK), 0)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK")
|
||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_DISABLE_COMPLEX_ALIGN), 0)
|
ifeq ($(KOKKOS_INTERNAL_DISABLE_COMPLEX_ALIGN), 0)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_COMPLEX_ALIGN")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_COMPLEX_ALIGN")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_PROFILING_LOAD_PRINT")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_PROFILING_LOAD_PRINT")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_TUNING), 1)
|
||||||
|
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_TUNING")
|
||||||
|
endif
|
||||||
|
|
||||||
|
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_LIBDL")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1)
|
||||||
ifneq ($(KOKKOS_CMAKE), yes)
|
ifneq ($(KOKKOS_CMAKE), yes)
|
||||||
ifneq ($(HWLOC_PATH),)
|
ifneq ($(HWLOC_PATH),)
|
||||||
@ -611,11 +620,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1)
|
|||||||
KOKKOS_LIBS += -lhwloc
|
KOKKOS_LIBS += -lhwloc
|
||||||
KOKKOS_TPL_LIBRARY_NAMES += hwloc
|
KOKKOS_TPL_LIBRARY_NAMES += hwloc
|
||||||
endif
|
endif
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_HWLOC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_HWLOC")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_USE_LIBRT")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_USE_LIBRT")
|
||||||
KOKKOS_LIBS += -lrt
|
KOKKOS_LIBS += -lrt
|
||||||
KOKKOS_TPL_LIBRARY_NAMES += rt
|
KOKKOS_TPL_LIBRARY_NAMES += rt
|
||||||
endif
|
endif
|
||||||
@ -632,50 +641,36 @@ ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1)
|
|||||||
KOKKOS_LIBS += -lmemkind -lnuma
|
KOKKOS_LIBS += -lmemkind -lnuma
|
||||||
KOKKOS_TPL_LIBRARY_NAMES += memkind numa
|
KOKKOS_TPL_LIBRARY_NAMES += memkind numa
|
||||||
endif
|
endif
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_HBWSPACE")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_HBWSPACE")
|
||||||
endif
|
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 0)
|
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_PROFILING")
|
|
||||||
endif
|
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 0)
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_DEPRECATED_CODE), 1)
|
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_DEPRECATED_CODE")
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_ETI")
|
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_LARGE_MEM_TESTS), 1)
|
ifeq ($(KOKKOS_INTERNAL_ENABLE_LARGE_MEM_TESTS), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_LARGE_MEM_TESTS")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_LARGE_MEM_TESTS")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
tmp := $(call kokkos_append_header,"/* Optimization Settings */")
|
tmp := $(call kokkos_append_header,"/* Optimization Settings */")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION), 1)
|
ifeq ($(KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_OPT_RANGE_AGGRESSIVE_VECTORIZATION")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
tmp := $(call kokkos_append_header,"/* Cuda Settings */")
|
tmp := $(call kokkos_append_header,"/* Cuda Settings */")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||||
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1)
|
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LDG_INTRINSIC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_LDG_INTRINSIC")
|
||||||
else
|
else
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LDG_INTRINSIC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_LDG_INTRINSIC")
|
||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1)
|
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_UVM")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_UVM")
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1)
|
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE")
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
||||||
KOKKOS_CXXFLAGS += -fcuda-rdc
|
KOKKOS_CXXFLAGS += -fcuda-rdc
|
||||||
KOKKOS_LDFLAGS += -fcuda-rdc
|
KOKKOS_LDFLAGS += -fcuda-rdc
|
||||||
@ -696,7 +691,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
|||||||
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1)
|
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1)
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
|
||||||
ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0)
|
ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LAMBDA")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_LAMBDA")
|
||||||
KOKKOS_CXXFLAGS += -expt-extended-lambda
|
KOKKOS_CXXFLAGS += -expt-extended-lambda
|
||||||
else
|
else
|
||||||
$(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.)
|
$(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.)
|
||||||
@ -704,14 +699,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_LAMBDA")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_LAMBDA")
|
||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_CONSTEXPR), 1)
|
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_CONSTEXPR), 1)
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
|
||||||
ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -ge 80; echo $$?),0)
|
ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -ge 80; echo $$?),0)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_CONSTEXPR")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_CONSTEXPR")
|
||||||
KOKKOS_CXXFLAGS += -expt-relaxed-constexpr
|
KOKKOS_CXXFLAGS += -expt-relaxed-constexpr
|
||||||
else
|
else
|
||||||
$(warning Warning: Cuda relaxed constexpr support was requested but NVCC version is too low. This requires NVCC for Cuda version 8.0 or higher. Disabling relaxed constexpr support now.)
|
$(warning Warning: Cuda relaxed constexpr support was requested but NVCC version is too low. This requires NVCC for Cuda version 8.0 or higher. Disabling relaxed constexpr support now.)
|
||||||
@ -719,25 +714,25 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA_CONSTEXPR")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CUDA_CONSTEXPR")
|
||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_IMPL_CUDA_CLANG_WORKAROUND")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_IMPL_CUDA_CLANG_WORKAROUND")
|
||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
|
||||||
ifeq ($(KOKKOS_INTERNAL_HPX_ENABLE_ASYNC_DISPATCH), 1)
|
ifeq ($(KOKKOS_INTERNAL_HPX_ENABLE_ASYNC_DISPATCH), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_HPX_ASYNC_DISPATCH")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_HPX_ASYNC_DISPATCH")
|
||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
# Add Architecture flags.
|
# Add Architecture flags.
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV80), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV80), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV80")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV80")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
||||||
KOKKOS_CXXFLAGS +=
|
KOKKOS_CXXFLAGS +=
|
||||||
@ -754,7 +749,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV80), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV81")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV81")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
||||||
KOKKOS_CXXFLAGS +=
|
KOKKOS_CXXFLAGS +=
|
||||||
@ -770,9 +765,9 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1)
|
|||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_EPYC), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AMD_EPYC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_ZEN")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AMD_AVX2")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_AVX2")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
KOKKOS_CXXFLAGS += -mavx2
|
KOKKOS_CXXFLAGS += -mavx2
|
||||||
@ -783,9 +778,22 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_EPYC), 1)
|
|||||||
endif
|
endif
|
||||||
endif
|
endif
|
||||||
|
|
||||||
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN2), 1)
|
||||||
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_ZEN2")
|
||||||
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_AVX2")
|
||||||
|
|
||||||
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
|
KOKKOS_CXXFLAGS += -mavx2
|
||||||
|
KOKKOS_LDFLAGS += -mavx2
|
||||||
|
else
|
||||||
|
KOKKOS_CXXFLAGS += -march=znver2 -mtune=znver2
|
||||||
|
KOKKOS_LDFLAGS += -march=znver2 -mtune=znver2
|
||||||
|
endif
|
||||||
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV80")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV80")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV8_THUNDERX")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV8_THUNDERX")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
||||||
KOKKOS_CXXFLAGS +=
|
KOKKOS_CXXFLAGS +=
|
||||||
@ -802,8 +810,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV81")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV81")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV8_THUNDERX2")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_ARMV8_THUNDERX2")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
|
||||||
KOKKOS_CXXFLAGS +=
|
KOKKOS_CXXFLAGS +=
|
||||||
@ -820,7 +828,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_SSE42), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_SSE42), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_SSE42")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_SSE42")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
KOKKOS_CXXFLAGS += -xSSE4.2
|
KOKKOS_CXXFLAGS += -xSSE4.2
|
||||||
@ -842,7 +850,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_SSE42), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
KOKKOS_CXXFLAGS += -mavx
|
KOKKOS_CXXFLAGS += -mavx
|
||||||
@ -864,7 +872,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER7), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER7), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_POWER7")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_POWER7")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
||||||
|
|
||||||
@ -876,7 +884,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER7), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER8), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER8), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_POWER8")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_POWER8")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
||||||
|
|
||||||
@ -897,7 +905,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER8), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_POWER9")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_POWER9")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
|
||||||
|
|
||||||
@ -918,7 +926,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_HSW), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_HSW), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX2")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX2")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
KOKKOS_CXXFLAGS += -xCORE-AVX2
|
KOKKOS_CXXFLAGS += -xCORE-AVX2
|
||||||
@ -940,7 +948,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_HSW), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_BDW), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_BDW), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX2")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX2")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
KOKKOS_CXXFLAGS += -xCORE-AVX2
|
KOKKOS_CXXFLAGS += -xCORE-AVX2
|
||||||
@ -962,7 +970,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_BDW), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX512MIC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX512MIC")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
KOKKOS_CXXFLAGS += -xMIC-AVX512
|
KOKKOS_CXXFLAGS += -xMIC-AVX512
|
||||||
@ -983,7 +991,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AVX512XEON")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AVX512XEON")
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1)
|
||||||
KOKKOS_CXXFLAGS += -xCORE-AVX512
|
KOKKOS_CXXFLAGS += -xCORE-AVX512
|
||||||
@ -1004,7 +1012,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON), 1)
|
|||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KNC), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KNC), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KNC")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KNC")
|
||||||
KOKKOS_CXXFLAGS += -mmic
|
KOKKOS_CXXFLAGS += -mmic
|
||||||
KOKKOS_LDFLAGS += -mmic
|
KOKKOS_LDFLAGS += -mmic
|
||||||
endif
|
endif
|
||||||
@ -1039,65 +1047,70 @@ endif
|
|||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_CUDA_ARCH), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_CUDA_ARCH), 1)
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER30")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER30")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_30
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_30
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER32), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER32), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER32")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER32")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_32
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_32
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER35), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER35), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER35")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER35")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_35
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_35
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER37), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER37), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_KEPLER37")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_KEPLER37")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_37
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_37
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_MAXWELL")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL50")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_MAXWELL50")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_50
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_50
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_MAXWELL")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL52")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_MAXWELL52")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_52
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_52
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_MAXWELL")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_MAXWELL53")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_MAXWELL53")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_53
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_53
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL60), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL60), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_PASCAL")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL60")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_PASCAL60")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_60
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_60
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_PASCAL")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_PASCAL61")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_PASCAL61")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_61
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_61
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VOLTA70), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VOLTA70), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VOLTA")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA70")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VOLTA70")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_70
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_70
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VOLTA72), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VOLTA72), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VOLTA")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA72")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VOLTA72")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_72
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_72
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_TURING75), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_TURING75), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_TURING")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_TURING")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_TURING75")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_TURING75")
|
||||||
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_75
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_75
|
||||||
endif
|
endif
|
||||||
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMPERE80), 1)
|
||||||
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE")
|
||||||
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMPERE80")
|
||||||
|
KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_80
|
||||||
|
endif
|
||||||
|
|
||||||
ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0)
|
ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0)
|
||||||
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)
|
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)
|
||||||
@ -1121,13 +1134,13 @@ endif
|
|||||||
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
||||||
# Lets start with adding architecture defines
|
# Lets start with adding architecture defines
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA900), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA900), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_HIP 900")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_HIP 900")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VEGA900")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA900")
|
||||||
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx900
|
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx900
|
||||||
endif
|
endif
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA906), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA906), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_HIP 906")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_HIP 906")
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VEGA906")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA906")
|
||||||
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx906
|
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx906
|
||||||
endif
|
endif
|
||||||
|
|
||||||
@ -1138,7 +1151,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
|||||||
KOKKOS_LDFLAGS+=$(KOKKOS_INTERNAL_HIP_ARCH_FLAG)
|
KOKKOS_LDFLAGS+=$(KOKKOS_INTERNAL_HIP_ARCH_FLAG)
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_HIP_USE_RELOC), 1)
|
ifeq ($(KOKKOS_INTERNAL_HIP_USE_RELOC), 1)
|
||||||
tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE")
|
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_HIP_RELOCATABLE_DEVICE_CODE")
|
||||||
KOKKOS_CXXFLAGS+=-fgpu-rdc
|
KOKKOS_CXXFLAGS+=-fgpu-rdc
|
||||||
KOKKOS_LDFLAGS+=-fgpu-rdc
|
KOKKOS_LDFLAGS+=-fgpu-rdc
|
||||||
else
|
else
|
||||||
@ -1171,9 +1184,6 @@ KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/containers/src/impl/*.cpp)
|
|||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||||
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp)
|
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp)
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/Cuda/*.cpp)
|
|
||||||
endif
|
|
||||||
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp)
|
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp)
|
||||||
ifneq ($(CUDA_PATH),)
|
ifneq ($(CUDA_PATH),)
|
||||||
KOKKOS_CPPLAGS += -I$(CUDA_PATH)/include
|
KOKKOS_CPPLAGS += -I$(CUDA_PATH)/include
|
||||||
@ -1211,9 +1221,6 @@ endif
|
|||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
|
||||||
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/OpenMP/*.cpp)
|
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/OpenMP/*.cpp)
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/OpenMP/*.cpp)
|
|
||||||
endif
|
|
||||||
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/OpenMP/*.hpp)
|
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/OpenMP/*.hpp)
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
|
ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1)
|
||||||
@ -1228,9 +1235,6 @@ endif
|
|||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
||||||
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.cpp)
|
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.cpp)
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/Threads/*.cpp)
|
|
||||||
endif
|
|
||||||
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.hpp)
|
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Threads/*.hpp)
