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Merge branch 'master' into fep

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This commit is contained in:
Agilio Padua
2021-03-03 14:01:43 +01:00
parent 74fe20b9a9 0f63f07ce5
commit 390e6eb965
557 changed files with 24327 additions and 11432 deletions
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7
cmake/CMakeLists.txt
View File

@ -156,8 +156,7 @@ if(BUILD_MPI)
endif()
endif()
else()
enable_language(C)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
@ -778,9 +777,7 @@ if(PKG_GPU)
message(STATUS "<<< GPU package settings >>>
-- GPU API: ${GPU_API}")
if(GPU_API STREQUAL "CUDA")
message(STATUS "GPU architecture: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "OPENCL")
message(STATUS "OpenCL tuning: ${OCL_TUNE}")
message(STATUS "GPU default architecture: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "HIP")
message(STATUS "HIP platform: ${HIP_PLATFORM}")
message(STATUS "HIP architecture: ${HIP_ARCH}")

6
cmake/Modules/Documentation.cmake
View File

@ -50,9 +50,9 @@ if(BUILD_DOC)
OUTPUT ${DOC_BUILD_DIR}/requirements.txt
DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
)
# download mathjax distribution and unpack to folder "mathjax"

16
cmake/Modules/GTest.cmake
View File

@ -20,10 +20,10 @@ ExternalProject_Add(googletest
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
<BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
@ -39,10 +39,10 @@ file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
ExternalProject_Get_Property(googletest BINARY_DIR)
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
# Prevent GoogleTest from overriding our compiler/linker options
# when building with Visual Studio

48
cmake/Modules/OpenCLLoader.cmake Normal file
View File

@ -0,0 +1,48 @@
message(STATUS "Downloading and building OpenCL loader library")
include(ExternalProject)
set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
mark_as_advanced(OPENCL_LOADER_URL)
ExternalProject_Add(opencl_loader
URL ${OPENCL_LOADER_URL}
URL_MD5 011cdcbd41030be94f3fced6d763a52a
SOURCE_DIR "${CMAKE_BINARY_DIR}/opencl_loader-src"
BINARY_DIR "${CMAKE_BINARY_DIR}/opencl_loader-build"
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
LOG_DOWNLOAD ON
LOG_CONFIGURE ON
LOG_BUILD ON
INSTALL_COMMAND ""
TEST_COMMAND "")
ExternalProject_Get_Property(opencl_loader SOURCE_DIR)
set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
# workaround for CMake 3.10 on ubuntu 18.04
file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
ExternalProject_Get_Property(opencl_loader BINARY_DIR)
set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
find_package(Threads QUIET)
if(NOT WIN32)
set(OPENCL_LOADER_DEP_LIBS "Threads::Threads;${CMAKE_DL_LIBS}")
else()
set(OPENCL_LOADER_DEP_LIBS "cfgmgr32;runtimeobject")
endif()
add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
add_dependencies(OpenCL::OpenCL opencl_loader)
set_target_properties(OpenCL::OpenCL PROPERTIES
IMPORTED_LOCATION ${OPENCL_LOADER_LIBRARY_PATH}
INTERFACE_INCLUDE_DIRECTORIES ${OPENCL_LOADER_INCLUDE_DIR}
INTERFACE_LINK_LIBRARIES "${OPENCL_LOADER_DEP_LIBS}")

44
cmake/Modules/Packages/GPU.cmake
View File

@ -1,7 +1,9 @@
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h
${GPU_SOURCES_DIR}/fix_gpu.cpp)
${GPU_SOURCES_DIR}/fix_gpu.cpp
${GPU_SOURCES_DIR}/fix_nh_gpu.h
${GPU_SOURCES_DIR}/fix_nh_gpu.cpp)
target_compile_definitions(lammps PRIVATE -DLMP_GPU)
set(GPU_API "opencl" CACHE STRING "API used by GPU package")
@ -97,9 +99,13 @@ if(GPU_API STREQUAL "CUDA")
if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
endif()
# Ampere (GPU Arch 8.0 and 8.6) is supported by CUDA 11 and later
# Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80] -gencode arch=compute_86,code=[sm_86,compute_86]")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
endif()
# Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
endif()
if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
message(WARNING "Unsupported CUDA version. Use at your own risk.")
@ -139,27 +145,13 @@ if(GPU_API STREQUAL "CUDA")
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
elseif(GPU_API STREQUAL "OPENCL")
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
# download and unpack support binaries for compilation of windows binaries.
set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
endif()
set_target_properties(OpenCL::OpenCL PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
mark_as_advanced(USE_STATIC_OPENCL_LOADER)
if (USE_STATIC_OPENCL_LOADER)
include(OpenCLLoader)
else()
find_package(OpenCL REQUIRED)
endif()
set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
validate_option(OCL_TUNE OCL_TUNE_VALUES)
string(TOUPPER ${OCL_TUNE} OCL_TUNE)
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
@ -203,7 +195,7 @@ elseif(GPU_API STREQUAL "OPENCL")
add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
target_link_libraries(lammps PRIVATE gpu)
@ -211,6 +203,7 @@ elseif(GPU_API STREQUAL "OPENCL")
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
add_dependencies(ocl_get_devices OpenCL::OpenCL)
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
@ -393,13 +386,10 @@ elseif(GPU_API STREQUAL "HIP")
target_link_libraries(lammps PRIVATE gpu)
endif()
# GPU package
FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
# detects styles which have GPU version
# detect styles which have a GPU version
RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)

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

@ -69,14 +69,14 @@ if(DOWNLOAD_KIM)
BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
)
else()
if(KIM-API_FOUND AND KIM_API_VERSION VERSION_GREATER_EQUAL 2.2.0)
if(KIM-API_FOUND AND KIM-API_VERSION VERSION_GREATER_EQUAL 2.2.0)
# For kim-api >= 2.2.0
find_package(KIM-API ${KIM-API_MIN_VERSION} CONFIG REQUIRED)
find_package(KIM-API 2.2.0 CONFIG REQUIRED)
target_link_libraries(lammps PRIVATE KIM-API::kim-api)
else()
# For kim-api 2.1.3 (consistent with previous version of this file)
find_package(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=KIM-API_MIN_VERSION)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
endif()
endif()

5
cmake/Modules/Packages/MESSAGE.cmake
View File

@ -2,9 +2,8 @@ if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
endif()
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
file(GLOB_RECURSE cslib_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
add_library(cslib STATIC ${cslib_SOURCES})
target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})

4
cmake/Modules/YAML.cmake
View File

@ -12,7 +12,7 @@ ExternalProject_Add(libyaml
CXX=${CMAKE_CXX_COMPILER}
CC=${CMAKE_C_COMPILER}
--prefix=<INSTALL_DIR> --disable-shared
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
TEST_COMMAND "")
ExternalProject_Get_Property(libyaml INSTALL_DIR)
@ -23,7 +23,7 @@ set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a)
set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
add_library(Yaml::Yaml UNKNOWN IMPORTED)
set_target_properties(Yaml::Yaml PROPERTIES

8
doc/Makefile
View File

@ -47,6 +47,8 @@ HAS_PDFLATEX = YES
endif
endif
# override settings for PIP commands
# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
@ -228,13 +230,13 @@ $(VENV):
@( \
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install --upgrade pip; \
pip install -r $(BUILDDIR)/utils/requirements.txt; \
pip $(PIP_OPTIONS) install --upgrade pip; \
pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
deactivate;\
)
$(MATHJAX):
@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
$(TXT2RST) $(ANCHORCHECK): $(VENV)
@( \

2
doc/src/Build_basics.rst
View File

@ -95,7 +95,7 @@ standard. A more detailed discussion of that is below.
.. note::
The file ``src/STUBS/mpi.c`` provides a CPU timer function
The file ``src/STUBS/mpi.cpp`` provides a CPU timer function
called ``MPI_Wtime()`` that calls ``gettimeofday()``. If your
operating system does not support ``gettimeofday()``, you will
need to insert code to call another timer. Note that the

33
doc/src/Build_extras.rst
View File

@ -120,8 +120,6 @@ CMake build
-D GPU_API=value # value = opencl (default) or cuda or hip
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_50
@ -135,6 +133,8 @@ CMake build
# value = yes (default) or no
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
# value = yes (default) or no
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
@ -161,6 +161,12 @@ When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
If you are compiling for OpenCL, the default setting is to download, build, and
link with a static OpenCL ICD loader library and standard OpenCL headers. This
way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
@ -258,18 +264,18 @@ To build with this package, the KIM library with API v2 must be downloaded
and built on your system. It must include the KIM models that you want to
use with LAMMPS.
If you would like to use the :doc:`kim_query <kim_commands>`
If you would like to use the :doc:`kim query <kim_commands>`
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
If you would like to use the :doc:`kim_property <kim_commands>`
If you would like to use the :doc:`kim property <kim_commands>`
command, you need to build LAMMPS with the PYTHON package installed
and linked to Python 3.6 or later. See the :ref:`PYTHON package build info <python>`
for more details on this. After successfully building LAMMPS with Python, you
also need to install the kim-property Python package, which can be easily done using
*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
``conda install kim-property`` if LAMMPS is built in Conda. More detailed
information is available at:
also need to install the ``kim-property`` Python package, which can be easily
done using *pip* as ``pip install kim-property``, or from the *conda-forge*
channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
In addition to installing the KIM API, it is also necessary to install the
@ -309,7 +315,7 @@ minutes to hours) to build. Of course you only need to do that once.)
You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``. You can also do
this in one step from the lammps/src dir, using a command like
this in one step from the lammps/src directory, using a command like
these, which simply invoke the ``lib/kim/Install.py`` script with
the specified args.
@ -329,7 +335,7 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: make
LMP_INC = -DLMP_NO_SSL_CHECK
LMP_INC = -DLMP_NO_SSL_CHECK
Debugging OpenKIM web queries in LAMMPS
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -377,10 +383,11 @@ Enabling the extra unit tests have some requirements,
Conda. More detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
* It is also necessary to install
``EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000``, and
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-build binary of the OpenKIM Repository of
to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see
`Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
to learn how to install the specific KIM models.

16
doc/src/Build_link.rst
View File

@ -20,16 +20,8 @@ the suffix ``.so.0`` (or some other number).
.. note::
Care should be taken to use the same MPI library for the calling code
and the LAMMPS library. The ``library.h`` file includes ``mpi.h``
and uses definitions from it so those need to be available and
consistent. When LAMMPS is compiled with the included STUBS MPI
library, then its ``mpi.h`` file needs to be included. While it is
technically possible to use a full MPI library in the calling code
and link to a serial LAMMPS library compiled with MPI STUBS, it is
recommended to use the *same* MPI library for both, and then use
``MPI_Comm_split()`` in the calling code to pass a suitable
communicator with a subset of MPI ranks to the function creating the
LAMMPS instance.
and the LAMMPS library unless LAMMPS is to be compiled without (real)
MPI support using the include STUBS MPI library.
Link with LAMMPS as a static library
------------------------------------
@ -110,7 +102,7 @@ executable, that are also required to link the LAMMPS executable.
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
gcc -c -O -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
-llammps_serial -lpoems -lmpi_stubs
@ -174,7 +166,7 @@ the POEMS package installed becomes:
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
gcc -c -O -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
Locating liblammps.so at runtime

11
doc/src/Build_manual.rst
View File

@ -74,7 +74,11 @@ For the documentation build a python virtual environment is set up in
the folder ``doc/docenv`` and various python packages are installed into
that virtual environment via the ``pip`` tool. For rendering embedded
LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
engine needs to be downloaded.
engine needs to be downloaded. If you need to pass additional options
to the pip commands to work (e.g. to use a web proxy or to point to
additional SSL certificates) you can set them via the ``PIP_OPTIONS``
environment variable or uncomment and edit the ``PIP_OPTIONS`` setting
at beginning of the makefile.
The actual translation is then done via ``make`` commands in the doc
folder. The following ``make`` commands are available:
@ -108,7 +112,10 @@ installation of the HTML manual pages into the "install" step when
installing LAMMPS after the CMake build via ``cmake --build . --target
install``. The documentation build is included in the default build
target, but can also be requested independently with
``cmake --build . --target doc``.
``cmake --build . --target doc``. If you need to pass additional options
to the pip commands to work (e.g. to use a web proxy or to point to
additional SSL certificates) you can set them via the ``PIP_OPTIONS``
environment variable.
.. code-block:: bash

6
doc/src/Commands_all.rst
View File

@ -60,11 +60,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`include <include>`
* :doc:`info <info>`
* :doc:`jump <jump>`
* :doc:`kim_init <kim_commands>`
* :doc:`kim_interactions <kim_commands>`
* :doc:`kim_param <kim_commands>`
* :doc:`kim_property <kim_commands>`
* :doc:`kim_query <kim_commands>`
* :doc:`kim <kim_commands>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`

8
doc/src/Commands_fix.rst
View File

@ -114,7 +114,7 @@ OPT.
* :doc:`nph/eff <fix_nh_eff>`
* :doc:`nph/sphere (o) <fix_nph_sphere>`
* :doc:`nphug <fix_nphug>`
* :doc:`npt (iko) <fix_nh>`
* :doc:`npt (giko) <fix_nh>`
* :doc:`npt/asphere (o) <fix_npt_asphere>`
* :doc:`npt/body <fix_npt_body>`
* :doc:`npt/cauchy <fix_npt_cauchy>`
@ -122,8 +122,8 @@ OPT.
* :doc:`npt/sphere (o) <fix_npt_sphere>`
* :doc:`npt/uef <fix_nh_uef>`
* :doc:`numdiff <fix_numdiff>`
* :doc:`nve (iko) <fix_nve>`
* :doc:`nve/asphere (i) <fix_nve_asphere>`
* :doc:`nve (giko) <fix_nve>`
* :doc:`nve/asphere (gi) <fix_nve_asphere>`
* :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
* :doc:`nve/awpmd <fix_nve_awpmd>`
* :doc:`nve/body <fix_nve_body>`
@ -138,7 +138,7 @@ OPT.
* :doc:`nve/spin <fix_nve_spin>`
* :doc:`nve/tri <fix_nve_tri>`
* :doc:`nvk <fix_nvk>`
* :doc:`nvt (iko) <fix_nh>`
* :doc:`nvt (giko) <fix_nh>`
* :doc:`nvt/asphere (o) <fix_nvt_asphere>`
* :doc:`nvt/body <fix_nvt_body>`
* :doc:`nvt/eff <fix_nh_eff>`

2
doc/src/Commands_pair.rst
View File

@ -122,7 +122,7 @@ OPT.
* :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>`
* :doc:`line/lj <pair_line_lj>`
* :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
* :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`

3
doc/src/Developer_utils.rst
View File

@ -104,6 +104,9 @@ and parsing files or arguments.
.. doxygenfunction:: strmatch
:project: progguide
.. doxygenfunction:: strfind
:project: progguide
.. doxygenfunction:: is_integer
:project: progguide

17
doc/src/Install_tarball.rst
View File

@ -33,22 +33,19 @@ in its name, e.g. lammps-23Jun18.
----------
You can also download a zip file via the "Clone or download" button on
the `LAMMPS GitHub site <git_>`_. The file name will be lammps-master.zip
which can be unzipped with the following command, to create
a lammps-master dir:
You can also download a compressed tar or zip archives from the
"Assets" sections of the `LAMMPS GitHub releases site <git_>`_.
The file name will be lammps-<version>.zip which can be unzipped
with the following command, to create a lammps-<version> dir:
.. code-block:: bash
$ unzip lammps*.zip
This version is the most up-to-date LAMMPS development version. It
will have the date of the most recent patch release (see the file
src/version.h). But it will also include any new bug-fixes or
features added since the last patch release. They will be included in
the next patch release tarball.
This version corresponds to the selected LAMMPS patch or stable
release.
.. _git: https://github.com/lammps/lammps
.. _git: https://github.com/lammps/lammps/releases
----------

2
doc/src/Intro_features.rst
View File

@ -85,7 +85,7 @@ commands)
* water potentials: TIP3P, TIP4P, SPC
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>`
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials

22
doc/src/Packages_details.rst
View File

@ -367,17 +367,19 @@ KIM package
**Contents:**
This package contains a set of commands that serve as a wrapper on the
This package contains a command with a set of sub-commands that serve as a
wrapper on the
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
repository of interatomic models (IMs) enabling compatible ones to be used in
LAMMPS simulations.
This includes :doc:`kim_init <kim_commands>`, and
:doc:`kim_interactions <kim_commands>` commands to select, initialize and
instantiate the IM, a :doc:`kim_query <kim_commands>` command to perform web
This includes :doc:`kim init <kim_commands>`, and
:doc:`kim interactions <kim_commands>` commands to select, initialize and
instantiate the IM, a :doc:`kim query <kim_commands>` command to perform web
queries for material property predictions of OpenKIM IMs, a
:doc:`kim_param <kim_commands>` command to access KIM Model Parameters from
LAMMPS, and a :doc:`kim_property <kim_commands>` command to write material
:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
LAMMPS, and a :doc:`kim property <kim_commands>` command to write material
properties computed in LAMMPS to standard KIM property instance format.
Support for KIM IMs that conform to the
@ -386,8 +388,8 @@ is provided by the :doc:`pair_style kim <pair_kim>` command.
.. note::
The command *pair_style kim* is called by *kim_interactions* and
is not recommended to be directly used in input scripts.
The command *pair_style kim* is called by *kim interactions* and is not
recommended to be directly used in input scripts.
To use this package you must have the KIM API library available on your
system. The KIM API is available for download on the
@ -404,7 +406,7 @@ and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
API and the *pair_style kim* command. Yaser Afshar (U Minnesota),
Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and
Daniel Karls (U Minnesota) contributed to the
:doc:`kim_commands <kim_commands>` interface in close collaboration with
:doc:`kim command <kim_commands>` interface in close collaboration with
Ryan Elliott.
**Install:**
@ -414,7 +416,7 @@ This package has :ref:`specific installation instructions <kim>` on the
**Supporting info:**
* :doc:`kim_commands <kim_commands>`
* :doc:`kim command <kim_commands>`
* :doc:`pair_style kim <pair_kim>`
* src/KIM: filenames -> commands
* src/KIM/README

2
doc/src/Python_atoms.rst
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@ -50,7 +50,7 @@ against invalid accesses.
**Numpy Methods**:
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
.. tab:: PyLammps/IPyLammps API

11
doc/src/Python_formats.rst Normal file
View File

@ -0,0 +1,11 @@
Output Readers
==============
.. py:module:: lammps.formats
The Python package contains the :py:mod:`lammps.formats` module, which
provides classes to post-process some of the output files generated by LAMMPS.
.. automodule:: lammps.formats
:members:
:noindex:

1
doc/src/Python_head.rst
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@ -13,6 +13,7 @@ together.
Python_module
Python_ext
Python_call
Python_formats
Python_examples
Python_error
Python_trouble