|
||||||
KOKKOS_LIBS += -lpthread
|
KOKKOS_LIBS += -lpthread
|
||||||
KOKKOS_TPL_LIBRARY_NAMES += pthread
|
KOKKOS_TPL_LIBRARY_NAMES += pthread
|
||||||
@ -1279,9 +1283,6 @@ endif
|
|||||||
# Don't include Kokkos_Serial.cpp or Kokkos_Serial_Task.cpp if not using Serial
|
# Don't include Kokkos_Serial.cpp or Kokkos_Serial_Task.cpp if not using Serial
|
||||||
# device to avoid a link warning.
|
# device to avoid a link warning.
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
KOKKOS_SRC += $(wildcard $(KOKKOS_ETI_PATH)/Serial/*.cpp)
|
|
||||||
endif
|
|
||||||
endif
|
endif
|
||||||
ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
||||||
KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial.cpp,$(KOKKOS_SRC))
|
KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial.cpp,$(KOKKOS_SRC))
|
||||||
|
|||||||
@ -26,21 +26,17 @@ Kokkos_Spinwait.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Spi
|
|||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Spinwait.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Spinwait.cpp
|
||||||
Kokkos_HostBarrier.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp
|
Kokkos_HostBarrier.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostBarrier.cpp
|
||||||
Kokkos_Profiling_Interface.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling_Interface.cpp
|
Kokkos_Profiling.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling_Interface.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling.cpp
|
||||||
Kokkos_SharedAlloc.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_SharedAlloc.cpp
|
Kokkos_SharedAlloc.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_SharedAlloc.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_SharedAlloc.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_SharedAlloc.cpp
|
||||||
Kokkos_MemoryPool.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp
|
Kokkos_MemoryPool.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemoryPool.cpp
|
||||||
|
Kokkos_MemorySpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_MemorySpace.cpp
|
||||||
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_MemorySpace.cpp
|
||||||
Kokkos_HostSpace_deepcopy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp
|
Kokkos_HostSpace_deepcopy.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HostSpace_deepcopy.cpp
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
include $(KOKKOS_ETI_PATH)/Serial/Makefile.eti_Serial
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
|
||||||
Kokkos_Cuda_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Instance.cpp
|
Kokkos_Cuda_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Instance.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Instance.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Instance.cpp
|
||||||
@ -50,9 +46,6 @@ Kokkos_Cuda_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cu
|
|||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Task.cpp
|
||||||
Kokkos_Cuda_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
|
Kokkos_Cuda_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Cuda/Kokkos_Cuda_Locks.cpp
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
include $(KOKKOS_ETI_PATH)/Cuda/Makefile.eti_Cuda
|
|
||||||
endif
|
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
|
||||||
@ -75,9 +68,6 @@ Kokkos_ROCm_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_RO
|
|||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Task.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Task.cpp
|
||||||
Kokkos_ROCm_Impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
|
Kokkos_ROCm_Impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
include $(KOKKOS_ETI_PATH)/ROCm/Makefile.eti_ROCm
|
|
||||||
endif
|
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
|
||||||
@ -85,9 +75,6 @@ Kokkos_ThreadsExec_base.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads
|
|||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec_base.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec_base.cpp
|
||||||
Kokkos_ThreadsExec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp
|
Kokkos_ThreadsExec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec.cpp
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
include $(KOKKOS_ETI_PATH)/Threads/Makefile.eti_Threads
|
|
||||||
endif
|
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
|
||||||
@ -95,9 +82,6 @@ Kokkos_OpenMP_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokko
|
|||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp
|
||||||
Kokkos_OpenMP_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
|
Kokkos_OpenMP_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
|
||||||
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
|
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp
|
||||||
ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1)
|
|
||||||
include $(KOKKOS_ETI_PATH)/OpenMP/Makefile.eti_OpenMP
|
|
||||||
endif
|
|
||||||
endif
|
endif
|
||||||
|
|
||||||
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
|
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
|
||||||
|
|||||||
@ -151,7 +151,7 @@ Full details are given in the [build instructions](BUILD.md). Basic setups are s
|
|||||||
## CMake
|
## CMake
|
||||||
|
|
||||||
The best way to install Kokkos is using the CMake build system. Assuming Kokkos lives in `$srcdir`:
|
The best way to install Kokkos is using the CMake build system. Assuming Kokkos lives in `$srcdir`:
|
||||||
````
|
````bash
|
||||||
cmake $srcdir \
|
cmake $srcdir \
|
||||||
-DCMAKE_CXX_COMPILER=$path_to_compiler \
|
-DCMAKE_CXX_COMPILER=$path_to_compiler \
|
||||||
-DCMAKE_INSTALL_PREFIX=$path_to_install \
|
-DCMAKE_INSTALL_PREFIX=$path_to_install \
|
||||||
@ -170,7 +170,7 @@ and run `make test` after completing the build.
|
|||||||
|
|
||||||
For your CMake project using Kokkos, code such as the following:
|
For your CMake project using Kokkos, code such as the following:
|
||||||
|
|
||||||
````
|
````cmake
|
||||||
find_package(Kokkos)
|
find_package(Kokkos)
|
||||||
...
|
...
|
||||||
target_link_libraries(myTarget Kokkos::kokkos)
|
target_link_libraries(myTarget Kokkos::kokkos)
|
||||||
@ -187,17 +187,15 @@ for the install location given above.
|
|||||||
|
|
||||||
## Spack
|
## Spack
|
||||||
An alternative to manually building with the CMake is to use the Spack package manager.
|
An alternative to manually building with the CMake is to use the Spack package manager.
|
||||||
To do so, download the `kokkos-spack` git repo and add to the package list:
|
To get started, download the Spack [repo](https://github.com/spack/spack).
|
||||||
````
|
|
||||||
spack repo add $path-to-kokkos-spack
|
|
||||||
````
|
````
|
||||||
A basic installation would be done as:
|
A basic installation would be done as:
|
||||||
````
|
````bash
|
||||||
spack install kokkos
|
> spack install kokkos
|
||||||
````
|
````
|
||||||
Spack allows options and and compilers to be tuned in the install command.
|
Spack allows options and and compilers to be tuned in the install command.
|
||||||
````
|
````bash
|
||||||
spack install kokkos@3.0 %gcc@7.3.0 +openmp
|
> spack install kokkos@3.0 %gcc@7.3.0 +openmp
|
||||||
````
|
````
|
||||||
This example illustrates the three most common parameters to Spack:
|
This example illustrates the three most common parameters to Spack:
|
||||||
* Variants: specified with, e.g. `+openmp`, this activates (or deactivates with, e.g. `~openmp`) certain options.
|
* Variants: specified with, e.g. `+openmp`, this activates (or deactivates with, e.g. `~openmp`) certain options.
|
||||||
@ -205,33 +203,33 @@ This example illustrates the three most common parameters to Spack:
|
|||||||
* Compiler: a default compiler will be chosen if not specified, but an exact compiler version can be given with the `%`option.
|
* Compiler: a default compiler will be chosen if not specified, but an exact compiler version can be given with the `%`option.
|
||||||
|
|
||||||
For a complete list of Kokkos options, run:
|
For a complete list of Kokkos options, run:
|
||||||
````
|
````bash
|
||||||
spack info kokkos
|
> spack info kokkos
|
||||||
````
|
````
|
||||||
Spack currently installs packages to a location determined by a unique hash. This hash name is not really "human readable".
|
Spack currently installs packages to a location determined by a unique hash. This hash name is not really "human readable".
|
||||||
Generally, Spack usage should never really require you to reference the computer-generated unique install folder.
|
Generally, Spack usage should never really require you to reference the computer-generated unique install folder.
|
||||||
More details are given in the [build instructions](BUILD.md). If you must know, you can locate Spack Kokkos installations with:
|
More details are given in the [build instructions](BUILD.md). If you must know, you can locate Spack Kokkos installations with:
|
||||||
````
|
````bash
|
||||||
spack find -p kokkos ...
|
> spack find -p kokkos ...
|
||||||
````
|
````
|
||||||
where `...` is the unique spec identifying the particular Kokkos configuration and version.
|
where `...` is the unique spec identifying the particular Kokkos configuration and version.
|
||||||
|
Some more details can found in the Kokkos spack [documentation](Spack.md) or the Spack [website](https://spack.readthedocs.io/en/latest).
|
||||||
|
|
||||||
## Raw Makefile
|
## Raw Makefile
|
||||||
A bash script is provided to generate raw makefiles.
|
A bash script is provided to generate raw makefiles.
|
||||||
To install Kokkos as a library create a build directory and run the following
|
To install Kokkos as a library create a build directory and run the following
|
||||||
````
|
````bash
|
||||||
$KOKKOS_PATH/generate_makefile.bash --prefix=$path_to_install
|
> $KOKKOS_PATH/generate_makefile.bash --prefix=$path_to_install
|
||||||
````
|
````
|
||||||
Once the Makefile is generated, run:
|
Once the Makefile is generated, run:
|
||||||
````
|
````bash
|
||||||
make kokkoslib
|
> make kokkoslib
|
||||||
make install
|
> make install
|
||||||
````
|
````
|
||||||
To additionally run the unit tests:
|
To additionally run the unit tests:
|
||||||
````
|
````bash
|
||||||
make build-test
|
> make build-test
|
||||||
make test
|
> make test
|
||||||
````
|
````
|
||||||
Run `generate_makefile.bash --help` for more detailed options such as
|
Run `generate_makefile.bash --help` for more detailed options such as
|
||||||
changing the device type for which to build.
|
changing the device type for which to build.
|
||||||
@ -274,7 +272,7 @@ more than a single GPU is used by a single process.
|
|||||||
|
|
||||||
If you publish work which mentions Kokkos, please cite the following paper:
|
If you publish work which mentions Kokkos, please cite the following paper:
|
||||||
|
|
||||||
````
|
````BibTeX
|
||||||
@article{CarterEdwards20143202,
|
@article{CarterEdwards20143202,
|
||||||
title = "Kokkos: Enabling manycore performance portability through polymorphic memory access patterns ",
|
title = "Kokkos: Enabling manycore performance portability through polymorphic memory access patterns ",
|
||||||
journal = "Journal of Parallel and Distributed Computing ",
|
journal = "Journal of Parallel and Distributed Computing ",
|
||||||
|
|||||||
267
lib/kokkos/Spack.md
Normal file
267
lib/kokkos/Spack.md
Normal file
@ -0,0 +1,267 @@
|
|||||||
|
|
||||||
|
|
||||||
|
# Kokkos Spack
|
||||||
|
|
||||||
|
This gives instructions for using Spack to install Kokkos and developing packages that depend on Kokkos.
|
||||||
|
|
||||||
|
## Getting Started
|
||||||
|
|
||||||
|
Make sure you have downloaded [Spack](https://github.com/spack/spack).
|
||||||
|
The easiest way to configure the Spack environment is:
|
||||||
|
````bash
|
||||||
|
> source spack/share/spack/setup-env.sh
|
||||||
|
````
|
||||||
|
with other scripts available for other shells.
|
||||||
|
You can display information about how to install packages with:
|
||||||
|
````bash
|
||||||
|
> spack info kokkos
|
||||||
|
````
|
||||||
|
This will print all the information about how to install Kokkos with Spack.
|
||||||
|
For detailed instructions on how to use Spack, see the [User Manual](https://spack.readthedocs.io).
|
||||||
|
|
||||||
|
## Setting Up Spack: Avoiding the Package Cascade
|
||||||
|
By default, Spack doesn't 'see' anything on your system - including things like CMake and CUDA.
|
||||||
|
This can be limited by adding a `packages.yaml` to your `$HOME/.spack` folder that includes CMake (and CUDA, if applicable). For example, your `packages.yaml` file could be:
|
||||||
|
````yaml
|
||||||
|
packages:
|
||||||
|
cuda:
|
||||||
|
modules:
|
||||||
|
cuda@10.1.243: [cuda/10.1.243]
|
||||||
|
paths:
|
||||||
|
cuda@10.1.243:
|
||||||
|
/opt/local/ppc64le-pwr8-nvidia/cuda/10.1.243
|
||||||
|
buildable: false
|
||||||
|
cmake:
|
||||||
|
modules:
|
||||||
|
cmake: [cmake/3.16.8]
|
||||||
|
paths:
|
||||||
|
cmake:
|
||||||
|
/opt/local/ppc64le/cmake/3.16.8
|
||||||
|
buildable: false
|
||||||
|
````
|
||||||
|
The `modules` entry is only necessary on systems that require loading Modules (i.e. most DOE systems).
|
||||||
|
The `buildable` flag is useful to make sure Spack crashes if there is a path error,
|
||||||
|
rather than having a type-o and Spack rebuilding everything because `cmake` isn't found.
|
||||||
|
You can verify your environment is set up correctly by running `spack graph` or `spack spec`.
|
||||||
|
For example:
|
||||||
|
````bash
|
||||||
|
> spack graph kokkos +cuda
|
||||||
|
o kokkos
|
||||||
|
|\
|
||||||
|
o | cuda
|
||||||
|
/
|
||||||
|
o cmake
|
||||||
|
````
|
||||||
|
Without the existing CUDA and CMake being identified in `packages.yaml`, a (subset!) of the output would be:
|
||||||
|
````bash
|
||||||
|
o kokkos
|
||||||
|
|\
|
||||||
|
| o cmake
|
||||||
|
| |\
|
||||||
|
| | | |\
|
||||||
|
| | | | | |\
|
||||||
|
| | | | | | | |\
|
||||||
|
| | | | | | | | | |\
|
||||||
|
| | | | | | | o | | | libarchive
|
||||||
|
| | | | | | | |\ \ \ \
|
||||||
|
| | | | | | | | | |\ \ \ \
|
||||||
|
| | | | | | | | | | | | |_|/
|
||||||
|
| | | | | | | | | | | |/| |
|
||||||
|
| | | | | | | | | | | | | o curl
|
||||||
|
| | |_|_|_|_|_|_|_|_|_|_|/|
|
||||||
|
| |/| | | |_|_|_|_|_|_|_|/
|
||||||
|
| | | | |/| | | | | | | |
|
||||||
|
| | | | o | | | | | | | | openssl
|
||||||
|
| |/| | | | | | | | | | |
|
||||||
|
| | | | | | | | | | o | | libxml2
|
||||||
|
| | |_|_|_|_|_|_|_|/| | |
|
||||||
|
| | | | | | | | | | |\ \ \
|
||||||
|
| o | | | | | | | | | | | | zlib
|
||||||
|
| / / / / / / / / / / / /
|
||||||
|
| o | | | | | | | | | | | xz
|
||||||
|
| / / / / / / / / / / /
|
||||||
|
| o | | | | | | | | | | rhash
|
||||||
|
| / / / / / / / / / /
|
||||||
|
| | | | o | | | | | | nettle
|
||||||
|
| | | | |\ \ \ \ \ \ \
|
||||||
|
| | | o | | | | | | | | libuv
|
||||||
|
| | | | o | | | | | | | autoconf
|
||||||
|
| | |_|/| | | | | | | |
|
||||||
|
| | | | |/ / / / / / /
|
||||||
|
| o | | | | | | | | | perl
|
||||||
|
| o | | | | | | | | | gdbm
|
||||||
|
| o | | | | | | | | | readline
|
||||||
|
````
|
||||||
|
|
||||||
|
## Configuring Kokkos as a Project Dependency
|
||||||
|
Say you have a project "SuperScience" which needs to use Kokkos.