12
doc/src/Python_module.rst
View File

@ -61,7 +61,7 @@ functions. Below is a detailed documentation of the API.
.. autoclass:: lammps.lammps
:members:
.. autoclass:: lammps.numpy::numpy_wrapper
.. autoclass:: lammps.numpy_wrapper::numpy_wrapper
:members:
----------
@ -134,8 +134,8 @@ Style Constants
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`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
:py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_type_constants:
@ -149,8 +149,8 @@ Type Constants
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`, :py:func:`lammps.extract_fix`, and their NumPy variants
:py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
:py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
:py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
.. _py_vartype_constants:
@ -170,6 +170,6 @@ Classes representing internal objects
:members:
:no-undoc-members:
.. autoclass:: lammps.numpy::NumPyNeighList
.. autoclass:: lammps.numpy_wrapper::NumPyNeighList
:members:
:no-undoc-members:

4
doc/src/Python_neighbor.rst
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@ -14,5 +14,5 @@ Neighbor list access
**NumPy Methods:**
* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)
* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)

12
doc/src/Python_objects.rst
View File

@ -36,9 +36,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
Python subscripting. The values will be zero for atoms not in the
specified group.
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>` are
:py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
:py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
:py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
@ -54,9 +54,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
**NumPy Methods**:
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
* :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
.. tab:: PyLammps/IPyLammps API

64
doc/src/Speed_gpu.rst
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@ -1,11 +1,14 @@
GPU package
===========
The GPU package was developed by Mike Brown while at SNL and ORNL
and his collaborators, particularly Trung Nguyen (now at Northwestern).
It provides GPU versions of many pair styles and for parts of the
:doc:`kspace_style pppm <kspace_style>` for long-range Coulombics.
It has the following general features:
The GPU package was developed by Mike Brown while at SNL and ORNL (now
at Intel Corp.) and his collaborators, particularly Trung Nguyen (now at
Northwestern). Support for AMD GPUs via HIP was added by Vsevolod Nikolskiy
and coworkers at HSE University.
The GPU package provides GPU versions of many pair styles and for
parts of the :doc:`kspace_style pppm <kspace_style>` for long-range
Coulombics. It has the following general features:
* It is designed to exploit common GPU hardware configurations where one
or more GPUs are coupled to many cores of one or more multi-core CPUs,
@ -24,8 +27,9 @@ It has the following general features:
force vectors.
* LAMMPS-specific code is in the GPU package. It makes calls to a
generic GPU library in the lib/gpu directory. This library provides
NVIDIA support as well as more general OpenCL support, so that the
same functionality is supported on a variety of hardware.
either Nvidia support, AMD support, or more general OpenCL support
(for Nvidia GPUs, AMD GPUs, Intel GPUs, and multi-core CPUs).
so that the same functionality is supported on a variety of hardware.
**Required hardware/software:**
@ -45,12 +49,23 @@ to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
In OpenCL mode, the acceleration depends on having an `OpenCL Installable Client Driver (ICD) <https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader>`_
installed. There can be multiple of them for the same or different hardware
(GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
as 'platforms'. The GPU library will select the **first** suitable platform,
but this can be overridden using the device option of the :doc:`package <package>`
as 'platforms'. The GPU library will try to auto-select the best suitable platform,
but this can be overridden using the platform option of the :doc:`package <package>`
command. run lammps/lib/gpu/ocl_get_devices to get a list of available
platforms and devices with a suitable ICD available.
To compute and use this package in HIP mode, you have to have the AMD ROCm
To compile and use this package for Intel GPUs, OpenCL or the Intel oneAPI
HPC Toolkit can be installed using linux package managers. The latter also
provides optimized C++, MPI, and many other libraries and tools. See:
* https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit/download.html
If you do not have a discrete GPU card installed, this package can still provide
significant speedups on some CPUs that include integrated GPUs. Additionally, for
many macs, OpenCL is already included with the OS and Makefiles are available
in the lib/gpu directory.
To compile and use this package in HIP mode, you have to have the AMD ROCm
software installed. Versions of ROCm older than 3.5 are currently deprecated
by AMD.
@ -75,10 +90,20 @@ automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.
The GPU package also has limited support for OpenMP for both
multi-threading and vectorization of routines that are run on the CPUs.
This requires that the GPU library and LAMMPS are built with flags to
enable OpenMP support (e.g. -fopenmp). Some styles for time integration
are also available in the GPU package. These run completely on the CPUs
in full double precision, but exploit multi-threading and vectorization
for faster performance.
Use the "-sf gpu" :doc:`command-line switch <Run_options>`, which will
automatically append "gpu" to styles that support it. Use the "-pk
gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of
GPUs/node to use.
GPUs/node to use. If Ng is 0, the number is selected automatically as
the number of matching GPUs that have the highest number of compute
cores.
.. code-block:: bash
@ -87,8 +112,8 @@ GPUs/node to use.
mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
Note that if the "-sf gpu" switch is used, it also issues a default
:doc:`package gpu 1 <package>` command, which sets the number of
GPUs/node to 1.
:doc:`package gpu 0 <package>` command, which will result in
automatic selection of the number of GPUs to use.
Using the "-pk" switch explicitly allows for setting of the number of
GPUs/node to use and additional options. Its syntax is the same as
@ -138,6 +163,13 @@ Likewise, you should experiment with the precision setting for the GPU
library to see if single or mixed precision will give accurate
results, since they will typically be faster.
MPI parallelism typically outperforms OpenMP parallelism, but in some
cases using fewer MPI tasks and multiple OpenMP threads with the GPU
package can give better performance. 3-body potentials can often perform
better with multiple OMP threads because the inter-process communication
is higher for these styles with the GPU package in order to allow
deterministic results.
**Guidelines for best performance:**
* Using multiple MPI tasks per GPU will often give the best performance,
@ -161,6 +193,12 @@ results, since they will typically be faster.
:doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
:doc:`improper <improper_style>`, and :doc:`long-range <kspace_style>`
calculations will not be included in the "Pair" time.
* Since only part of the pppm kspace style is GPU accelerated, it
may be faster to only use GPU acceleration for Pair styles with
long-range electrostatics. See the "pair/only" keyword of the
package command for a shortcut to do that. The work between kspace
on the CPU and non-bonded interactions on the GPU can be balanced
through adjusting the coulomb cutoff without loss of accuracy.
* When the *mode* setting for the package gpu command is force/neigh,
the time for neighbor list calculations on the GPU will be added into
the "Pair" time, not the "Neigh" time. An additional breakdown of the

8
doc/src/Speed_packages.rst
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@ -16,7 +16,7 @@ These are the accelerator packages currently in LAMMPS, either as
standard or user packages:
+-----------------------------------------+-------------------------------------------------------+
| :doc:`GPU Package <Speed_gpu>` | for NVIDIA GPUs as well as OpenCL support |
| :doc:`GPU Package <Speed_gpu>` | for GPUs via CUDA, OpenCL, or ROCm HIP |
+-----------------------------------------+-------------------------------------------------------+
| :doc:`USER-INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi |
+-----------------------------------------+-------------------------------------------------------+
@ -43,7 +43,7 @@ three kinds of hardware, via the listed packages:
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Many-core CPUs | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`USER-OMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| NVIDIA/AMD GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
| GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
| Intel Phi/AVX | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages |
+-----------------+-----------------------------------------------------------------------------------------------------------------------------+
@ -154,8 +154,8 @@ Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
* Styles with a "gpu" suffix are part of the GPU package and can be run
on NVIDIA or AMD GPUs. The speed-up on a GPU depends on a variety of
factors, discussed in the accelerator sections.
on Intel, NVIDIA, or AMD GPUs. The speed-up on a GPU depends on a
variety of factors, discussed in the accelerator sections.
* Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,

2
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@ -163,7 +163,7 @@ the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+

2
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@ -153,7 +153,7 @@ temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>
compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1 temp
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
fix 1 all ave/time 100 1 100 c_myChunk[1] file tmp.out mode vector
----------

4
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@ -128,9 +128,9 @@ formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`born/coul/long, born/coul/msm <pair_born>` | coulombic_cutoff | type global |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | coulombic_cutoff | type global |
| :doc:`buck/coul/long, buck/coul/msm <pair_buck>` | a,c,coulombic_cutoff | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+--------------------------------------------------+-------------+

2
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@ -120,7 +120,7 @@ styles and their energy formulas for the meaning of these parameters:
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`born <pair_born>` | a,b,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck <pair_buck>` | a,c | type pairs |
| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm <pair_buck>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+
| :doc:`buck/mdf <pair_mdf>` | a,c | type pairs |
+------------------------------------------------------------------------------+-------------------------+------------+

6
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@ -1,8 +1,10 @@
.. index:: fix nvt
.. index:: fix nvt/gpu
.. index:: fix nvt/intel
.. index:: fix nvt/kk
.. index:: fix nvt/omp
.. index:: fix npt
.. index:: fix npt/gpu
.. index:: fix npt/intel
.. index:: fix npt/kk
.. index:: fix npt/omp
@ -13,12 +15,12 @@
fix nvt command
===============
Accelerator Variants: *nvt/intel*, *nvt/kk*, *nvt/omp*
Accelerator Variants: *nvt/gpu*, *nvt/intel*, *nvt/kk*, *nvt/omp*
fix npt command
===============
Accelerator Variants: *npt/intel*, *npt/kk*, *npt/omp*
Accelerator Variants: *npt/gpu*, *npt/intel*, *npt/kk*, *npt/omp*
fix nph command
===============