|
||||||
|
In your `package.py` file, you would generally include something like:
|
||||||
|
````python
|
||||||
|
class SuperScience(CMakePackage):
|
||||||
|
...
|
||||||
|
depends_on("kokkos")
|
||||||
|
````
|
||||||
|
Often projects want to tweak behavior when using certain features, e.g.
|
||||||
|
````python
|
||||||
|
depends_on("kokkos+cuda", when="+cuda")
|
||||||
|
````
|
||||||
|
if your project needs CUDA-specific logic to configure and build.
|
||||||
|
This illustrates the general principle in Spack of "flowing-up".
|
||||||
|
A user requests a feature in the final app:
|
||||||
|
````bash
|
||||||
|
> spack install superscience+cuda
|
||||||
|
````
|
||||||
|
This flows upstream to the Kokkos dependency, causing the `kokkos+cuda` variant to build.
|
||||||
|
The downstream app (SuperScience) tells the upstream app (Kokkos) how to build.
|
||||||
|
|
||||||
|
Because Kokkos is a performance portability library, it somewhat inverts this principle.
|
||||||
|
Kokkos "flows-down", telling your application how best to configure for performance.
|
||||||
|
Rather than a downstream app (SuperScience) telling the upstream (Kokkos) what variants to build,
|
||||||
|
a pre-built Kokkos should be telling the downstream app SuperScience what variants to use.
|
||||||
|
Kokkos works best when there is an "expert" configuration installed on your system.
|
||||||
|
Your build should simply request `-DKokkos_ROOT=<BEST_KOKKOS_FOR_MY_SYSTEM>` and configure appropriately based on the Kokkos it finds.
|
||||||
|
|
||||||
|
Kokkos has many, many build variants.
|
||||||
|
Where possible, projects should only depend on a general Kokkos, not specific variants.
|
||||||
|
We recommend instead adding for each system you build on a Kokkos configuration to your `packages.yaml` file (usually found in `~/.spack` for specific users).
|
||||||
|
For a Xeon + Volta system, this could look like:
|
||||||
|
````yaml
|
||||||
|
kokkos:
|
||||||
|
variants: +cuda +openmp +cuda_lambda +wrapper ^cuda@10.1 cuda_arch=70
|
||||||
|
compiler: [gcc@7.2.0]
|
||||||
|
````
|
||||||
|
which gives the "best" Kokkos configuration as CUDA+OpenMP optimized for a Volta 70 architecture using CUDA 10.1.
|
||||||
|
It also enables support for CUDA Lambdas.
|
||||||
|
The `+wrapper` option tells Kokkos to build with the special `nvcc_wrapper` (more below).
|
||||||
|
Note here that we use the built-in `cuda_arch` variant of Spack to specify the archicture.
|
||||||
|
For a Haswell system, we use
|
||||||
|
````yaml
|
||||||
|
kokkos:
|
||||||
|
variants: +openmp std=14 target=haswell
|
||||||
|
compiler: [intel@18]
|
||||||
|
````
|
||||||
|
which uses the built-in microarchitecture variants of Spack.
|
||||||
|
Consult the Spack documentation for more details of Spack microarchitectures
|
||||||
|
and CUDA architectures.
|
||||||
|
Spack does not currently provide an AMD GPU microarchitecture option.
|
||||||
|
If building for HIP or an AMD GPU, Kokkos provides an `amd_gpu_arch` similar to `cuda_arch`.
|
||||||
|
````yaml
|
||||||
|
kokkos:
|
||||||
|
variants: +hip amd_gpu_arch=vega900
|
||||||
|
````
|
||||||
|
|
||||||
|
Without an optimal default in your `packages.yaml` file, it is highly likely that the default Kokkos configuration you get will not be what you want.
|
||||||
|
For example, CUDA is not enabled by default (there is no easy logic to conditionally activate this for CUDA-enabled systems).
|
||||||
|
If you don't specify a CUDA build variant in a `packages.yaml` and you build your Kokkos-dependent project:
|
||||||
|
````bash
|
||||||
|
> spack install superscience
|
||||||
|
````
|
||||||
|
you may end up just getting the default Kokkos (i.e. Serial).
|
||||||
|
Some examples are included in the `config/yaml` folder for common platforms.
|
||||||
|
Before running `spack install <package>` we recommend running `spack spec <package>` to confirm your dependency tree is correct.
|
||||||
|
For example, with Kokkos Kernels:
|
||||||
|
````bash
|
||||||
|
kokkos-kernels@3.0%gcc@8.3.0~blas build_type=RelWithDebInfo ~cblas~complex_double~complex_float~cublas~cuda cuda_arch=none ~cusparse~diy+double execspace_cuda=auto execspace_openmp=auto execspace_serial=auto execspace_threads=auto ~float~lapack~lapacke+layoutleft~layoutright memspace_cudaspace=auto memspace_cudauvmspace=auto +memspace_hostspace~mkl+offset_int+offset_size_t~openmp+ordinal_int~ordinal_int64_t~serial~superlu arch=linux-rhel7-skylake_avx512
|
||||||
|
^cmake@3.16.2%gcc@8.3.0~doc+ncurses+openssl+ownlibs~qt arch=linux-rhel7-skylake_avx512
|
||||||
|
^kokkos@3.0%gcc@8.3.0~aggressive_vectorization~amdavx~armv80~armv81~armv8_thunderx~armv8_tx2~bdw~bgq build_type=RelWithDebInfo ~carrizo~compiler_warnings+cuda cuda_arch=none +cuda_lambda~cuda_ldg_intrinsic~cuda_relocatable_device_code~cuda_uvm~debug~debug_bounds_check~debug_dualview_modify_check~deprecated_code~diy~epyc~examples~explicit_instantiation~fiji~gfx901~hpx~hpx_async_dispatch~hsw~hwloc~kaveri~kepler30~kepler32~kepler35~kepler37~knc~knl~maxwell50~maxwell52~maxwell53~memkind~numactl+openmp~pascal60~pascal61~power7~power8~power9+profiling~profiling_load_print~pthread~qthread~rocm~ryzen~serial~skx~snb std=14 ~tests~turing75~vega+volta70~volta72+wrapper~wsm arch=linux-rhel7-skylake_avx512
|
||||||
|
^cuda@10.1%gcc@8.3.0 arch=linux-rhel7-skylake_avx512
|
||||||
|
^kokkos-nvcc-wrapper@old%gcc@8.3.0 build_type=RelWithDebInfo +mpi arch=linux-rhel7-skylake_avx512
|
||||||
|
^openmpi@4.0.2%gcc@8.3.0~cuda+cxx_exceptions fabrics=none ~java~legacylaunchers~memchecker patches=073477a76bba780c67c36e959cd3ee6910743e2735c7e76850ffba6791d498e4 ~pmi schedulers=none ~sqlite3~thread_multiple+vt arch=linux-rhel7-skylake_avx512
|
||||||
|
````
|
||||||
|
The output can be very verbose, but we can verify the expected `kokkos`:
|
||||||
|
````bash
|
||||||
|
kokkos@3.0%gcc@8.3.0~aggressive_vectorization~amdavx~armv80~armv81~armv8_thunderx~armv8_tx2~bdw~bgq build_type=RelWithDebInfo ~carrizo~compiler_warnings+cuda cuda_arch=none +cuda_lambda~cuda_ldg_intrinsic~cuda_relocatable_device_code~cuda_uvm~debug~debug_bounds_check~debug_dualview_modify_check~deprecated_code~diy~epyc~examples~explicit_instantiation~fiji~gfx901~hpx~hpx_async_dispatch~hsw~hwloc~kaveri~kepler30~kepler32~kepler35~kepler37~knc~knl~maxwell50~maxwell52~maxwell53~memkind~numactl+openmp~pascal60~pascal61~power7~power8~power9+profiling~profiling_load_print~pthread~qthread~rocm~ryzen~serial~skx~snb std=11 ~tests~turing75~vega+volta70~volta72+wrapper~wsm arch=linux-rhel7-skylake_avx512
|
||||||
|
````
|
||||||
|
We see that we do have `+volta70` and `+wrapper`, e.g.
|
||||||
|
|
||||||
|
### Spack Environments
|
||||||
|
The encouraged way to use Spack is with Spack environments ([more details here](https://spack-tutorial.readthedocs.io/en/latest/tutorial_environments.html#dealing-with-many-specs-at-once)).
|
||||||
|
Rather than installing packages one-at-a-time, you add packages to an environment.
|
||||||
|
After adding all packages, you concretize and install them all.
|
||||||
|
Using environments, one can explicitly add a desired Kokkos for the environment, e.g.
|
||||||
|
````bash
|
||||||
|
> spack add kokkos +cuda +cuda_lambda +volta70
|
||||||
|
> spack add my_project +my_variant
|
||||||
|
> ...
|
||||||
|
> spack install
|
||||||
|
````
|
||||||
|
All packages within the environment will build against the CUDA-enabled Kokkos,
|
||||||
|
even if they only request a default Kokkos.
|
||||||
|
|
||||||
|
## NVCC Wrapper
|
||||||
|
Kokkos is a C++ project, but often builds for the CUDA backend.
|
||||||
|
This is particularly problematic with CMake. At this point, `nvcc` does not accept all the flags that normally get passed to a C++ compiler.
|
||||||
|
Kokkos provides `nvcc_wrapper` that identifies correctly as a C++ compiler to CMake and accepts C++ flags, but uses `nvcc` as the underlying compiler.
|
||||||
|
`nvcc` itself also uses an underlying host compiler, e.g. GCC.
|
||||||
|
|
||||||
|
In Spack, the underlying host compiler is specified as below, e.g.:
|
||||||
|
````bash
|
||||||
|
> spack install package %gcc@8.0.0
|
||||||
|
````
|
||||||
|
This is still valid for Kokkos. To use the special wrapper for CUDA builds, request a desired compiler and simply add the `+wrapper` variant.
|
||||||
|
````bash
|
||||||
|
> spack install kokkos +cuda +wrapper %gcc@7.2.0
|
||||||
|
````
|
||||||
|
Downstream projects depending on Kokkos need to override their compiler.
|
||||||
|
Kokkos provides the compiler in a `kokkos_cxx` variable,
|
||||||
|
which points to either `nvcc_wrapper` when needed or the regular compiler otherwise.
|
||||||
|
Spack projects already do this to use MPI compiler wrappers.
|
||||||
|
````python
|
||||||
|
def cmake_args(self):
|
||||||
|
options = []
|
||||||
|
...
|
||||||
|
options.append("-DCMAKE_CXX_COMPILER=%s" % self.spec["kokkos"].kokkos_cxx)
|
||||||
|
...
|
||||||
|
return options
|
||||||
|
````
|
||||||
|
Note: `nvcc_wrapper` works with the MPI compiler wrappers.
|
||||||
|
If building your project with MPI, do NOT set your compiler to `nvcc_wrapper`.
|
||||||
|
Instead set your compiler to `mpicxx` and `nvcc_wrapper` will be used under the hood.
|
||||||
|
````python
|
||||||
|
def cmake_args(self):
|
||||||
|
options = []
|
||||||
|
...
|
||||||
|
options.append("-DCMAKE_CXX_COMPILER=%s" % self.spec["mpi"].mpicxx)
|
||||||
|
...
|
||||||
|
return options
|
||||||
|
````
|
||||||
|
To accomplish this, `nvcc_wrapper` must depend on MPI (even though it uses no MPI).
|
||||||
|
This has the unfortunate consequence that Kokkos CUDA projects not using MPI will implicitly depend on MPI anyway.
|
||||||
|
This behavior is necessary for now, but will hopefully be removed later.
|
||||||
|
When using environments, if MPI is not needed, you can remove the MPI dependency with:
|
||||||
|
````bash
|
||||||
|
> spack add kokkos-nvcc-wrapper ~mpi
|
||||||
|
````
|
||||||
|
|
||||||
|
## Developing With Spack
|
||||||
|
|
||||||
|
Spack has historically been much more suited to *deployment* of mature packages than active testing or developing.
|
||||||
|
However, recent features have improved support for development.
|
||||||
|
Future releases are likely to make this even easier and incorporate Git integration.
|
||||||
|
The most common commands will do a full build and install of the packages.
|
||||||
|
If doing development, you may wish to merely set up a build environment.
|
||||||
|
This allows you to modify the source and re-build.
|
||||||
|
In this case, you can stop after configuring.
|
||||||
|
Suppose you have Kokkos checkout in the folder `kokkos-src`:
|
||||||
|
````bash
|
||||||
|
> spack dev-build -d kokkos-src -u cmake kokkos@develop +wrapper +openmp
|
||||||
|
````
|
||||||
|
This sets up a development environment for you in `kokkos-src` which you can use (Bash example shown):
|
||||||
|
Note: Always specify `develop` as the version when doing `dev-build`, except in rare cases.
|
||||||
|
You are usually developing a feature branch that will merge into `develop`,
|
||||||
|
hence you are making a new `develop` branch.
|
||||||
|
|
||||||
|
````bash
|
||||||
|
> cd kokko-src
|
||||||
|
> source spack-build-env.txt
|
||||||
|
> cd spack-build
|
||||||
|
> make
|
||||||
|
````
|
||||||
|
Before sourcing the Spack development environment, you may wish to save your current environment:
|
||||||
|
````bash
|
||||||
|
> declare -px > myenv.sh
|
||||||
|
````
|
||||||
|
When done with Spack, you can then restore your original environment:
|
||||||
|
````bash
|
||||||
|
> source myenv.sh
|
||||||
|
````
|
||||||
@ -2,7 +2,9 @@
|
|||||||
|
|
||||||
KOKKOS_SUBPACKAGE(Algorithms)
|
KOKKOS_SUBPACKAGE(Algorithms)
|
||||||
|
|
||||||
ADD_SUBDIRECTORY(src)
|
IF (NOT Kokkos_INSTALL_TESTING)
|
||||||
|
ADD_SUBDIRECTORY(src)
|
||||||
|
ENDIF()
|
||||||
|
|
||||||
KOKKOS_ADD_TEST_DIRECTORIES(unit_tests)
|
KOKKOS_ADD_TEST_DIRECTORIES(unit_tests)
|
||||||
|
|
||||||
|
|||||||
@ -7,9 +7,15 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
|
|||||||
|
|
||||||
#-----------------------------------------------------------------------------
|
#-----------------------------------------------------------------------------
|
||||||
|
|
||||||
FILE(GLOB HEADERS *.hpp)
|
FILE(GLOB ALGO_HEADERS *.hpp)
|
||||||
FILE(GLOB SOURCES *.cpp)
|
FILE(GLOB ALGO_SOURCES *.cpp)
|
||||||
LIST(APPEND HEADERS ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME}_config.h)
|
LIST(APPEND ALGO_HEADERS ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME}_config.h)
|
||||||
|
|
||||||
|
INSTALL (
|
||||||
|
DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/"
|
||||||
|
DESTINATION ${KOKKOS_HEADER_DIR}
|
||||||
|
FILES_MATCHING PATTERN "*.hpp"
|
||||||
|
)
|
||||||
|
|
||||||
#-----------------------------------------------------------------------------
|
#-----------------------------------------------------------------------------
|
||||||
|
|
||||||
@ -17,8 +23,8 @@ LIST(APPEND HEADERS ${CMAKE_CURRENT_BINARY_DIR}/${PACKAGE_NAME}_config.h)
|
|||||||
# These will get ignored for standalone CMake and a true interface library made
|
# These will get ignored for standalone CMake and a true interface library made
|
||||||
KOKKOS_ADD_INTERFACE_LIBRARY(
|
KOKKOS_ADD_INTERFACE_LIBRARY(
|
||||||
kokkosalgorithms
|
kokkosalgorithms
|
||||||
HEADERS ${HEADERS}
|
HEADERS ${ALGO_HEADERS}
|
||||||
SOURCES ${SOURCES}
|
SOURCES ${ALGO_SOURCES}
|
||||||
)
|
)
|
||||||
KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkosalgorithms
|
KOKKOS_LIB_INCLUDE_DIRECTORIES(kokkosalgorithms
|
||||||
${KOKKOS_TOP_BUILD_DIR}
|
${KOKKOS_TOP_BUILD_DIR}
|
||||||
|
|||||||
@ -94,9 +94,9 @@ namespace Kokkos {
|
|||||||
class Pool {
|
class Pool {
|
||||||
public:
|
public:
|
||||||
//The Kokkos device type
|
//The Kokkos device type
|
||||||
typedef Device device_type;
|
using device_type = Device;
|
||||||
//The actual generator type
|
//The actual generator type
|
||||||
typedef Generator<Device> generator_type;
|
using generator_type = Generator<Device>;
|
||||||
|
|
||||||
//Default constructor: does not initialize a pool
|
//Default constructor: does not initialize a pool
|
||||||
Pool();
|
Pool();
|
||||||
@ -124,7 +124,7 @@ namespace Kokkos {
|
|||||||
class Generator {
|
class Generator {
|
||||||
public:
|
public:
|
||||||
//The Kokkos device type
|
//The Kokkos device type
|
||||||
typedef DeviceType device_type;
|
using device_type = DeviceType;
|
||||||
|
|
||||||
//Max return values of respective [X]rand[S]() functions
|
//Max return values of respective [X]rand[S]() functions
|
||||||
enum {MAX_URAND = 0xffffffffU};
|
enum {MAX_URAND = 0xffffffffU};
|
||||||
@ -138,75 +138,75 @@ namespace Kokkos {
|
|||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
Generator (STATE_ARGUMENTS, int state_idx = 0);
|
Generator (STATE_ARGUMENTS, int state_idx = 0);
|
||||||
|
|
||||||
//Draw a equidistributed uint32_t in the range (0,MAX_URAND]
|
//Draw a equidistributed uint32_t in the range [0,MAX_URAND)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
uint32_t urand();
|
uint32_t urand();
|
||||||
|
|
||||||
//Draw a equidistributed uint64_t in the range (0,MAX_URAND64]
|
//Draw a equidistributed uint64_t in the range [0,MAX_URAND64)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
uint64_t urand64();
|
uint64_t urand64();
|
||||||
|
|
||||||
//Draw a equidistributed uint32_t in the range (0,range]
|
//Draw a equidistributed uint32_t in the range [0,range)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
uint32_t urand(const uint32_t& range);
|
uint32_t urand(const uint32_t& range);
|
||||||
|
|
||||||
//Draw a equidistributed uint32_t in the range (start,end]
|
//Draw a equidistributed uint32_t in the range [start,end)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
uint32_t urand(const uint32_t& start, const uint32_t& end );
|
uint32_t urand(const uint32_t& start, const uint32_t& end );
|
||||||
|
|
||||||
//Draw a equidistributed uint64_t in the range (0,range]
|
//Draw a equidistributed uint64_t in the range [0,range)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
uint64_t urand64(const uint64_t& range);
|
uint64_t urand64(const uint64_t& range);
|
||||||
|
|
||||||
//Draw a equidistributed uint64_t in the range (start,end]
|
//Draw a equidistributed uint64_t in the range [start,end)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
uint64_t urand64(const uint64_t& start, const uint64_t& end );
|
uint64_t urand64(const uint64_t& start, const uint64_t& end );
|
||||||
|
|
||||||
//Draw a equidistributed int in the range (0,MAX_RAND]
|
//Draw a equidistributed int in the range [0,MAX_RAND)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
int rand();
|
int rand();
|
||||||
|
|
||||||
//Draw a equidistributed int in the range (0,range]
|
//Draw a equidistributed int in the range [0,range)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
int rand(const int& range);
|
int rand(const int& range);
|
||||||
|
|
||||||
//Draw a equidistributed int in the range (start,end]
|
//Draw a equidistributed int in the range [start,end)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
int rand(const int& start, const int& end );
|
int rand(const int& start, const int& end );
|
||||||
|
|
||||||
//Draw a equidistributed int64_t in the range (0,MAX_RAND64]
|
//Draw a equidistributed int64_t in the range [0,MAX_RAND64)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
int64_t rand64();
|
int64_t rand64();
|
||||||
|
|
||||||
//Draw a equidistributed int64_t in the range (0,range]
|
//Draw a equidistributed int64_t in the range [0,range)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
int64_t rand64(const int64_t& range);
|
int64_t rand64(const int64_t& range);
|
||||||
|
|
||||||
//Draw a equidistributed int64_t in the range (start,end]
|
//Draw a equidistributed int64_t in the range [start,end)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
int64_t rand64(const int64_t& start, const int64_t& end );
|
int64_t rand64(const int64_t& start, const int64_t& end );
|
||||||
|
|
||||||
//Draw a equidistributed float in the range (0,1.0]
|
//Draw a equidistributed float in the range [0,1.0)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
float frand();
|
float frand();
|
||||||
|
|
||||||
//Draw a equidistributed float in the range (0,range]
|
//Draw a equidistributed float in the range [0,range)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
float frand(const float& range);
|
float frand(const float& range);
|
||||||
|
|
||||||
//Draw a equidistributed float in the range (start,end]
|
//Draw a equidistributed float in the range [start,end)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
float frand(const float& start, const float& end );
|
float frand(const float& start, const float& end );
|
||||||
|
|
||||||
//Draw a equidistributed double in the range (0,1.0]
|
//Draw a equidistributed double in the range [0,1.0)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
double drand();
|
double drand();
|
||||||
|
|
||||||
//Draw a equidistributed double in the range (0,range]
|
//Draw a equidistributed double in the range [0,range)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
double drand(const double& range);
|
double drand(const double& range);
|
||||||
|
|
||||||
//Draw a equidistributed double in the range (start,end]
|
//Draw a equidistributed double in the range [start,end)
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
double drand(const double& start, const double& end );
|
double drand(const double& start, const double& end );
|
||||||
|
|
||||||
@ -221,11 +221,11 @@ namespace Kokkos {
|
|||||||
|
|
||||||
//Additional Functions:
|
//Additional Functions:
|
||||||
|
|
||||||
//Fills view with random numbers in the range (0,range]
|
//Fills view with random numbers in the range [0,range)
|
||||||
template<class ViewType, class PoolType>
|
template<class ViewType, class PoolType>
|
||||||
void fill_random(ViewType view, PoolType pool, ViewType::value_type range);
|
void fill_random(ViewType view, PoolType pool, ViewType::value_type range);
|
||||||
|
|
||||||
//Fills view with random numbers in the range (start,end]
|
//Fills view with random numbers in the range [start,end)
|
||||||
template<class ViewType, class PoolType>
|
template<class ViewType, class PoolType>
|
||||||
void fill_random(ViewType view, PoolType pool,
|
void fill_random(ViewType view, PoolType pool,
|
||||||
ViewType::value_type start, ViewType::value_type end);
|
ViewType::value_type start, ViewType::value_type end);
|
||||||
@ -381,7 +381,7 @@ struct rand<Generator, unsigned long> {
|
|||||||
// NOTE (mfh 26 oct 2014) This is a partial specialization for long
|
// NOTE (mfh 26 oct 2014) This is a partial specialization for long
|
||||||
// long, a C99 / C++11 signed type which is guaranteed to be at
|
// long, a C99 / C++11 signed type which is guaranteed to be at
|
||||||
// least 64 bits. Do NOT write a partial specialization for
|
// least 64 bits. Do NOT write a partial specialization for
|
||||||
// int64_t!!! This is just a typedef! It could be either long or
|
// int64_t!!! This is just an alias! It could be either long or
|
||||||
// long long. We don't know which a priori, and I've seen both.
|
// long long. We don't know which a priori, and I've seen both.
|
||||||
// The types long and long long are guaranteed to differ, so it's
|
// The types long and long long are guaranteed to differ, so it's
|
||||||
// always safe to specialize for both.
|
// always safe to specialize for both.