3
doc/src/fix_nve.rst
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@ -1,4 +1,5 @@
.. index:: fix nve
.. index:: fix nve/gpu
.. index:: fix nve/intel
.. index:: fix nve/kk
.. index:: fix nve/omp
@ -6,7 +7,7 @@
fix nve command
===============
Accelerator Variants: *nve/intel*, *nve/kk*, *nve/omp*
Accelerator Variants: *nve/gpu*, *nve/intel*, *nve/kk*, *nve/omp*
Syntax
""""""

3
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@ -1,10 +1,11 @@
.. index:: fix nve/asphere
.. index:: fix nve/asphere/gpu
.. index:: fix nve/asphere/intel
fix nve/asphere command
=======================
Accelerator Variants: *nve/asphere/intel*
Accelerator Variants: *nve/asphere/gpu*, *nve/asphere/intel*
Syntax
""""""

2
doc/src/fix_wall_body_polygon.rst
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@ -15,7 +15,7 @@ Syntax
* k_n = normal repulsion strength (force/distance or pressure units)
* c_n = normal damping coefficient (force/distance or pressure units)
* c_t = tangential damping coefficient (force/distance or pressure units)
* wallstyle = *xplane* or *yplane* or *zplane* or *zcylinder*
* wallstyle = *xplane* or *yplane* or *zcylinder*
* args = list of arguments for a particular style
.. parsed-literal::

6
doc/src/fix_wall_gran.rst
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@ -199,11 +199,11 @@ the following table:
| 1 | 1.0 if particle is in contact with wall, | |
| | 0.0 otherwise | |
+-------+----------------------------------------------------+----------------+
| 2 | Force :math:`f_x` exerted on the wall | force units |
| 2 | Force :math:`f_x` exerted by the wall | force units |
+-------+----------------------------------------------------+----------------+
| 3 | Force :math:`f_y` exerted on the wall | force units |
| 3 | Force :math:`f_y` exerted by the wall | force units |
+-------+----------------------------------------------------+----------------+
| 4 | Force :math:`f_z` exerted on the wall | force units |
| 4 | Force :math:`f_z` exerted by the wall | force units |
+-------+----------------------------------------------------+----------------+
| 5 | :math:`x`-coordinate of contact point on wall | distance units |
+-------+----------------------------------------------------+----------------+

6
doc/src/fix_wall_gran_region.rst
View File

@ -240,11 +240,11 @@ the following table:
| 1 | 1.0 if particle is in contact with wall, | |
| | 0.0 otherwise | |
+-------+----------------------------------------------------+----------------+
| 2 | Force :math:`f_x` exerted on the wall | force units |
| 2 | Force :math:`f_x` exerted by the wall | force units |
+-------+----------------------------------------------------+----------------+
| 3 | Force :math:`f_y` exerted on the wall | force units |
| 3 | Force :math:`f_y` exerted by the wall | force units |
+-------+----------------------------------------------------+----------------+
| 4 | Force :math:`f_z` exerted on the wall | force units |
| 4 | Force :math:`f_z` exerted by the wall | force units |
+-------+----------------------------------------------------+----------------+
| 5 | :math:`x`-coordinate of contact point on wall | distance units |
+-------+----------------------------------------------------+----------------+

1352
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242
doc/src/package.rst
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@ -18,7 +18,7 @@ Syntax
*gpu* args = Ngpu keyword value ...
Ngpu = # of GPUs per node
zero or more keyword/value pairs may be appended
keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *device* or *blocksize*
keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *blocksize* or *platform* or *device_type* or *ocl_args*
*neigh* value = *yes* or *no*
yes = neighbor list build on GPU (default)
no = neighbor list build on CPU
@ -32,17 +32,20 @@ Syntax
size = bin size for neighbor list construction (distance units)
*split* = fraction
fraction = fraction of atoms assigned to GPU (default = 1.0)
*gpuID* values = first last
first = ID of first GPU to be used on each node
last = ID of last GPU to be used on each node
*tpa* value = Nthreads
Nthreads = # of GPU threads used per atom
*device* value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13
platform_id = numerical OpenCL platform id (default: -1)
device_type = *kepler* or *fermi* or *cypress* or *intel* or *phi* or *generic* or *custom*
val1,val2,... = custom OpenCL tune parameters (see below for details)
*tpa* value = Nlanes
Nlanes = # of GPU vector lanes (CUDA threads) used per atom
*blocksize* value = size
size = thread block size for pair force computation
*omp* value = Nthreads
Nthreads = number of OpenMP threads to use on CPU (default = 0)
*platform* value = id
id = For OpenCL, platform ID for the GPU or accelerator
*gpuID* values = id
id = ID of first GPU to be used on each node
*device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom,val1,val2,...*
val1,val2,... = custom OpenCL accelerator configuration parameters (see below for details)
*ocl_args* value = args
args = List of additional OpenCL compiler arguments delimited by colons
*intel* args = NPhi keyword value ...
Nphi = # of co-processors per node
zero or more keyword/value pairs may be appended
@ -100,7 +103,7 @@ Syntax
off = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default)
on = use device acceleration only for pair styles (and host acceleration for others)
*omp* args = Nthreads keyword value ...
Nthread = # of OpenMP threads to associate with each MPI process
Nthreads = # of OpenMP threads to associate with each MPI process
zero or more keyword/value pairs may be appended
keywords = *neigh*
*neigh* value = *yes* or *no*
@ -112,12 +115,10 @@ Examples
.. code-block:: LAMMPS
package gpu 1
package gpu 0
package gpu 1 split 0.75
package gpu 2 split -1.0
package gpu 1 device kepler
package gpu 1 device 2:generic
package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128
package gpu 0 omp 2 device_type intelgpu
package kokkos neigh half comm device
package omp 0 neigh no
package omp 4
@ -174,10 +175,18 @@ simulations.
The *gpu* style invokes settings associated with the use of the GPU
package.
The *Ngpu* argument sets the number of GPUs per node. There must be
at least as many MPI tasks per node as GPUs, as set by the mpirun or
mpiexec command. If there are more MPI tasks (per node)
than GPUs, multiple MPI tasks will share each GPU.
The *Ngpu* argument sets the number of GPUs per node. If *Ngpu* is 0
and no other keywords are specified, GPU or accelerator devices are
auto-selected. In this process, all platforms are searched for
accelerator devices and GPUs are chosen if available. The device with
the highest number of compute cores is selected. The number of devices
is increased to be the number of matching accelerators with the same
number of compute cores. If there are more devices than MPI tasks,
the additional devices will be unused. The auto-selection of GPUs/
accelerator devices and platforms can be restricted by specifying
a non-zero value for *Ngpu* and / or using the *gpuID*, *platform*,
and *device_type* keywords as described below. If there are more MPI
tasks (per node) than GPUs, multiple MPI tasks will share each GPU.
Optional keyword/value pairs can also be specified. Each has a
default value as listed below.
@ -212,18 +221,8 @@ overlapped with all other computations on the CPU.
The *binsize* keyword sets the size of bins used to bin atoms in
neighbor list builds performed on the GPU, if *neigh* = *yes* is set.
If *binsize* is set to 0.0 (the default), then bins = the size of the
pairwise cutoff + neighbor skin distance. This is 2x larger than the
LAMMPS default used for neighbor list building on the CPU. This will
be close to optimal for the GPU, so you do not normally need to use
this keyword. Note that if you use a longer-than-usual pairwise
cutoff, e.g. to allow for a smaller fraction of KSpace work with a
:doc:`long-range Coulombic solver <kspace_style>` because the GPU is
faster at performing pairwise interactions, then it may be optimal to
make the *binsize* smaller than the default. For example, with a
cutoff of 20\*sigma in LJ :doc:`units <units>` and a neighbor skin
distance of sigma, a *binsize* = 5.25\*sigma can be more efficient than
the default.
If *binsize* is set to 0.0 (the default), then the binsize is set
automatically using heuristics in the GPU package.
The *split* keyword can be used for load balancing force calculations
between CPU and GPU cores in GPU-enabled pair styles. If 0 < *split* <
@ -257,63 +256,79 @@ cores would perform force calculations for some fraction of the
particles at the same time the GPUs performed force calculation for
the other particles.
The *gpuID* keyword allows selection of which GPUs on each node will
be used for a simulation. The *first* and *last* values specify the
GPU IDs to use (from 0 to Ngpu-1). By default, first = 0 and last =
Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
of physical GPUs. If you only wish to use a subset, set Ngpu to a
smaller number and first/last to a sub-range of the available GPUs.
The *gpuID* keyword is used to specify the first ID for the GPU or
other accelerator that LAMMPS will use. For example, if the ID is
1 and *Ngpu* is 3, GPUs 1-3 will be used. Device IDs should be
determined from the output of nvc_get_devices, ocl_get_devices,
or hip_get_devices
as provided in the lib/gpu directory. When using OpenCL with
accelerators that have main memory NUMA, the accelerators can be
split into smaller virtual accelerators for more efficient use
with MPI.
The *tpa* keyword sets the number of GPU thread per atom used to
The *tpa* keyword sets the number of GPU vector lanes per atom used to
perform force calculations. With a default value of 1, the number of
threads will be chosen based on the pair style, however, the value can
lanes will be chosen based on the pair style, however, the value can
be set explicitly with this keyword to fine-tune performance. For
large cutoffs or with a small number of particles per GPU, increasing
the value can improve performance. The number of threads per atom must
be a power of 2 and currently cannot be greater than 32.
The *device* keyword can be used to tune parameters optimized for a
specific accelerator and platform when using OpenCL. OpenCL supports
the concept of a **platform**\ , which represents one or more devices that
share the same driver (e.g. there would be a different platform for
GPUs from different vendors or for CPU based accelerator support).
In LAMMPS only one platform can be active at a time and by default
the first platform with an accelerator is selected. This is equivalent
to using a platform ID of -1. The platform ID is a number corresponding
to the output of the ocl_get_devices tool. The platform ID is passed
to the GPU library, by prefixing the *device* keyword with that number
separated by a colon. For CUDA, the *device* keyword is ignored.
Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA
Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device.
More devices may be added later. The default device type can be
specified when building LAMMPS with the GPU library, via setting a
variable in the lib/gpu/Makefile that is used.
In addition, a device type *custom* is available, which is followed by
13 comma separated numbers, which allows to set those tweakable parameters
from the package command. It can be combined with the (colon separated)
platform id. The individual settings are:
* MEM_THREADS
* THREADS_PER_ATOM
* THREADS_PER_CHARGE
* BLOCK_PAIR
* MAX_SHARED_TYPES
* BLOCK_NBOR_BUILD
* BLOCK_BIO_PAIR
* BLOCK_ELLIPSE
* WARP_SIZE
* PPPM_BLOCK_1D
* BLOCK_CELL_2D
* BLOCK_CELL_ID
* MAX_BIO_SHARED_TYPES
the value can improve performance. The number of lanes per atom must
be a power of 2 and currently cannot be greater than the SIMD width
for the GPU / accelerator. In the case it exceeds the SIMD width, it
will automatically be decreased to meet the restriction.
The *blocksize* keyword allows you to tweak the number of threads used
per thread block. This number should be a multiple of 32 (for GPUs)
and its maximum depends on the specific GPU hardware. Typical choices
are 64, 128, or 256. A larger block size increases occupancy of
individual GPU cores, but reduces the total number of thread blocks,
thus may lead to load imbalance.
thus may lead to load imbalance. On modern hardware, the sensitivity
to the blocksize is typically low.
The *Nthreads* value for the *omp* keyword sets the number of OpenMP
threads allocated for each MPI task. This setting controls OpenMP
parallelism only for routines run on the CPUs. For more details on
setting the number of OpenMP threads, see the discussion of the
*Nthreads* setting on this doc page for the "package omp" command.
The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL,
and GPU packages.
The *platform* keyword is only used with OpenCL to specify the ID for
an OpenCL platform. See the output from ocl_get_devices in the lib/gpu
directory. In LAMMPS only one platform can be active at a time and by
default (id=-1) the platform is auto-selected to find the GPU with the
most compute cores. When *Ngpu* or other keywords are specified, the
auto-selection is appropriately restricted. For example, if *Ngpu* is
3, only platforms with at least 3 accelerators are considered. Similar
restrictions can be enforced by the *gpuID* and *device_type* keywords.
The *device_type* keyword can be used for OpenCL to specify the type of
GPU to use or specify a custom configuration for an accelerator. In most
cases this selection will be automatic and there is no need to use the
keyword. The *applegpu* type is not specific to a particular GPU vendor,
but is separate due to the more restrictive Apple OpenCL implementation.
For expert users, to specify a custom configuration, the *custom* keyword
followed by the next parameters can be specified:
CONFIG_ID, SIMD_SIZE, MEM_THREADS, SHUFFLE_AVAIL, FAST_MATH,
THREADS_PER_ATOM, THREADS_PER_CHARGE, THREADS_PER_THREE, BLOCK_PAIR,
BLOCK_BIO_PAIR, BLOCK_ELLIPSE, PPPM_BLOCK_1D, BLOCK_NBOR_BUILD,
BLOCK_CELL_2D, BLOCK_CELL_ID, MAX_SHARED_TYPES, MAX_BIO_SHARED_TYPES,
PPPM_MAX_SPLINE.
CONFIG_ID can be 0. SHUFFLE_AVAIL in {0,1} indicates that inline-PTX
(NVIDIA) or OpenCL extensions (Intel) should be used for horizontal
vector operations. FAST_MATH in {0,1} indicates that OpenCL fast math
optimizations are used during the build and hardware-accelerated
transcendental functions are used when available. THREADS_PER_* give the
default *tpa* values for ellipsoidal models, styles using charge, and
any other styles. The BLOCK_* parameters specify the block sizes for
various kernel calls and the MAX_*SHARED*_ parameters are used to
determine the amount of local shared memory to use for storing model
parameters.
For OpenCL, the routines are compiled at runtime for the specified GPU
or accelerator architecture. The *ocl_args* keyword can be used to
specify additional flags for the runtime build.
----------
@ -331,44 +346,13 @@ built with co-processor support.
Optional keyword/value pairs can also be specified. Each has a
default value as listed below.
The *omp* keyword determines the number of OpenMP threads allocated
for each MPI task when any portion of the interactions computed by a
USER-INTEL pair style are run on the CPU. This can be the case even
if LAMMPS was built with co-processor support; see the *balance*
keyword discussion below. If you are running with less MPI tasks/node
than there are CPUs, it can be advantageous to use OpenMP threading on
the CPUs.
.. note::
The *omp* keyword has nothing to do with co-processor threads on
the Xeon Phi; see the *tpc* and *tptask* keywords below for a
discussion of co-processor threads.
The *Nthread* value for the *omp* keyword sets the number of OpenMP
threads allocated for each MPI task. Setting *Nthread* = 0 (the
default) instructs LAMMPS to use whatever value is the default for the
given OpenMP environment. This is usually determined via the
*OMP_NUM_THREADS* environment variable or the compiler runtime, which
is usually a value of 1.
For more details, including examples of how to set the OMP_NUM_THREADS
environment variable, see the discussion of the *Nthreads* setting on
this doc page for the "package omp" command. Nthreads is a required
argument for the USER-OMP package. Its meaning is exactly the same
for the USER-INTEL package.
.. note::
If you build LAMMPS with both the USER-INTEL and USER-OMP
packages, be aware that both packages allow setting of the *Nthreads*
value via their package commands, but there is only a single global
*Nthreads* value used by OpenMP. Thus if both package commands are
invoked, you should insure the two values are consistent. If they are
not, the last one invoked will take precedence, for both packages.
Also note that if the :doc:`-sf hybrid intel omp command-line switch <Run_options>` is used, it invokes a "package intel"
command, followed by a "package omp" command, both with a setting of
*Nthreads* = 0.
The *Nthreads* value for the *omp* keyword sets the number of OpenMP
threads allocated for each MPI task. This setting controls OpenMP
parallelism only for routines run on the CPUs. For more details on
setting the number of OpenMP threads, see the discussion of the
*Nthreads* setting on this doc page for the "package omp" command.
The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL,
and GPU packages.
The *mode* keyword determines the precision mode to use for
computing pair style forces, either on the CPU or on the co-processor,
@ -574,7 +558,7 @@ result in better performance for certain configurations and system sizes.
The *omp* style invokes settings associated with the use of the
USER-OMP package.
The *Nthread* argument sets the number of OpenMP threads allocated for
The *Nthreads* argument sets the number of OpenMP threads allocated for
each MPI task. For example, if your system has nodes with dual
quad-core processors, it has a total of 8 cores per node. You could
use two MPI tasks per node (e.g. using the -ppn option of the mpirun
@ -583,7 +567,7 @@ This would use all 8 cores on each node. Note that the product of MPI
tasks \* threads/task should not exceed the physical number of cores
(on a node), otherwise performance will suffer.
Setting *Nthread* = 0 instructs LAMMPS to use whatever value is the
Setting *Nthreads* = 0 instructs LAMMPS to use whatever value is the
default for the given OpenMP environment. This is usually determined
via the *OMP_NUM_THREADS* environment variable or the compiler
runtime. Note that in most cases the default for OpenMP capable
@ -614,6 +598,24 @@ input. Not all features of LAMMPS support OpenMP threading via the
USER-OMP package and the parallel efficiency can be very different,
too.
.. note::
If you build LAMMPS with the GPU, USER-INTEL, and / or USER-OMP
packages, be aware these packages all allow setting of the *Nthreads*
value via their package commands, but there is only a single global
*Nthreads* value used by OpenMP. Thus if multiple package commands are
invoked, you should insure the values are consistent. If they are
not, the last one invoked will take precedence, for all packages.
Also note that if the :doc:`-sf hybrid intel omp command-line switch <Run_options>` is used, it invokes a "package intel" command, followed by a
"package omp" command, both with a setting of *Nthreads* = 0. Likewise
for a hybrid suffix for gpu and omp. Note that KOKKOS also supports
setting the number of OpenMP threads from the command line using the
"-k on" :doc:`command-line switch <Run_options>`. The default for
KOKKOS is 1 thread per MPI task, so any other number of threads should
be explicitly set using the "-k on" command-line switch (and this
setting should be consistent with settings from any other packages
used).
Optional keyword/value pairs can also be specified. Each has a
default value as listed below.
@ -658,9 +660,9 @@ Related commands
Default
"""""""
For the GPU package, the default is Ngpu = 1 and the option defaults
For the GPU package, the default is Ngpu = 0 and the option defaults
are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
to Ngpu-1, tpa = 1, and device = not used. These settings are made
to Ngpu-1, tpa = 1, omp = 0, and platform=-1. These settings are made
automatically if the "-sf gpu" :doc:`command-line switch <Run_options>`
is used. If it is not used, you must invoke the package gpu command
in your input script or via the "-pk gpu" :doc:`command-line switch <Run_options>`.