|
||||||
@ -413,7 +413,7 @@ struct rand<Generator, long long> {
|
|||||||
// NOTE (mfh 26 oct 2014) This is a partial specialization for
|
// NOTE (mfh 26 oct 2014) This is a partial specialization for
|
||||||
// unsigned long long, a C99 / C++11 unsigned type which is
|
// unsigned long long, a C99 / C++11 unsigned type which is
|
||||||
// guaranteed to be at least 64 bits. Do NOT write a partial
|
// guaranteed to be at least 64 bits. Do NOT write a partial
|
||||||
// specialization for uint64_t!!! This is just a typedef! It could
|
// specialization for uint64_t!!! This is just an alias! It could
|
||||||
// be either unsigned long or unsigned long long. We don't know
|
// be either unsigned long or unsigned long long. We don't know
|
||||||
// which a priori, and I've seen both. The types unsigned long and
|
// which a priori, and I've seen both. The types unsigned long and
|
||||||
// unsigned long long are guaranteed to differ, so it's always safe
|
// unsigned long long are guaranteed to differ, so it's always safe
|
||||||
@ -604,11 +604,7 @@ struct Random_UniqueIndex {
|
|||||||
KOKKOS_FUNCTION
|
KOKKOS_FUNCTION
|
||||||
static int get_state_idx(const locks_view_type) {
|
static int get_state_idx(const locks_view_type) {
|
||||||
#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
|
#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST
|
||||||
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE
|
|
||||||
const int i = ExecutionSpace::hardware_thread_id();
|
|
||||||
#else
|
|
||||||
const int i = ExecutionSpace::impl_hardware_thread_id();
|
const int i = ExecutionSpace::impl_hardware_thread_id();
|
||||||
#endif
|
|
||||||
return i;
|
return i;
|
||||||
#else
|
#else
|
||||||
return 0;
|
return 0;
|
||||||
@ -652,15 +648,13 @@ struct Random_UniqueIndex<Kokkos::Experimental::HIP> {
|
|||||||
static int get_state_idx(const locks_view_type& locks_) {
|
static int get_state_idx(const locks_view_type& locks_) {
|
||||||
#ifdef __HIP_DEVICE_COMPILE__
|
#ifdef __HIP_DEVICE_COMPILE__
|
||||||
const int i_offset =
|
const int i_offset =
|
||||||
(hipThreadIdx_x * hipBlockDim_y + hipThreadIdx_y) * hipBlockDim_z +
|
(threadIdx.x * blockDim.y + threadIdx.y) * blockDim.z + threadIdx.z;
|
||||||
hipThreadIdx_z;
|
int i = (((blockIdx.x * gridDim.y + blockIdx.y) * gridDim.z + blockIdx.z) *
|
||||||
int i = (((hipBlockIdx_x * hipGridDim_y + hipBlockIdx_y) * hipGridDim_z +
|
blockDim.x * blockDim.y * blockDim.z +
|
||||||
hipBlockIdx_z) *
|
|
||||||
hipBlockDim_x * hipBlockDim_y * hipBlockDim_z +
|
|
||||||
i_offset) %
|
i_offset) %
|
||||||
locks_.extent(0);
|
locks_.extent(0);
|
||||||
while (Kokkos::atomic_compare_exchange(&locks_(i), 0, 1)) {
|
while (Kokkos::atomic_compare_exchange(&locks_(i), 0, 1)) {
|
||||||
i += hipBlockDim_x * hipBlockDim_y * hipBlockDim_z;
|
i += blockDim.x * blockDim.y * blockDim.z;
|
||||||
if (i >= static_cast<int>(locks_.extent(0))) {
|
if (i >= static_cast<int>(locks_.extent(0))) {
|
||||||
i = i_offset;
|
i = i_offset;
|
||||||
}
|
}
|
||||||
@ -687,7 +681,7 @@ class Random_XorShift64 {
|
|||||||
friend class Random_XorShift64_Pool<DeviceType>;
|
friend class Random_XorShift64_Pool<DeviceType>;
|
||||||
|
|
||||||
public:
|
public:
|
||||||
typedef DeviceType device_type;
|
using device_type = DeviceType;
|
||||||
|
|
||||||
constexpr static uint32_t MAX_URAND = std::numeric_limits<uint32_t>::max();
|
constexpr static uint32_t MAX_URAND = std::numeric_limits<uint32_t>::max();
|
||||||
constexpr static uint64_t MAX_URAND64 = std::numeric_limits<uint64_t>::max();
|
constexpr static uint64_t MAX_URAND64 = std::numeric_limits<uint64_t>::max();
|
||||||
@ -805,11 +799,6 @@ class Random_XorShift64 {
|
|||||||
// number
|
// number
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
double normal() {
|
double normal() {
|
||||||
#ifndef __HIP_DEVICE_COMPILE__ // FIXME_HIP
|
|
||||||
using std::sqrt;
|
|
||||||
#else
|
|
||||||
using ::sqrt;
|
|
||||||
#endif
|
|
||||||
double S = 2.0;
|
double S = 2.0;
|
||||||
double U;
|
double U;
|
||||||
while (S >= 1.0) {
|
while (S >= 1.0) {
|
||||||
@ -817,7 +806,7 @@ class Random_XorShift64 {
|
|||||||
const double V = 2.0 * drand() - 1.0;
|
const double V = 2.0 * drand() - 1.0;
|
||||||
S = U * U + V * V;
|
S = U * U + V * V;
|
||||||
}
|
}
|
||||||
return U * sqrt(-2.0 * log(S) / S);
|
return U * std::sqrt(-2.0 * log(S) / S);
|
||||||
}
|
}
|
||||||
|
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
@ -830,15 +819,15 @@ template <class DeviceType = Kokkos::DefaultExecutionSpace>
|
|||||||
class Random_XorShift64_Pool {
|
class Random_XorShift64_Pool {
|
||||||
private:
|
private:
|
||||||
using execution_space = typename DeviceType::execution_space;
|
using execution_space = typename DeviceType::execution_space;
|
||||||
typedef View<int*, execution_space> locks_type;
|
using locks_type = View<int*, execution_space>;
|
||||||
typedef View<uint64_t*, DeviceType> state_data_type;
|
using state_data_type = View<uint64_t*, DeviceType>;
|
||||||
locks_type locks_;
|
locks_type locks_;
|
||||||
state_data_type state_;
|
state_data_type state_;
|
||||||
int num_states_;
|
int num_states_;
|
||||||
|
|
||||||
public:
|
public:
|
||||||
typedef Random_XorShift64<DeviceType> generator_type;
|
using generator_type = Random_XorShift64<DeviceType>;
|
||||||
typedef DeviceType device_type;
|
using device_type = DeviceType;
|
||||||
|
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
Random_XorShift64_Pool() { num_states_ = 0; }
|
Random_XorShift64_Pool() { num_states_ = 0; }
|
||||||
@ -923,8 +912,8 @@ class Random_XorShift1024 {
|
|||||||
friend class Random_XorShift1024_Pool<DeviceType>;
|
friend class Random_XorShift1024_Pool<DeviceType>;
|
||||||
|
|
||||||
public:
|
public:
|
||||||
typedef Random_XorShift1024_Pool<DeviceType> pool_type;
|
using pool_type = Random_XorShift1024_Pool<DeviceType>;
|
||||||
typedef DeviceType device_type;
|
using device_type = DeviceType;
|
||||||
|
|
||||||
constexpr static uint32_t MAX_URAND = std::numeric_limits<uint32_t>::max();
|
constexpr static uint32_t MAX_URAND = std::numeric_limits<uint32_t>::max();
|
||||||
constexpr static uint64_t MAX_URAND64 = std::numeric_limits<uint64_t>::max();
|
constexpr static uint64_t MAX_URAND64 = std::numeric_limits<uint64_t>::max();
|
||||||
@ -1046,11 +1035,6 @@ class Random_XorShift1024 {
|
|||||||
// number
|
// number
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
double normal() {
|
double normal() {
|
||||||
#ifndef KOKKOS_ENABLE_HIP // FIXME_HIP
|
|
||||||
using std::sqrt;
|
|
||||||
#else
|
|
||||||
using ::sqrt;
|
|
||||||
#endif
|
|
||||||
double S = 2.0;
|
double S = 2.0;
|
||||||
double U;
|
double U;
|
||||||
while (S >= 1.0) {
|
while (S >= 1.0) {
|
||||||
@ -1058,7 +1042,7 @@ class Random_XorShift1024 {
|
|||||||
const double V = 2.0 * drand() - 1.0;
|
const double V = 2.0 * drand() - 1.0;
|
||||||
S = U * U + V * V;
|
S = U * U + V * V;
|
||||||
}
|
}
|
||||||
return U * sqrt(-2.0 * log(S) / S);
|
return U * std::sqrt(-2.0 * log(S) / S);
|
||||||
}
|
}
|
||||||
|
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
@ -1071,9 +1055,9 @@ template <class DeviceType = Kokkos::DefaultExecutionSpace>
|
|||||||
class Random_XorShift1024_Pool {
|
class Random_XorShift1024_Pool {
|
||||||
private:
|
private:
|
||||||
using execution_space = typename DeviceType::execution_space;
|
using execution_space = typename DeviceType::execution_space;
|
||||||
typedef View<int*, execution_space> locks_type;
|
using locks_type = View<int*, execution_space>;
|
||||||
typedef View<int*, DeviceType> int_view_type;
|
using int_view_type = View<int*, DeviceType>;
|
||||||
typedef View<uint64_t * [16], DeviceType> state_data_type;
|
using state_data_type = View<uint64_t * [16], DeviceType>;
|
||||||
|
|
||||||
locks_type locks_;
|
locks_type locks_;
|
||||||
state_data_type state_;
|
state_data_type state_;
|
||||||
@ -1082,9 +1066,9 @@ class Random_XorShift1024_Pool {
|
|||||||
friend class Random_XorShift1024<DeviceType>;
|
friend class Random_XorShift1024<DeviceType>;
|
||||||
|
|
||||||
public:
|
public:
|
||||||
typedef Random_XorShift1024<DeviceType> generator_type;
|
using generator_type = Random_XorShift1024<DeviceType>;
|
||||||
|
|
||||||
typedef DeviceType device_type;
|
using device_type = DeviceType;
|
||||||
|
|
||||||
KOKKOS_INLINE_FUNCTION
|
KOKKOS_INLINE_FUNCTION
|
||||||
Random_XorShift1024_Pool() { num_states_ = 0; }
|
Random_XorShift1024_Pool() { num_states_ = 0; }
|
||||||
@ -1176,14 +1160,13 @@ struct fill_random_functor_begin_end;
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 1, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 1, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1203,14 +1186,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 1, IndexType> {
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 2, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 2, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1232,14 +1214,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 2, IndexType> {
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 3, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 3, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1262,14 +1243,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 3, IndexType> {
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 4, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 4, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1293,14 +1273,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 4, IndexType> {
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 5, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 5, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1326,14 +1305,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 5, IndexType> {
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 6, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 6, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1361,14 +1339,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 6, IndexType> {
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 7, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 7, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1398,14 +1375,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 7, IndexType> {
|
|||||||
|
|
||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_range<ViewType, RandomPool, loops, 8, IndexType> {
|
struct fill_random_functor_range<ViewType, RandomPool, loops, 8, IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type range;
|
typename ViewType::const_value_type range;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_range(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type range_)
|
typename ViewType::const_value_type range_)
|
||||||
@ -1437,14 +1413,13 @@ struct fill_random_functor_range<ViewType, RandomPool, loops, 8, IndexType> {
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 1,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 1,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
@ -1466,14 +1441,13 @@ struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 1,
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 2,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 2,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
@ -1497,14 +1471,13 @@ struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 2,
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 3,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 3,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
@ -1529,14 +1502,13 @@ struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 3,
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 4,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 4,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
@ -1562,14 +1534,13 @@ struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 4,
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 5,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 5,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
@ -1597,14 +1568,13 @@ struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 5,
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 6,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 6,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
@ -1634,14 +1604,13 @@ struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 6,
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 7,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 7,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
@ -1673,14 +1642,13 @@ struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 7,
|
|||||||
template <class ViewType, class RandomPool, int loops, class IndexType>
|
template <class ViewType, class RandomPool, int loops, class IndexType>
|
||||||
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 8,
|
struct fill_random_functor_begin_end<ViewType, RandomPool, loops, 8,
|
||||||
IndexType> {
|
IndexType> {
|
||||||
typedef typename ViewType::execution_space execution_space;
|
using execution_space = typename ViewType::execution_space;
|
||||||
ViewType a;
|
ViewType a;
|
||||||
RandomPool rand_pool;
|
RandomPool rand_pool;
|
||||||
typename ViewType::const_value_type begin, end;
|
typename ViewType::const_value_type begin, end;
|
||||||
|
|
||||||
typedef rand<typename RandomPool::generator_type,
|
using Rand = rand<typename RandomPool::generator_type,
|
||||||
typename ViewType::non_const_value_type>
|
typename ViewType::non_const_value_type>;
|
||||||
Rand;
|
|
||||||
|
|
||||||
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
fill_random_functor_begin_end(ViewType a_, RandomPool rand_pool_,
|
||||||
typename ViewType::const_value_type begin_,
|
typename ViewType::const_value_type begin_,
|
||||||
|
|||||||
@ -95,9 +95,9 @@ class BinSort {
|
|||||||
public:
|
public:
|
||||||
template <class DstViewType, class SrcViewType>
|
template <class DstViewType, class SrcViewType>
|
||||||
struct copy_functor {
|
struct copy_functor {
|
||||||
typedef typename SrcViewType::const_type src_view_type;
|
using src_view_type = typename SrcViewType::const_type;
|
||||||
|
|
||||||
typedef Impl::CopyOp<DstViewType, src_view_type> copy_op;
|
using copy_op = Impl::CopyOp<DstViewType, src_view_type>;
|
||||||
|
|
||||||
DstViewType dst_values;
|
DstViewType dst_values;
|
||||||
src_view_type src_values;
|
src_view_type src_values;
|
||||||
@ -120,17 +120,17 @@ class BinSort {
|
|||||||
// If a Kokkos::View then can generate constant random access
|
// If a Kokkos::View then can generate constant random access
|
||||||
// otherwise can only use the constant type.
|
// otherwise can only use the constant type.
|
||||||
|
|
||||||
typedef typename std::conditional<
|
using src_view_type = typename std::conditional<
|
||||||
Kokkos::is_view<SrcViewType>::value,
|
Kokkos::is_view<SrcViewType>::value,
|
||||||
Kokkos::View<typename SrcViewType::const_data_type,
|
Kokkos::View<typename SrcViewType::const_data_type,
|
||||||
typename SrcViewType::array_layout,
|
typename SrcViewType::array_layout,
|
||||||
typename SrcViewType::device_type,
|
typename SrcViewType::device_type,
|
||||||
Kokkos::MemoryTraits<Kokkos::RandomAccess> >,
|
Kokkos::MemoryTraits<Kokkos::RandomAccess> >,
|
||||||
typename SrcViewType::const_type>::type src_view_type;
|
typename SrcViewType::const_type>::type;
|
||||||
|
|
||||||
typedef typename PermuteViewType::const_type perm_view_type;
|
using perm_view_type = typename PermuteViewType::const_type;
|
||||||
|
|
||||||
typedef Impl::CopyOp<DstViewType, src_view_type> copy_op;
|
using copy_op = Impl::CopyOp<DstViewType, src_view_type>;
|
||||||
|
|
||||||
DstViewType dst_values;
|
DstViewType dst_values;
|
||||||
perm_view_type sort_order;
|
perm_view_type sort_order;
|
||||||
@ -151,8 +151,8 @@ class BinSort {
|
|||||||
}
|
}
|
||||||
};
|
};
|
||||||
|
|
||||||
typedef typename Space::execution_space execution_space;
|
using execution_space = typename Space::execution_space;
|
||||||
typedef BinSortOp bin_op_type;
|
using bin_op_type = BinSortOp;
|
||||||
|
|
||||||
struct bin_count_tag {};
|
struct bin_count_tag {};
|
||||||
struct bin_offset_tag {};
|
struct bin_offset_tag {};
|
||||||
@ -160,30 +160,30 @@ class BinSort {
|
|||||||
struct bin_sort_bins_tag {};
|
struct bin_sort_bins_tag {};
|
||||||
|
|
||||||
public:
|
public:
|
||||||
typedef SizeType size_type;
|
using size_type = SizeType;
|
||||||
typedef size_type value_type;
|
using value_type = size_type;
|
||||||
|
|
||||||
typedef Kokkos::View<size_type*, Space> offset_type;
|
using offset_type = Kokkos::View<size_type*, Space>;
|
||||||
typedef Kokkos::View<const int*, Space> bin_count_type;
|
using bin_count_type = Kokkos::View<const int*, Space>;
|
||||||
|
|
||||||
typedef typename KeyViewType::const_type const_key_view_type;
|
using const_key_view_type = typename KeyViewType::const_type;
|
||||||
|
|
||||||
// If a Kokkos::View then can generate constant random access
|
// If a Kokkos::View then can generate constant random access
|
||||||
// otherwise can only use the constant type.
|
// otherwise can only use the constant type.