2
doc/src/pair_adp.rst
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@ -59,7 +59,7 @@ command to specify them.
* The OpenKIM Project at
`https://openkim.org/browse/models/by-type <https://openkim.org/browse/models/by-type>`_
provides ADP potentials that can be used directly in LAMMPS with the
:doc:`kim_commands <kim_commands>` interface.
:doc:`kim command <kim_commands>` interface.
----------

3
doc/src/pair_charmm.rst
View File

@ -1,4 +1,5 @@
.. index:: pair_style lj/charmm/coul/charmm
.. index:: pair_style lj/charmm/coul/charmm/gpu
.. index:: pair_style lj/charmm/coul/charmm/intel
.. index:: pair_style lj/charmm/coul/charmm/kk
.. index:: pair_style lj/charmm/coul/charmm/omp
@ -19,7 +20,7 @@
pair_style lj/charmm/coul/charmm command
========================================
Accelerator Variants: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp*
Accelerator Variants: *lj/charmm/coul/charmm/gpu*, *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp*
pair_style lj/charmm/coul/charmm/implicit command
=================================================

2
doc/src/pair_eam.rst
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@ -141,7 +141,7 @@ interatomic potentials and file formats.
The OpenKIM Project at
`https://openkim.org/browse/models/by-type <https://openkim.org/browse/models/by-type>`_
provides EAM potentials that can be used directly in LAMMPS with the
:doc:`kim_commands <kim_commands>` interface.
:doc:`kim command <kim_commands>` interface.
----------

21
doc/src/pair_kim.rst
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@ -23,29 +23,30 @@ Examples
Description
"""""""""""
This pair style is a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_ repository of interatomic
potentials to enable their use in LAMMPS scripts.
This pair style is a wrapper on the
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
repository of interatomic potentials to enable their use in LAMMPS scripts.
The preferred interface for using interatomic models archived in
OpenKIM is the :doc:`kim_commands interface <kim_commands>`. That
OpenKIM is the :doc:`kim command <kim_commands>` interface. That
interface supports both "KIM Portable Models" (PMs) that conform to the
KIM API Portable Model Interface (PMI) and can be used by any
simulation code that conforms to the KIM API/PMI, and
"KIM Simulator Models" that are natively implemented within a single
"KIM Simulator Models" (SMs) that are natively implemented within a single
simulation code (like LAMMPS) and can only be used with it.
The *pair_style kim* command is limited to KIM PMs. It is
used by the :doc:`kim_commands interface <kim_commands>` as needed.
used by the :doc:`kim command <kim_commands>` interface as needed.
.. note::
Since *pair_style kim* is called by *kim_interactions* as needed,
is not recommended to be directly used in input scripts.
Since *pair_style kim* is called by *kim interactions* as needed,
it is not recommended to be directly used in input scripts.
----------
The argument *model* is the name of the KIM PM.
For potentials archived in OpenKIM
this is the extended KIM ID (see :doc:`kim_commands <kim_commands>`
this is the extended KIM ID (see :doc:`kim command <kim_commands>`
for details). LAMMPS can invoke any KIM PM, however there can
be incompatibilities (for example due to unit matching issues).
In the event of an incompatibility, the code will terminate with
@ -106,7 +107,7 @@ Restrictions
""""""""""""
This pair style is part of the KIM package. See details on
restrictions in :doc:`kim_commands <kim_commands>`.
restrictions in :doc:`kim command <kim_commands>`.
This current version of pair_style kim is compatible with the
kim-api package version 2.0.0 and higher.
@ -114,7 +115,7 @@ kim-api package version 2.0.0 and higher.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`kim_commands <kim_commands>`
:doc:`pair_coeff <pair_coeff>`, :doc:`kim command <kim_commands>`
Default
"""""""

2
doc/utils/requirements.txt
View File

@ -1,6 +1,6 @@
Sphinx
sphinxcontrib-spelling
git+https://github.com/akohlmey/sphinx-fortran@parallel-read
git+git://github.com/akohlmey/sphinx-fortran@parallel-read
sphinx_tabs
breathe
Pygments

4
doc/utils/sphinx-config/LAMMPSLexer.py
View File

@ -8,8 +8,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
"delete_bonds", "dielectric", "dihedral_coeff", "dihedral_style", "dimension",
"displace_atoms", "dump_modify", "dynamical_matrix", "echo",
"fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
"improper_style", "include", "info", "jump", "kim_init", "kim_interactions",
"kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice",
"improper_style", "include", "info", "jump", "kim",
"kspace_modify", "kspace_style", "label", "lattice",
"log", "mass", "message", "minimize", "min_modify", "min_style", "molecule",
"ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next",
"package", "pair_coeff", "pair_modify", "pair_style", "pair_write",

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -2297,6 +2297,7 @@ omegaz
Omelyan
omp
OMP
oneAPI
onelevel
oneway
onn
@ -2366,6 +2367,7 @@ parmin
Parrinello
Partay
Particuology
Pascuet
pastewka
Pastewka
pathangle
@ -2528,6 +2530,7 @@ ptm
PTM
ptol
ptr
PTX
pu
purdue
Purohit

2
examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
View File

@ -22,7 +22,7 @@ improper_style class2
read_data tiny_nylon.data
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian

2
examples/VISCOSITY/profile.13Oct16.mp.2d.g++.1
View File

@ -1,4 +1,4 @@
# Chunk-averaged data for fix 5 and group file
# Chunk-averaged data for fix 5 and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount vx
6000 20 800

2
examples/VISCOSITY/profile.13Oct16.nemd.2d.g++.1
View File

@ -1,4 +1,4 @@
# Chunk-averaged data for fix 4 and group file
# Chunk-averaged data for fix 4 and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount vx
10000 20 800

2
examples/VISCOSITY/profile.13Oct16.wall.2d.g++.1
View File

@ -1,4 +1,4 @@
# Chunk-averaged data for fix 4 and group file
# Chunk-averaged data for fix 4 and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount vx
10000 20 1020

42
examples/kim/in.kim-ex.melt
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@ -1,35 +1,35 @@
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# the kim-api package are installed. see the `./lib/kim/README` or
# `./lib/kim/Install.py` files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init LennardJones_Ar real
kim init LennardJones_Ar real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Ar
kim interactions Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

38
examples/kim/in.kim-pm-property
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@ -1,19 +1,19 @@
# kim-property example
# kim property example
#
# For detailed information of this example please refer to:
# https://openkim.org/doc/evaluation/tutorial-lammps/
# `https://openkim.org/doc/evaluation/tutorial-lammps/`
#
# Description:
#
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# https://openkim.org/doc/schema/properties-framework/ and
# https://lammps.sandia.gov/doc/kim_commands.html for further details).
# Then the created property instance is written to a file named results.edn
# using the `kim_property dump` commands.
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
@ -28,7 +28,7 @@
# This example requires that the KIM Portable Model (PM)
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed. This can be done with the command
# `kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
@ -38,14 +38,14 @@
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
# Initialize interatomic potential (KIM model) and units
atom_style atomic
# Set the OpenKIM model that will be used
kim_init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
# the equilibrium lattice constant for the fcc structure
variable lattice_constant equal 5.248509056866169
@ -55,14 +55,14 @@ boundary p p p
# Create an FCC lattice with the lattice spacing
# using a single conventional (orthogonal) unit cell
lattice fcc ${lattice_constant}
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
lattice fcc ${lattice_constant}
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
create_atoms 1 box
mass 1 39.948
mass 1 39.948
# Specify the KIM interactions
kim_interactions Ar
kim interactions Ar
# Compute energy
run 0
@ -72,10 +72,10 @@ variable natoms equal "count(all)"
variable ecohesive equal "-pe/v_natoms"
# Create a property instance
kim_property create 1 cohesive-potential-energy-cubic-crystal
kim property create 1 cohesive-potential-energy-cubic-crystal
# Set all the key-value pairs for this property instance
kim_property modify 1 key short-name source-value 1 fcc &
kim property modify 1 key short-name source-value 1 fcc &
key species source-value 1 Ar &
key a source-value ${lattice_constant} &
source-unit angstrom &
@ -88,4 +88,4 @@ kim_property modify 1 key short-name source-value 1 fcc
source-unit eV
# Dump the results in a file
kim_property dump "results.edn"
kim property dump "results.edn"

44
examples/kim/in.kim-pm-query.melt
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@ -1,7 +1,7 @@
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
@ -13,34 +13,34 @@
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
lattice fcc ${a0}
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc ${a0}
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Si
kim interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

42
examples/kim/in.kim-pm.melt
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@ -1,7 +1,7 @@
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
@ -13,33 +13,33 @@
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions Si
kim interactions Si
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

76
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@ -0,0 +1,76 @@
# kim query example
#
# Requirement:
#
# This example requires LAMMPS is built with KIM package. A requirement for
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models
# `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# and
# `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
# are installed.
#
# This can be done with the commands
# `kim-api-collections-management install user `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# `kim-api-collections-management install user `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
#
# If these commands do not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
# Get the lattice contant from a different model
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
clear
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
clear
# -----------------------------------------------
# Get an equilibrium hcp crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal
kim query latconst split get_lattice_constant_hexagonal crystal=["hcp"] species=["Zr"] units=["angstrom"]
print "HCP lattice constants = ${latconst_1}, ${latconst_2}"
clear
# -----------------------------------------------
# Query for KIM models from openkim.org
# Get all the EAM models that support Al
# -----------------------------------------------
kim query model index get_available_models species=[Al] potential_type=[eam]
label model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
print "FCC lattice constant (${model}) = ${latconst}"
next model
jump SELF model_loop
clear