|
||||||
|
|
||||||
typedef typename std::conditional<
|
using const_rnd_key_view_type = typename std::conditional<
|
||||||
Kokkos::is_view<KeyViewType>::value,
|
Kokkos::is_view<KeyViewType>::value,
|
||||||
Kokkos::View<typename KeyViewType::const_data_type,
|
Kokkos::View<typename KeyViewType::const_data_type,
|
||||||
typename KeyViewType::array_layout,
|
typename KeyViewType::array_layout,
|
||||||
typename KeyViewType::device_type,
|
typename KeyViewType::device_type,
|
||||||
Kokkos::MemoryTraits<Kokkos::RandomAccess> >,
|
Kokkos::MemoryTraits<Kokkos::RandomAccess> >,
|
||||||
const_key_view_type>::type const_rnd_key_view_type;
|
const_key_view_type>::type;
|
||||||
|
|
||||||
typedef typename KeyViewType::non_const_value_type non_const_key_scalar;
|
using non_const_key_scalar = typename KeyViewType::non_const_value_type;
|
||||||
typedef typename KeyViewType::const_value_type const_key_scalar;
|
using const_key_scalar = typename KeyViewType::const_value_type;
|
||||||
|
|
||||||
typedef Kokkos::View<int*, Space, Kokkos::MemoryTraits<Kokkos::Atomic> >
|
using bin_count_atomic_type =
|
||||||
bin_count_atomic_type;
|
Kokkos::View<int*, Space, Kokkos::MemoryTraits<Kokkos::Atomic> >;
|
||||||
|
|
||||||
private:
|
private:
|
||||||
const_key_view_type keys;
|
const_key_view_type keys;
|
||||||
@ -266,10 +266,10 @@ class BinSort {
|
|||||||
template <class ValuesViewType>
|
template <class ValuesViewType>
|
||||||
void sort(ValuesViewType const& values, int values_range_begin,
|
void sort(ValuesViewType const& values, int values_range_begin,
|
||||||
int values_range_end) const {
|
int values_range_end) const {
|
||||||
typedef Kokkos::View<typename ValuesViewType::data_type,
|
using scratch_view_type =
|
||||||
|
Kokkos::View<typename ValuesViewType::data_type,
|
||||||
typename ValuesViewType::array_layout,
|
typename ValuesViewType::array_layout,
|
||||||
typename ValuesViewType::device_type>
|
typename ValuesViewType::device_type>;
|
||||||
scratch_view_type;
|
|
||||||
|
|
||||||
const size_t len = range_end - range_begin;
|
const size_t len = range_end - range_begin;
|
||||||
const size_t values_len = values_range_end - values_range_begin;
|
const size_t values_len = values_range_end - values_range_begin;
|
||||||
@ -278,13 +278,6 @@ class BinSort {
|
|||||||
"BinSort::sort: values range length != permutation vector length");
|
"BinSort::sort: values range length != permutation vector length");
|
||||||
}
|
}
|
||||||
|
|
||||||
#ifdef KOKKOS_ENABLE_DEPRECATED_CODE
|
|
||||||
scratch_view_type sorted_values(
|
|
||||||
ViewAllocateWithoutInitializing(
|
|
||||||
"Kokkos::SortImpl::BinSortFunctor::sorted_values"),
|
|
||||||
len, values.extent(1), values.extent(2), values.extent(3),
|
|
||||||
values.extent(4), values.extent(5), values.extent(6), values.extent(7));
|
|
||||||
#else
|
|
||||||
scratch_view_type sorted_values(
|
scratch_view_type sorted_values(
|
||||||
ViewAllocateWithoutInitializing(
|
ViewAllocateWithoutInitializing(
|
||||||
"Kokkos::SortImpl::BinSortFunctor::sorted_values"),
|
"Kokkos::SortImpl::BinSortFunctor::sorted_values"),
|
||||||
@ -303,7 +296,6 @@ class BinSort {
|
|||||||
: KOKKOS_IMPL_CTOR_DEFAULT_ARG,
|
: KOKKOS_IMPL_CTOR_DEFAULT_ARG,
|
||||||
values.rank_dynamic > 7 ? values.extent(7)
|
values.rank_dynamic > 7 ? values.extent(7)
|
||||||
: KOKKOS_IMPL_CTOR_DEFAULT_ARG);
|
: KOKKOS_IMPL_CTOR_DEFAULT_ARG);
|
||||||
#endif
|
|
||||||
|
|
||||||
{
|
{
|
||||||
copy_permute_functor<scratch_view_type /* DstViewType */
|
copy_permute_functor<scratch_view_type /* DstViewType */
|
||||||
@ -511,8 +503,8 @@ bool try_std_sort(ViewType view) {
|
|||||||
|
|
||||||
template <class ViewType>
|
template <class ViewType>
|
||||||
struct min_max_functor {
|
struct min_max_functor {
|
||||||
typedef Kokkos::MinMaxScalar<typename ViewType::non_const_value_type>
|
using minmax_scalar =
|
||||||
minmax_scalar;
|
Kokkos::MinMaxScalar<typename ViewType::non_const_value_type>;
|
||||||
|
|
||||||
ViewType view;
|
ViewType view;
|
||||||
min_max_functor(const ViewType& view_) : view(view_) {}
|
min_max_functor(const ViewType& view_) : view(view_) {}
|
||||||
@ -531,7 +523,7 @@ void sort(ViewType const& view, bool const always_use_kokkos_sort = false) {
|
|||||||
if (!always_use_kokkos_sort) {
|
if (!always_use_kokkos_sort) {
|
||||||
if (Impl::try_std_sort(view)) return;
|
if (Impl::try_std_sort(view)) return;
|
||||||
}
|
}
|
||||||
typedef BinOp1D<ViewType> CompType;
|
using CompType = BinOp1D<ViewType>;
|
||||||
|
|
||||||
Kokkos::MinMaxScalar<typename ViewType::non_const_value_type> result;
|
Kokkos::MinMaxScalar<typename ViewType::non_const_value_type> result;
|
||||||
Kokkos::MinMax<typename ViewType::non_const_value_type> reducer(result);
|
Kokkos::MinMax<typename ViewType::non_const_value_type> reducer(result);
|
||||||
@ -548,8 +540,8 @@ void sort(ViewType const& view, bool const always_use_kokkos_sort = false) {
|
|||||||
|
|
||||||
template <class ViewType>
|
template <class ViewType>
|
||||||
void sort(ViewType view, size_t const begin, size_t const end) {
|
void sort(ViewType view, size_t const begin, size_t const end) {
|
||||||
typedef Kokkos::RangePolicy<typename ViewType::execution_space> range_policy;
|
using range_policy = Kokkos::RangePolicy<typename ViewType::execution_space>;
|
||||||
typedef BinOp1D<ViewType> CompType;
|
using CompType = BinOp1D<ViewType>;
|
||||||
|
|
||||||
Kokkos::MinMaxScalar<typename ViewType::non_const_value_type> result;
|
Kokkos::MinMaxScalar<typename ViewType::non_const_value_type> result;
|
||||||
Kokkos::MinMax<typename ViewType::non_const_value_type> reducer(result);
|
Kokkos::MinMax<typename ViewType::non_const_value_type> reducer(result);
|
||||||
|
|||||||
@ -20,14 +20,18 @@ KOKKOS_ADD_TEST_LIBRARY(
|
|||||||
HEADERS ${GTEST_SOURCE_DIR}/gtest/gtest.h
|
HEADERS ${GTEST_SOURCE_DIR}/gtest/gtest.h
|
||||||
SOURCES ${GTEST_SOURCE_DIR}/gtest/gtest-all.cc
|
SOURCES ${GTEST_SOURCE_DIR}/gtest/gtest-all.cc
|
||||||
)
|
)
|
||||||
# WORKAROUND FOR HIPCC
|
|
||||||
IF(Kokkos_ENABLE_HIP)
|
# avoid deprecation warnings from MSVC
|
||||||
TARGET_COMPILE_DEFINITIONS(kokkosalgorithms_gtest PUBLIC "-DGTEST_HAS_PTHREAD=0 --amdgpu-target=gfx906")
|
TARGET_COMPILE_DEFINITIONS(kokkosalgorithms_gtest PUBLIC GTEST_HAS_TR1_TUPLE=0 GTEST_HAS_PTHREAD=0)
|
||||||
ELSE()
|
|
||||||
TARGET_COMPILE_DEFINITIONS(kokkosalgorithms_gtest PUBLIC "-DGTEST_HAS_PTHREAD=0")
|
IF(NOT (Kokkos_ENABLE_CUDA AND WIN32))
|
||||||
|
TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_11)
|
||||||
ENDIF()
|
ENDIF()
|
||||||
|
|
||||||
TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_11)
|
# Suppress clang-tidy diagnostics on code that we do not have control over
|
||||||
|
IF(CMAKE_CXX_CLANG_TIDY)
|
||||||
|
SET_TARGET_PROPERTIES(kokkosalgorithms_gtest PROPERTIES CXX_CLANG_TIDY "")
|
||||||
|
ENDIF()
|
||||||
|
|
||||||
SET(SOURCES
|
SET(SOURCES
|
||||||
UnitTestMain.cpp
|
UnitTestMain.cpp
|
||||||
|
|||||||
@ -111,10 +111,10 @@ struct RandomProperties {
|
|||||||
|
|
||||||
template <class GeneratorPool, class Scalar>
|
template <class GeneratorPool, class Scalar>
|
||||||
struct test_random_functor {
|
struct test_random_functor {
|
||||||
typedef typename GeneratorPool::generator_type rnd_type;
|
using rnd_type = typename GeneratorPool::generator_type;
|
||||||
|
|
||||||
typedef RandomProperties value_type;
|
using value_type = RandomProperties;
|
||||||
typedef typename GeneratorPool::device_type device_type;
|
using device_type = typename GeneratorPool::device_type;
|
||||||
|
|
||||||
GeneratorPool rand_pool;
|
GeneratorPool rand_pool;
|
||||||
const double mean;
|
const double mean;
|
||||||
@ -125,12 +125,12 @@ struct test_random_functor {
|
|||||||
// implementations might violate this upper bound, due to rounding
|
// implementations might violate this upper bound, due to rounding
|
||||||
// error. Just in case, we leave an extra space at the end of each
|
// error. Just in case, we leave an extra space at the end of each
|
||||||
// dimension, in the View types below.
|
// dimension, in the View types below.
|
||||||
typedef Kokkos::View<int[HIST_DIM1D + 1], typename GeneratorPool::device_type>
|
using type_1d =
|
||||||
type_1d;
|
Kokkos::View<int[HIST_DIM1D + 1], typename GeneratorPool::device_type>;
|
||||||
type_1d density_1d;
|
type_1d density_1d;
|
||||||
typedef Kokkos::View<int[HIST_DIM3D + 1][HIST_DIM3D + 1][HIST_DIM3D + 1],
|
using type_3d =
|
||||||
typename GeneratorPool::device_type>
|
Kokkos::View<int[HIST_DIM3D + 1][HIST_DIM3D + 1][HIST_DIM3D + 1],
|
||||||
type_3d;
|
typename GeneratorPool::device_type>;
|
||||||
type_3d density_3d;
|
type_3d density_3d;
|
||||||
|
|
||||||
test_random_functor(GeneratorPool rand_pool_, type_1d d1d, type_3d d3d)
|
test_random_functor(GeneratorPool rand_pool_, type_1d d1d, type_3d d3d)
|
||||||
@ -200,9 +200,9 @@ struct test_random_functor {
|
|||||||
|
|
||||||
template <class DeviceType>
|
template <class DeviceType>
|
||||||
struct test_histogram1d_functor {
|
struct test_histogram1d_functor {
|
||||||
typedef RandomProperties value_type;
|
using value_type = RandomProperties;
|
||||||
typedef typename DeviceType::execution_space execution_space;
|
using execution_space = typename DeviceType::execution_space;
|
||||||
typedef typename DeviceType::memory_space memory_space;
|
using memory_space = typename DeviceType::memory_space;
|
||||||
|
|
||||||
// NOTE (mfh 03 Nov 2014): Kokkos::rand::max() is supposed to define
|
// NOTE (mfh 03 Nov 2014): Kokkos::rand::max() is supposed to define
|
||||||
// an exclusive upper bound on the range of random numbers that
|
// an exclusive upper bound on the range of random numbers that
|
||||||
@ -210,7 +210,7 @@ struct test_histogram1d_functor {
|
|||||||
// implementations might violate this upper bound, due to rounding
|
// implementations might violate this upper bound, due to rounding
|
||||||
// error. Just in case, we leave an extra space at the end of each
|
// error. Just in case, we leave an extra space at the end of each
|
||||||
// dimension, in the View type below.
|
// dimension, in the View type below.
|
||||||
typedef Kokkos::View<int[HIST_DIM1D + 1], memory_space> type_1d;
|
using type_1d = Kokkos::View<int[HIST_DIM1D + 1], memory_space>;
|
||||||
type_1d density_1d;
|
type_1d density_1d;
|
||||||
double mean;
|
double mean;
|
||||||
|
|
||||||
@ -219,7 +219,7 @@ struct test_histogram1d_functor {
|
|||||||
|
|
||||||
KOKKOS_INLINE_FUNCTION void operator()(
|
KOKKOS_INLINE_FUNCTION void operator()(
|
||||||
const typename memory_space::size_type i, RandomProperties& prop) const {
|
const typename memory_space::size_type i, RandomProperties& prop) const {
|
||||||
typedef typename memory_space::size_type size_type;
|
using size_type = typename memory_space::size_type;
|
||||||
const double count = density_1d(i);
|
const double count = density_1d(i);
|
||||||
prop.mean += count;
|
prop.mean += count;
|
||||||
prop.variance += 1.0 * (count - mean) * (count - mean);
|
prop.variance += 1.0 * (count - mean) * (count - mean);
|
||||||
@ -234,9 +234,9 @@ struct test_histogram1d_functor {
|
|||||||
|
|
||||||
template <class DeviceType>
|
template <class DeviceType>
|
||||||
struct test_histogram3d_functor {
|
struct test_histogram3d_functor {
|
||||||
typedef RandomProperties value_type;
|
using value_type = RandomProperties;
|
||||||
typedef typename DeviceType::execution_space execution_space;
|
using execution_space = typename DeviceType::execution_space;
|
||||||
typedef typename DeviceType::memory_space memory_space;
|
using memory_space = typename DeviceType::memory_space;
|
||||||
|
|
||||||
// NOTE (mfh 03 Nov 2014): Kokkos::rand::max() is supposed to define
|
// NOTE (mfh 03 Nov 2014): Kokkos::rand::max() is supposed to define
|
||||||
// an exclusive upper bound on the range of random numbers that
|
// an exclusive upper bound on the range of random numbers that
|
||||||
@ -244,9 +244,9 @@ struct test_histogram3d_functor {
|
|||||||
// implementations might violate this upper bound, due to rounding
|
// implementations might violate this upper bound, due to rounding
|
||||||
// error. Just in case, we leave an extra space at the end of each
|
// error. Just in case, we leave an extra space at the end of each
|
||||||
// dimension, in the View type below.
|
// dimension, in the View type below.
|
||||||
typedef Kokkos::View<int[HIST_DIM3D + 1][HIST_DIM3D + 1][HIST_DIM3D + 1],
|
using type_3d =
|
||||||
memory_space>
|
Kokkos::View<int[HIST_DIM3D + 1][HIST_DIM3D + 1][HIST_DIM3D + 1],
|
||||||
type_3d;
|
memory_space>;
|
||||||
type_3d density_3d;
|
type_3d density_3d;
|
||||||
double mean;
|
double mean;
|
||||||
|
|
||||||
@ -255,7 +255,7 @@ struct test_histogram3d_functor {
|
|||||||
|
|
||||||
KOKKOS_INLINE_FUNCTION void operator()(
|
KOKKOS_INLINE_FUNCTION void operator()(
|
||||||
const typename memory_space::size_type i, RandomProperties& prop) const {
|
const typename memory_space::size_type i, RandomProperties& prop) const {
|
||||||
typedef typename memory_space::size_type size_type;
|
using size_type = typename memory_space::size_type;
|
||||||
const double count = density_3d(
|
const double count = density_3d(
|
||||||
i / (HIST_DIM3D * HIST_DIM3D),
|
i / (HIST_DIM3D * HIST_DIM3D),
|
||||||
(i % (HIST_DIM3D * HIST_DIM3D)) / HIST_DIM3D, i % HIST_DIM3D);
|
(i % (HIST_DIM3D * HIST_DIM3D)) / HIST_DIM3D, i % HIST_DIM3D);
|
||||||
@ -276,7 +276,7 @@ struct test_histogram3d_functor {
|
|||||||
//
|
//
|
||||||
template <class RandomGenerator, class Scalar>
|
template <class RandomGenerator, class Scalar>
|
||||||
struct test_random_scalar {
|
struct test_random_scalar {
|
||||||
typedef typename RandomGenerator::generator_type rnd_type;
|
using rnd_type = typename RandomGenerator::generator_type;
|
||||||
|
|
||||||
int pass_mean, pass_var, pass_covar;
|
int pass_mean, pass_var, pass_covar;
|
||||||
int pass_hist1d_mean, pass_hist1d_var, pass_hist1d_covar;
|
int pass_hist1d_mean, pass_hist1d_var, pass_hist1d_covar;
|
||||||
@ -294,7 +294,7 @@ struct test_random_scalar {
|
|||||||
cout << " -- Testing randomness properties" << endl;
|
cout << " -- Testing randomness properties" << endl;
|
||||||
|
|
||||||
RandomProperties result;
|
RandomProperties result;
|
||||||
typedef test_random_functor<RandomGenerator, Scalar> functor_type;
|
using functor_type = test_random_functor<RandomGenerator, Scalar>;
|
||||||
parallel_reduce(num_draws / 1024,
|
parallel_reduce(num_draws / 1024,
|
||||||
functor_type(pool, density_1d, density_3d), result);
|
functor_type(pool, density_1d, density_3d), result);
|
||||||
|
|
||||||
@ -325,8 +325,8 @@ struct test_random_scalar {
|
|||||||
cout << " -- Testing 1-D histogram" << endl;
|
cout << " -- Testing 1-D histogram" << endl;
|
||||||
|
|
||||||
RandomProperties result;
|
RandomProperties result;
|
||||||
typedef test_histogram1d_functor<typename RandomGenerator::device_type>
|
using functor_type =
|
||||||
functor_type;
|
test_histogram1d_functor<typename RandomGenerator::device_type>;
|
||||||
parallel_reduce(HIST_DIM1D, functor_type(density_1d, num_draws), result);
|
parallel_reduce(HIST_DIM1D, functor_type(density_1d, num_draws), result);
|
||||||
|
|
||||||
double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D);
|
double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D);
|
||||||
@ -357,8 +357,8 @@ struct test_random_scalar {
|
|||||||
cout << " -- Testing 3-D histogram" << endl;
|
cout << " -- Testing 3-D histogram" << endl;
|
||||||
|
|
||||||
RandomProperties result;
|
RandomProperties result;
|
||||||
typedef test_histogram3d_functor<typename RandomGenerator::device_type>
|
using functor_type =
|
||||||
functor_type;
|
test_histogram3d_functor<typename RandomGenerator::device_type>;
|
||||||
parallel_reduce(HIST_DIM1D, functor_type(density_3d, num_draws), result);
|
parallel_reduce(HIST_DIM1D, functor_type(density_3d, num_draws), result);
|
||||||
|
|
||||||
double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D);
|
double tolerance = 6 * std::sqrt(1.0 / HIST_DIM1D);
|
||||||
|
|||||||
@ -55,8 +55,8 @@ namespace Impl {
|
|||||||
|
|
||||||
template <class ExecutionSpace, class Scalar>
|
template <class ExecutionSpace, class Scalar>
|
||||||
struct is_sorted_struct {
|
struct is_sorted_struct {
|
||||||
typedef unsigned int value_type;
|
using value_type = unsigned int;
|
||||||
typedef ExecutionSpace execution_space;
|
using execution_space = ExecutionSpace;
|
||||||
|
|
||||||
Kokkos::View<Scalar*, ExecutionSpace> keys;
|
Kokkos::View<Scalar*, ExecutionSpace> keys;
|
||||||
|
|
||||||
@ -69,8 +69,8 @@ struct is_sorted_struct {
|
|||||||
|
|
||||||
template <class ExecutionSpace, class Scalar>
|
template <class ExecutionSpace, class Scalar>
|
||||||
struct sum {
|
struct sum {
|
||||||
typedef double value_type;
|
using value_type = double;
|
||||||
typedef ExecutionSpace execution_space;
|
using execution_space = ExecutionSpace;
|
||||||
|
|
||||||
Kokkos::View<Scalar*, ExecutionSpace> keys;
|
Kokkos::View<Scalar*, ExecutionSpace> keys;
|
||||||
|
|
||||||
@ -81,8 +81,8 @@ struct sum {
|
|||||||
|
|
||||||
template <class ExecutionSpace, class Scalar>
|
template <class ExecutionSpace, class Scalar>
|
||||||
struct bin3d_is_sorted_struct {
|
struct bin3d_is_sorted_struct {
|
||||||
typedef unsigned int value_type;
|
using value_type = unsigned int;
|
||||||
typedef ExecutionSpace execution_space;
|
using execution_space = ExecutionSpace;
|
||||||
|
|
||||||
Kokkos::View<Scalar * [3], ExecutionSpace> keys;
|
Kokkos::View<Scalar * [3], ExecutionSpace> keys;
|
||||||
|
|
||||||
@ -115,8 +115,8 @@ struct bin3d_is_sorted_struct {
|
|||||||
|
|
||||||
template <class ExecutionSpace, class Scalar>
|
template <class ExecutionSpace, class Scalar>
|
||||||
struct sum3D {
|
struct sum3D {
|
||||||
typedef double value_type;
|
using value_type = double;
|
||||||
typedef ExecutionSpace execution_space;
|
using execution_space = ExecutionSpace;
|
||||||
|
|
||||||
Kokkos::View<Scalar * [3], ExecutionSpace> keys;
|
Kokkos::View<Scalar * [3], ExecutionSpace> keys;
|
||||||
|
|
||||||
@ -131,7 +131,7 @@ struct sum3D {
|
|||||||
|
|
||||||
template <class ExecutionSpace, typename KeyType>
|
template <class ExecutionSpace, typename KeyType>
|
||||||
void test_1D_sort_impl(unsigned int n, bool force_kokkos) {
|
void test_1D_sort_impl(unsigned int n, bool force_kokkos) {
|
||||||
typedef Kokkos::View<KeyType*, ExecutionSpace> KeyViewType;
|
using KeyViewType = Kokkos::View<KeyType*, ExecutionSpace>;
|
||||||
KeyViewType keys("Keys", n);
|
KeyViewType keys("Keys", n);
|
||||||
|
|
||||||
// Test sorting array with all numbers equal
|
// Test sorting array with all numbers equal
|
||||||
@ -166,7 +166,7 @@ void test_1D_sort_impl(unsigned int n, bool force_kokkos) {
|
|||||||
|
|
||||||
template <class ExecutionSpace, typename KeyType>
|
template <class ExecutionSpace, typename KeyType>
|
||||||
void test_3D_sort_impl(unsigned int n) {
|
void test_3D_sort_impl(unsigned int n) {
|
||||||
typedef Kokkos::View<KeyType * [3], ExecutionSpace> KeyViewType;
|
using KeyViewType = Kokkos::View<KeyType * [3], ExecutionSpace>;
|
||||||
|
|
||||||
KeyViewType keys("Keys", n * n * n);
|
KeyViewType keys("Keys", n * n * n);
|
||||||
|
|
||||||
@ -186,7 +186,7 @@ void test_3D_sort_impl(unsigned int n) {
|
|||||||
typename KeyViewType::value_type min[3] = {0, 0, 0};
|
typename KeyViewType::value_type min[3] = {0, 0, 0};
|
||||||
typename KeyViewType::value_type max[3] = {100, 100, 100};
|
typename KeyViewType::value_type max[3] = {100, 100, 100};
|
||||||
|
|
||||||
typedef Kokkos::BinOp3D<KeyViewType> BinOp;
|
using BinOp = Kokkos::BinOp3D<KeyViewType>;
|
||||||
BinOp bin_op(bin_max, min, max);
|
BinOp bin_op(bin_max, min, max);
|
||||||
Kokkos::BinSort<KeyViewType, BinOp> Sorter(keys, bin_op, false);
|
Kokkos::BinSort<KeyViewType, BinOp> Sorter(keys, bin_op, false);
|
||||||
Sorter.create_permute_vector();
|
Sorter.create_permute_vector();
|
||||||
@ -215,9 +215,9 @@ void test_3D_sort_impl(unsigned int n) {
|
|||||||
|
|
||||||
template <class ExecutionSpace, typename KeyType>
|
template <class ExecutionSpace, typename KeyType>
|
||||||
void test_dynamic_view_sort_impl(unsigned int n) {
|
void test_dynamic_view_sort_impl(unsigned int n) {
|
||||||
typedef Kokkos::Experimental::DynamicView<KeyType*, ExecutionSpace>
|
using KeyDynamicViewType =
|
||||||
KeyDynamicViewType;
|
Kokkos::Experimental::DynamicView<KeyType*, ExecutionSpace>;
|
||||||
typedef Kokkos::View<KeyType*, ExecutionSpace> KeyViewType;
|
using KeyViewType = Kokkos::View<KeyType*, ExecutionSpace>;
|
||||||
|
|
||||||
const size_t upper_bound = 2 * n;
|
const size_t upper_bound = 2 * n;
|
||||||
const size_t min_chunk_size = 1024;
|
const size_t min_chunk_size = 1024;
|
||||||
@ -305,8 +305,8 @@ void test_issue_1160_impl() {
|
|||||||
Kokkos::deep_copy(x_, h_x);
|
Kokkos::deep_copy(x_, h_x);
|
||||||
Kokkos::deep_copy(v_, h_v);
|
Kokkos::deep_copy(v_, h_v);
|
||||||
|
|
||||||
typedef decltype(element_) KeyViewType;
|
using KeyViewType = decltype(element_);
|
||||||
typedef Kokkos::BinOp1D<KeyViewType> BinOp;
|
using BinOp = Kokkos::BinOp1D<KeyViewType>;
|
||||||
|
|
||||||
int begin = 3;
|
int begin = 3;
|
||||||
int end = 8;
|
int end = 8;
|
||||||
|
|||||||
@ -5,6 +5,6 @@ build_script:
|
|||||||
- cmd: >-
|
- cmd: >-
|
||||||
mkdir build &&
|
mkdir build &&
|
||||||
cd build &&
|
cd build &&
|
||||||
cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON -DKokkos_ENABLE_LIBDL=OFF -DKokkos_ENABLE_PROFILING=OFF &&
|
cmake c:\projects\source -DKokkos_ENABLE_TESTS=ON &&
|
||||||
cmake --build . --target install &&
|
cmake --build . --target install &&
|
||||||
ctest -C Debug -V
|
ctest -C Debug -V
|
||||||
|
|||||||
@ -69,13 +69,13 @@ int main(int argc, char* argv[]) {
|
|||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
int L = atoi(argv[1]);
|
int L = std::stoi(argv[1]);
|
||||||
int N = atoi(argv[2]);
|
int N = std::stoi(argv[2]);
|
||||||
int M = atoi(argv[3]);
|
int M = std::stoi(argv[3]);
|
||||||
int D = atoi(argv[4]);
|
int D = std::stoi(argv[4]);
|
||||||
int K = atoi(argv[5]);
|
int K = std::stoi(argv[5]);
|
||||||
int R = atoi(argv[6]);
|
int R = std::stoi(argv[6]);
|
||||||
int type = atoi(argv[7]);
|
int type = std::stoi(argv[7]);
|
||||||
|
|
||||||
Kokkos::View<int*> offsets("Offsets", L, M);
|
Kokkos::View<int*> offsets("Offsets", L, M);
|
||||||
Kokkos::Random_XorShift64_Pool<> pool(12371);
|
Kokkos::Random_XorShift64_Pool<> pool(12371);
|
||||||
|
|||||||