44
examples/kim/in.kim-sm.melt
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@ -1,8 +1,8 @@
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# is installed. This can be done with the command
# `Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000`
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
@ -13,33 +13,33 @@
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See https://openkim.org/doc/obtaining-models for alternative options.
# See `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
kim_interactions O
kim interactions O
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

44
examples/kim/in.lammps.melt
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@ -1,33 +1,33 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units real
units real
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
run 100

127
examples/kim/log.10Feb21.in.kim-ex.melt.clang.1 Normal file
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@ -0,0 +1,127 @@
LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the `./lib/kim/README` or
# `./lib/kim/Install.py` files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init LennardJones_Ar real
#=== BEGIN kim init ==========================================
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has No mutable parameters.
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003 seconds
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1153)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
pair_coeff * * Ar
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.450000000000001
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75
Loop time of 2.85673 on 1 procs for 100 steps with 32000 atoms
Performance: 3.024 ns/day, 7.935 hours/ns, 35.005 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4805 | 2.4805 | 2.4805 | 0.0 | 86.83
Neigh | 0.32948 | 0.32948 | 0.32948 | 0.0 | 11.53
Comm | 0.012038 | 0.012038 | 0.012038 | 0.0 | 0.42
Output | 7.4e-05 | 7.4e-05 | 7.4e-05 | 0.0 | 0.00
Modify | 0.023745 | 0.023745 | 0.023745 | 0.0 | 0.83
Other | | 0.01084 | | | 0.38
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911.0 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.92969
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02

127
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@ -0,0 +1,127 @@
LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the `./lib/kim/README` or
# `./lib/kim/Install.py` files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init LennardJones_Ar real
#=== BEGIN kim init ==========================================
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has No mutable parameters.
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide 'partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1153)
WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1159)
pair_coeff * * Ar
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.450000000000001
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75
Loop time of 0.843382 on 4 procs for 100 steps with 32000 atoms
Performance: 10.244 ns/day, 2.343 hours/ns, 118.570 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71505 | 0.71942 | 0.72345 | 0.4 | 85.30
Neigh | 0.089886 | 0.090153 | 0.090611 | 0.1 | 10.69
Comm | 0.016342 | 0.020141 | 0.024546 | 2.5 | 2.39
Output | 2.4e-05 | 2.625e-05 | 3.2e-05 | 0.0 | 0.00
Modify | 0.008197 | 0.0083267 | 0.008504 | 0.1 | 0.99
Other | | 0.005318 | | | 0.63
Nlocal: 8000.00 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131.00 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.92969
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (10 Feb 2021)
# kim property example
#
# For detailed information of this example please refer to:
# `https://openkim.org/doc/evaluation/tutorial-lammps/`
#
# Description:
#
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed. This can be done with the command
# kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
# Initialize interatomic potential (KIM model) and units
atom_style atomic
# Set the OpenKIM model that will be used
kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 3 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | epsilon | "Double" | 1
3 | sigma | "Double" | 1
#=== END kim init ============================================
# the equilibrium lattice constant for the fcc structure
variable lattice_constant equal 5.248509056866169
# Periodic boundary conditions along all three dimensions
boundary p p p
# Create an FCC lattice with the lattice spacing
# using a single conventional (orthogonal) unit cell
lattice fcc ${lattice_constant}
lattice fcc 5.24850905686617
Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091 5.2485091)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4 atoms
create_atoms CPU = 0.000 seconds
mass 1 39.948
# Specify the KIM interactions
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
pair_coeff * * Ar
#=== END kim interactions ====================================
# Compute energy
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_126566794224_004a} is archived in OpenKIM~\cite{MO_126566794224_004, MD_498634107543_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_126566794224_004.bib}
\end{document}
}
@Misc{MO_126566794224_004,
author = {Ellad Tadmor},
title = {{L}ennard-{J}ones model (shifted) for {A}r with parameters from {B}ernardes (1958) (medium precision cutoff) v004},
doi = {10.25950/9f98b989},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model, MO_126566794224_004},
publisher = {OpenKIM},
year = 2020,
}
@Misc{MD_498634107543_004,
author = {Ellad Tadmor},
title = {{D}river for the {L}ennard-{J}ones model uniformly shifted to have zero energy at the cutoff radius v004},
doi = {10.25950/bdffd6a6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model Driver, MD_498634107543_004},
publisher = {OpenKIM},
year = 2020,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_126566794224_004a,
author = {Newton Bernardes},
doi = {10.1103/PhysRev.112.1534},
issue = {5},
journal = {Physical Review},
pages = {1534--1539},
publisher = {American Physical Society},
title = {Theory of Solid {N}e, {A}, {K}r, and {X}e at 0{K}},
volume = {112},
year = {1958},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.5
ghost atom cutoff = 15.5
binsize = 7.75, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 15.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.119 | 3.119 | 3.119 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -0.34602203 0 -0.34602203 0.00061471244
Loop time of 3e-05 on 1 procs for 0 steps with 4 atoms
3.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3e-05 | | |100.00
Nlocal: 4.00000 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1094.00 ave 1094 max 1094 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1712.00 ave 1712 max 1712 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1712
Ave neighs/atom = 428.00000
Neighbor list builds = 0
Dangerous builds = 0
# Get cohesive energy
variable natoms equal "count(all)"
variable ecohesive equal "-pe/v_natoms"
# Create a property instance
kim property create 1 cohesive-potential-energy-cubic-crystal
#=== kim property ===========================================
# Set all the key-value pairs for this property instance
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value ${lattice_constant} source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value 0.0865055084950546 source-unit eV
#=== kim property ===========================================
# Dump the results in a file
kim property dump "results.edn"
#=== kim property ===========================================
Total wall time: 0:00:00

238
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LAMMPS (10 Feb 2021)
# kim property example
#
# For detailed information of this example please refer to:
# `https://openkim.org/doc/evaluation/tutorial-lammps/`
#
# Description:
#
# This example is designed to calculate the cohesive energy corresponding to
# the equilibrium FCC lattice constant for
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004` model for
# argon. The material properties computed in LAMMPS are represented as a
# standard KIM property instance format. (See
# `https://openkim.org/doc/schema/properties-framework/` and
# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
# Then the created property instance is written to a file named `results.edn`
# using the `kim property dump` command.
#
# Requirement:
#
# This example requires LAMMPS built with the Python 3.6 or later package
# installed. See the `https://lammps.sandia.gov/doc/python.html` doc page for
# more info on building LAMMPS with the version of Python on your system.
# After successfully building LAMMPS with Python, you need to install the
# kim-property Python package, See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for
# further details.
#
# This example requires that the KIM Portable Model (PM)
# `LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004`
# is installed. This can be done with the command
# kim-api-collections-management install user LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
# Initialize interatomic potential (KIM model) and units
atom_style atomic
# Set the OpenKIM model that will be used
kim init LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 3 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | epsilon | "Double" | 1
3 | sigma | "Double" | 1
#=== END kim init ============================================
# the equilibrium lattice constant for the fcc structure
variable lattice_constant equal 5.248509056866169
# Periodic boundary conditions along all three dimensions
boundary p p p
# Create an FCC lattice with the lattice spacing
# using a single conventional (orthogonal) unit cell
lattice fcc ${lattice_constant}
lattice fcc 5.24850905686617
Lattice spacing in x,y,z = 5.2485091 5.2485091 5.2485091
region box block 0 1 0 1 0 1 units lattice
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.2485091 5.2485091 5.2485091)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4 atoms
create_atoms CPU = 0.001 seconds
mass 1 39.948
# Specify the KIM interactions
kim interactions Ar
#=== BEGIN kim interactions ==================================
pair_style kim LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_004
pair_coeff * * Ar
#=== END kim interactions ====================================
# Compute energy
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_126566794224_004#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_126566794224_004a} is archived in OpenKIM~\cite{MO_126566794224_004, MD_498634107543_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_126566794224_004.bib}
\end{document}
}
@Misc{MO_126566794224_004,
author = {Ellad Tadmor},
title = {{L}ennard-{J}ones model (shifted) for {A}r with parameters from {B}ernardes (1958) (medium precision cutoff) v004},
doi = {10.25950/9f98b989},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model, MO_126566794224_004},
publisher = {OpenKIM},
year = 2020,
}
@Misc{MD_498634107543_004,
author = {Ellad Tadmor},
title = {{D}river for the {L}ennard-{J}ones model uniformly shifted to have zero energy at the cutoff radius v004},
doi = {10.25950/bdffd6a6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/9f98b989}},
keywords = {OpenKIM, Model Driver, MD_498634107543_004},
publisher = {OpenKIM},
year = 2020,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_126566794224_004a,
author = {Newton Bernardes},
doi = {10.1103/PhysRev.112.1534},
issue = {5},
journal = {Physical Review},
pages = {1534--1539},
publisher = {American Physical Society},
title = {Theory of Solid {N}e, {A}, {K}r, and {X}e at 0{K}},
volume = {112},
year = {1958},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 15.5
ghost atom cutoff = 15.5
binsize = 7.75, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 15.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.165 | 3.165 | 3.165 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -0.34602203 0 -0.34602203 0.00061471244
Loop time of 1.5e-06 on 4 procs for 0 steps with 4 atoms
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.5e-06 | | |100.00
Nlocal: 1.00000 ave 1 max 1 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 935.000 ave 935 max 935 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 428.000 ave 428 max 428 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1712
Ave neighs/atom = 428.00000
Neighbor list builds = 0
Dangerous builds = 0
# Get cohesive energy
variable natoms equal "count(all)"
variable ecohesive equal "-pe/v_natoms"
# Create a property instance
kim property create 1 cohesive-potential-energy-cubic-crystal
#=== kim property ===========================================
# Set all the key-value pairs for this property instance
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value ${lattice_constant} source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value ${ecohesive} source-unit eV
kim property modify 1 key short-name source-value 1 fcc key species source-value 1 Ar key a source-value 5.24850905686617 source-unit angstrom key basis-atom-coordinates source-value 1 1:3 0.0 0.0 0.0 source-value 2 1:3 0.0 0.5 0.5 source-value 3 1:3 0.5 0.0 0.5 source-value 4 1:3 0.5 0.5 0.0 key space-group source-value Fm-3m key cohesive-potential-energy source-value 0.0865055084950538 source-unit eV
#=== kim property ===========================================
# Dump the results in a file
kim property dump "results.edn"
#=== kim property ===========================================
Total wall time: 0:00:00