@ -73,15 +73,15 @@ int main(int argc, char* argv[]) {
|
|||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
int P = atoi(argv[1]);
|
int P = std::stoi(argv[1]);
|
||||||
int N = atoi(argv[2]);
|
int N = std::stoi(argv[2]);
|
||||||
int K = atoi(argv[3]);
|
int K = std::stoi(argv[3]);
|
||||||
int R = atoi(argv[4]);
|
int R = std::stoi(argv[4]);
|
||||||
int D = atoi(argv[5]);
|
int D = std::stoi(argv[5]);
|
||||||
int U = atoi(argv[6]);
|
int U = std::stoi(argv[6]);
|
||||||
int F = atoi(argv[7]);
|
int F = std::stoi(argv[7]);
|
||||||
int T = atoi(argv[8]);
|
int T = std::stoi(argv[8]);
|
||||||
int S = atoi(argv[9]);
|
int S = std::stoi(argv[9]);
|
||||||
|
|
||||||
if (U > 8) {
|
if (U > 8) {
|
||||||
printf("U must be 1-8\n");
|
printf("U must be 1-8\n");
|
||||||
|
|||||||
@ -72,13 +72,13 @@ int main(int argc, char* argv[]) {
|
|||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
int S = atoi(argv[1]);
|
int S = std::stoi(argv[1]);
|
||||||
int N = atoi(argv[2]);
|
int N = std::stoi(argv[2]);
|
||||||
int K = atoi(argv[3]);
|
int K = std::stoi(argv[3]);
|
||||||
int D = atoi(argv[4]);
|
int D = std::stoi(argv[4]);
|
||||||
int R = atoi(argv[5]);
|
int R = std::stoi(argv[5]);
|
||||||
int U = atoi(argv[6]);
|
int U = std::stoi(argv[6]);
|
||||||
int F = atoi(argv[7]);
|
int F = std::stoi(argv[7]);
|
||||||
|
|
||||||
if ((S != 1) && (S != 2) && (S != 4)) {
|
if ((S != 1) && (S != 2) && (S != 4)) {
|
||||||
printf("S must be one of 1,2,4\n");
|
printf("S must be one of 1,2,4\n");
|
||||||
|
|||||||
@ -50,58 +50,61 @@
|
|||||||
#define HLINE "-------------------------------------------------------------\n"
|
#define HLINE "-------------------------------------------------------------\n"
|
||||||
|
|
||||||
#if defined(KOKKOS_ENABLE_CUDA)
|
#if defined(KOKKOS_ENABLE_CUDA)
|
||||||
typedef Kokkos::View<int64_t*, Kokkos::CudaSpace>::HostMirror GUPSHostArray;
|
using GUPSHostArray = Kokkos::View<int64_t*, Kokkos::CudaSpace>::HostMirror;
|
||||||
typedef Kokkos::View<int64_t*, Kokkos::CudaSpace> GUPSDeviceArray;
|
using GUPSDeviceArray = Kokkos::View<int64_t*, Kokkos::CudaSpace>;
|
||||||
#else
|
#else
|
||||||
typedef Kokkos::View<int64_t*, Kokkos::HostSpace>::HostMirror GUPSHostArray;
|
using GUPSHostArray = Kokkos::View<int64_t*, Kokkos::HostSpace>::HostMirror;
|
||||||
typedef Kokkos::View<int64_t*, Kokkos::HostSpace> GUPSDeviceArray;
|
using GUPSDeviceArray = Kokkos::View<int64_t*, Kokkos::HostSpace>;
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
typedef int GUPSIndex;
|
using GUPSIndex = int;
|
||||||
|
|
||||||
double now() {
|
double now() {
|
||||||
struct timeval now;
|
struct timeval now;
|
||||||
gettimeofday(&now, nullptr);
|
gettimeofday(&now, nullptr);
|
||||||
|
|
||||||
return (double) now.tv_sec + ((double) now.tv_usec * 1.0e-6);
|
return (double)now.tv_sec + ((double)now.tv_usec * 1.0e-6);
|
||||||
}
|
}
|
||||||
|
|
||||||
void randomize_indices(GUPSHostArray& indices, GUPSDeviceArray& dev_indices, const int64_t dataCount) {
|
void randomize_indices(GUPSHostArray& indices, GUPSDeviceArray& dev_indices,
|
||||||
for( GUPSIndex i = 0; i < indices.extent(0); ++i ) {
|
const int64_t dataCount) {
|
||||||
|
for (GUPSIndex i = 0; i < indices.extent(0); ++i) {
|
||||||
indices[i] = lrand48() % dataCount;
|
indices[i] = lrand48() % dataCount;
|
||||||
}
|
}
|
||||||
|
|
||||||
Kokkos::deep_copy(dev_indices, indices);
|
Kokkos::deep_copy(dev_indices, indices);
|
||||||
}
|
}
|
||||||
|
|
||||||
void run_gups(GUPSDeviceArray& indices, GUPSDeviceArray& data, const int64_t datum,
|
void run_gups(GUPSDeviceArray& indices, GUPSDeviceArray& data,
|
||||||
const bool performAtomics) {
|
const int64_t datum, const bool performAtomics) {
|
||||||
|
if (performAtomics) {
|
||||||
if( performAtomics ) {
|
Kokkos::parallel_for(
|
||||||
Kokkos::parallel_for("bench-gups-atomic", indices.extent(0), KOKKOS_LAMBDA(const GUPSIndex i) {
|
"bench-gups-atomic", indices.extent(0),
|
||||||
Kokkos::atomic_fetch_xor( &data[indices[i]], datum );
|
KOKKOS_LAMBDA(const GUPSIndex i) {
|
||||||
|
Kokkos::atomic_fetch_xor(&data[indices[i]], datum);
|
||||||
});
|
});
|
||||||
} else {
|
} else {
|
||||||
Kokkos::parallel_for("bench-gups-non-atomic", indices.extent(0), KOKKOS_LAMBDA(const GUPSIndex i) {
|
Kokkos::parallel_for(
|
||||||
data[indices[i]] ^= datum;
|
"bench-gups-non-atomic", indices.extent(0),
|
||||||
});
|
KOKKOS_LAMBDA(const GUPSIndex i) { data[indices[i]] ^= datum; });
|
||||||
}
|
}
|
||||||
|
|
||||||
Kokkos::fence();
|
Kokkos::fence();
|
||||||
}
|
}
|
||||||
|
|
||||||
int run_benchmark(const GUPSIndex indicesCount, const GUPSIndex dataCount, const int repeats,
|
int run_benchmark(const GUPSIndex indicesCount, const GUPSIndex dataCount,
|
||||||
const bool useAtomics) {
|
const int repeats, const bool useAtomics) {
|
||||||
|
|
||||||
printf("Reports fastest timing per kernel\n");
|
printf("Reports fastest timing per kernel\n");
|
||||||
printf("Creating Views...\n");
|
printf("Creating Views...\n");
|
||||||
|
|
||||||
printf("Memory Sizes:\n");
|
printf("Memory Sizes:\n");
|
||||||
printf("- Elements: %15" PRIu64 " (%12.4f MB)\n", static_cast<uint64_t>(dataCount),
|
printf("- Elements: %15" PRIu64 " (%12.4f MB)\n",
|
||||||
1.0e-6 * ((double) dataCount * (double) sizeof(int64_t)));
|
static_cast<uint64_t>(dataCount),
|
||||||
printf("- Indices: %15" PRIu64 " (%12.4f MB)\n", static_cast<uint64_t>(indicesCount),
|
1.0e-6 * ((double)dataCount * (double)sizeof(int64_t)));
|
||||||
1.0e-6 * ((double) indicesCount * (double) sizeof(int64_t)));
|
printf("- Indices: %15" PRIu64 " (%12.4f MB)\n",
|
||||||
printf(" - Atomics: %15s\n", (useAtomics ? "Yes" : "No") );
|
static_cast<uint64_t>(indicesCount),
|
||||||
|
1.0e-6 * ((double)indicesCount * (double)sizeof(int64_t)));
|
||||||
|
printf(" - Atomics: %15s\n", (useAtomics ? "Yes" : "No"));
|
||||||
printf("Benchmark kernels will be performed for %d iterations.\n", repeats);
|
printf("Benchmark kernels will be performed for %d iterations.\n", repeats);
|
||||||
|
|
||||||
printf(HLINE);
|
printf(HLINE);
|
||||||
@ -118,24 +121,22 @@ int run_benchmark(const GUPSIndex indicesCount, const GUPSIndex dataCount, const
|
|||||||
printf("Initializing Views...\n");
|
printf("Initializing Views...\n");
|
||||||
|
|
||||||
#if defined(KOKKOS_HAVE_OPENMP)
|
#if defined(KOKKOS_HAVE_OPENMP)
|
||||||
Kokkos::parallel_for("init-data", Kokkos::RangePolicy<Kokkos::OpenMP>(0, dataCount),
|
Kokkos::parallel_for(
|
||||||
|
"init-data", Kokkos::RangePolicy<Kokkos::OpenMP>(0, dataCount),
|
||||||
#else
|
#else
|
||||||
Kokkos::parallel_for("init-data", Kokkos::RangePolicy<Kokkos::Serial>(0, dataCount),
|
Kokkos::parallel_for(
|
||||||
|
"init-data", Kokkos::RangePolicy<Kokkos::Serial>(0, dataCount),
|
||||||
#endif
|
#endif
|
||||||
KOKKOS_LAMBDA(const int i) {
|
KOKKOS_LAMBDA(const int i) { data[i] = 10101010101; });
|
||||||
|
|
||||||
data[i] = 10101010101;
|
|
||||||
});
|
|
||||||
|
|
||||||
#if defined(KOKKOS_HAVE_OPENMP)
|
#if defined(KOKKOS_HAVE_OPENMP)
|
||||||
Kokkos::parallel_for("init-indices", Kokkos::RangePolicy<Kokkos::OpenMP>(0, indicesCount),
|
Kokkos::parallel_for(
|
||||||
|
"init-indices", Kokkos::RangePolicy<Kokkos::OpenMP>(0, indicesCount),
|
||||||
#else
|
#else
|
||||||
Kokkos::parallel_for("init-indices", Kokkos::RangePolicy<Kokkos::Serial>(0, indicesCount),
|
Kokkos::parallel_for(
|
||||||
|
"init-indices", Kokkos::RangePolicy<Kokkos::Serial>(0, indicesCount),
|
||||||
#endif
|
#endif
|
||||||
KOKKOS_LAMBDA(const int i) {
|
KOKKOS_LAMBDA(const int i) { indices[i] = 0; });
|
||||||
|
|
||||||
indices[i] = 0;
|
|
||||||
});
|
|
||||||
|
|
||||||
Kokkos::deep_copy(dev_data, data);
|
Kokkos::deep_copy(dev_data, data);
|
||||||
Kokkos::deep_copy(dev_indices, indices);
|
Kokkos::deep_copy(dev_indices, indices);
|
||||||
@ -143,7 +144,7 @@ int run_benchmark(const GUPSIndex indicesCount, const GUPSIndex dataCount, const
|
|||||||
|
|
||||||
printf("Starting benchmarking...\n");
|
printf("Starting benchmarking...\n");
|
||||||
|
|
||||||
for( GUPSIndex k = 0; k < repeats; ++k ) {
|
for (GUPSIndex k = 0; k < repeats; ++k) {
|
||||||
randomize_indices(indices, dev_indices, data.extent(0));
|
randomize_indices(indices, dev_indices, data.extent(0));
|
||||||
|
|
||||||
start = now();
|
start = now();
|
||||||
@ -155,15 +156,15 @@ int run_benchmark(const GUPSIndex indicesCount, const GUPSIndex dataCount, const
|
|||||||
Kokkos::deep_copy(data, dev_data);
|
Kokkos::deep_copy(data, dev_data);
|
||||||
|
|
||||||
printf(HLINE);
|
printf(HLINE);
|
||||||
printf("GUP/s Random: %18.6f\n",
|
printf(
|
||||||
(1.0e-9 * ((double) repeats) * (double) dev_indices.extent(0)) / gupsTime);
|
"GUP/s Random: %18.6f\n",
|
||||||
|
(1.0e-9 * ((double)repeats) * (double)dev_indices.extent(0)) / gupsTime);
|
||||||
printf(HLINE);
|
printf(HLINE);
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
int main(int argc, char* argv[]) {
|
int main(int argc, char* argv[]) {
|
||||||
|
|
||||||
printf(HLINE);
|
printf(HLINE);
|
||||||
printf("Kokkos GUPS Benchmark\n");
|
printf("Kokkos GUPS Benchmark\n");
|
||||||
printf(HLINE);
|
printf(HLINE);
|
||||||
@ -177,17 +178,17 @@ int main(int argc, char* argv[]) {
|
|||||||
int64_t repeats = 10;
|
int64_t repeats = 10;
|
||||||
bool useAtomics = false;
|
bool useAtomics = false;
|
||||||
|
|
||||||
for( int i = 1; i < argc; ++i ) {
|
for (int i = 1; i < argc; ++i) {
|
||||||
if( strcmp( argv[i], "--indices" ) == 0 ) {
|
if (strcmp(argv[i], "--indices") == 0) {
|
||||||
indices = std::atoll(argv[i+1]);
|
indices = std::atoll(argv[i + 1]);
|
||||||
++i;
|
++i;
|
||||||
} else if( strcmp( argv[i], "--data" ) == 0 ) {
|
} else if (strcmp(argv[i], "--data") == 0) {
|
||||||
data = std::atoll(argv[i+1]);
|
data = std::atoll(argv[i + 1]);
|
||||||
++i;
|
++i;
|
||||||
} else if( strcmp( argv[i], "--repeats" ) == 0 ) {
|
} else if (strcmp(argv[i], "--repeats") == 0) {
|
||||||
repeats = std::atoll(argv[i+1]);
|
repeats = std::atoll(argv[i + 1]);
|
||||||
++i;
|
++i;
|
||||||
} else if( strcmp( argv[i], "--atomics" ) == 0 ) {
|
} else if (strcmp(argv[i], "--atomics") == 0) {
|
||||||
useAtomics = true;
|
useAtomics = true;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user