238
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LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim init ==========================================
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== END kim init ============================================
kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
#=== BEGIN kim-query =========================================
variable a0 string "4.146581932902336"
#=== END kim-query ===========================================
lattice fcc ${a0}
lattice fcc 4.146581932902336
Lattice spacing in x,y,z = 4.1465819 4.1465819 4.1465819
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (82.931639 82.931639 82.931639)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.004 seconds
kim interactions Si
#=== BEGIN kim interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
- OpenKIM query: https://doi.org/10.1063/5.0014267
@Article{karls:bierbaum:2020,
author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor},
title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine},
journal = {{T}he {J}ournal of {C}hemical {P}hysics},
year = 2020,
volume = 153,
number = 6,
pages = {064104},
doi = {10.1063/5.0014267}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 41 41 41
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685
Loop time of 18.2008 on 1 procs for 100 steps with 32000 atoms
Performance: 0.475 ns/day, 50.558 hours/ns, 5.494 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.058 | 18.058 | 18.058 | 0.0 | 99.21
Neigh | 0.097367 | 0.097367 | 0.097367 | 0.0 | 0.53
Comm | 0.009271 | 0.009271 | 0.009271 | 0.0 | 0.05
Output | 6.1e-05 | 6.1e-05 | 6.1e-05 | 0.0 | 0.00
Modify | 0.025469 | 0.025469 | 0.025469 | 0.0 | 0.14
Other | | 0.01084 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9667.00 ave 9667 max 9667 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 450192.0 ave 450192 max 450192 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 450192
Ave neighs/atom = 14.068500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:21

238
examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.4 Normal file
View File

@ -0,0 +1,238 @@
LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim init ==========================================
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== END kim init ============================================
kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
#=== BEGIN kim-query =========================================
variable a0 string "4.146581932902336"
#=== END kim-query ===========================================
lattice fcc ${a0}
lattice fcc 4.146581932902336
Lattice spacing in x,y,z = 4.1465819 4.1465819 4.1465819
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (82.931639 82.931639 82.931639)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
kim interactions Si
#=== BEGIN kim interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
- OpenKIM query: https://doi.org/10.1063/5.0014267
@Article{karls:bierbaum:2020,
author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor},
title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine},
journal = {{T}he {J}ournal of {C}hemical {P}hysics},
year = 2020,
volume = 153,
number = 6,
pages = {064104},
doi = {10.1063/5.0014267}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 41 41 41
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685
Loop time of 5.33871 on 4 procs for 100 steps with 32000 atoms
Performance: 1.618 ns/day, 14.830 hours/ns, 18.731 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.244 | 5.2604 | 5.2753 | 0.5 | 98.53
Neigh | 0.027617 | 0.027767 | 0.027955 | 0.1 | 0.52
Comm | 0.017101 | 0.031947 | 0.04856 | 6.3 | 0.60
Output | 3.4e-05 | 4.525e-05 | 5.6e-05 | 0.0 | 0.00
Modify | 0.011577 | 0.01165 | 0.011709 | 0.0 | 0.22
Other | | 0.0069 | | | 0.13
Nlocal: 8000.00 ave 8029 max 7968 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 4259.00 ave 4303 max 4202 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 112548.0 ave 113091 max 111995 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 450192
Ave neighs/atom = 14.068500
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:07

219
examples/kim/log.10Feb21.in.kim-pm.melt.clang.1 Normal file
View File

@ -0,0 +1,219 @@
LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim init ==========================================
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003 seconds
kim interactions Si
#=== BEGIN kim interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698
Loop time of 17.6645 on 1 procs for 100 steps with 32000 atoms
Performance: 0.489 ns/day, 49.068 hours/ns, 5.661 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.553 | 17.553 | 17.553 | 0.0 | 99.37
Neigh | 0.063346 | 0.063346 | 0.063346 | 0.0 | 0.36
Comm | 0.009667 | 0.009667 | 0.009667 | 0.0 | 0.05
Output | 6.6e-05 | 6.6e-05 | 6.6e-05 | 0.0 | 0.00
Modify | 0.02711 | 0.02711 | 0.02711 | 0.0 | 0.15
Other | | 0.01088 | | | 0.06
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7760.00 ave 7760 max 7760 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 402352.0 ave 402352 max 402352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 402352
Ave neighs/atom = 12.573500
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:17

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LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim init ==========================================
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
This model has 9 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | A | "Double" | 1
2 | B | "Double" | 1
3 | p | "Double" | 1
4 | q | "Double" | 1
5 | sigma | "Double" | 1
6 | gamma | "Double" | 1
7 | cutoff | "Double" | 1
8 | lambda | "Double" | 1
9 | costheta0 | "Double" | 1
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
kim interactions Si
#=== BEGIN kim interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_405512056662_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_405512056662_005.bib}
\end{document}
}
@Misc{MO_405512056662_005,
author = {Amit K Singh},
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
doi = {10.25950/c74b293f},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model, MO_405512056662_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_335816936951_004,
author = {Mingjian Wen},
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
doi = {10.25950/f3abd2d6},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_405512056662_005a,
author = {Stillinger, Frank H. and Weber, Thomas A.},
doi = {10.1103/PhysRevB.31.5262},
issue = {8},
journal = {Physical Review B},
month = {Apr},
pages = {5262--5271},
publisher = {American Physical Society},
title = {Computer simulation of local order in condensed phases of silicon},
volume = {31},
year = {1985},
}
@Book{MO_405512056662_005b,
author = {Tadmor, Ellad B. and Miller, Ronald E.},
doi = {10.1017/CBO9781139003582},
publisher = {Cambridge University Press},
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
year = {2011},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698
Loop time of 4.88034 on 4 procs for 100 steps with 32000 atoms
Performance: 1.770 ns/day, 13.556 hours/ns, 20.490 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8131 | 4.8235 | 4.8347 | 0.4 | 98.84
Neigh | 0.017627 | 0.017731 | 0.017825 | 0.1 | 0.36
Comm | 0.013892 | 0.025022 | 0.03536 | 5.0 | 0.51
Output | 3.4e-05 | 4.025e-05 | 4.7e-05 | 0.0 | 0.00
Modify | 0.008725 | 0.0087775 | 0.008862 | 0.1 | 0.18
Other | | 0.005278 | | | 0.11
Nlocal: 8000.00 ave 8014 max 7988 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 3374.75 ave 3389 max 3361 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 100588.0 ave 100856 max 100392 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 402352
Ave neighs/atom = 12.573500
Neighbor list builds = 4
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (10 Feb 2021)
# kim query example
#
# Requirement:
#
# This example requires LAMMPS is built with KIM package. A requirement for
# the KIM package, is the KIM API library that must be downloaded from the
# OpenKIM website and installed before LAMMPS is compiled. The 'kim query'
# command requires the libcurl library to be installed. See the
# `https://lammps.sandia.gov/doc/Build_extras.html#kim` doc page for further
# details
#
# This example requires that the KIM Models
# `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# and
# `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
# are installed.
#
# This can be done with the commands
# `kim-api-collections-management install user `EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`
# `kim-api-collections-management install user `EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000`
#
# If these commands do not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 6 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | deltaRho | "Double" | 1
3 | deltaR | "Double" | 1
4 | embeddingData | "Double" | 500
5 | rPhiData | "Double" | 500
6 | densityData | "Double" | 500
#=== END kim init ============================================
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
#=== BEGIN kim-query =========================================
variable latconst_1 string "4.032082033157349"
#=== END kim-query ===========================================
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = 4.032082033157349
# Get the lattice contant from a different model
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
#=== BEGIN kim-query =========================================
variable latconst_2 string "4.024845376610756"
#=== END kim-query ===========================================
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = 4.024845376610756
clear
# -----------------------------------------------
# Get an equilibrium fcc crystal lattice constant
# -----------------------------------------------
kim query latconst_1 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]
#=== BEGIN kim-query =========================================
variable latconst_1 string "4.032082033157349"
#=== END kim-query ===========================================
kim query latconst_2 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
#=== BEGIN kim-query =========================================
variable latconst_2 string "4.024845376610756"
#=== END kim-query ===========================================
print "FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = ${latconst_1}"
FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = 4.032082033157349
print "FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = ${latconst_2}"
FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = 4.024845376610756
clear
# -----------------------------------------------
# Get an equilibrium hcp crystal lattice constant
# -----------------------------------------------
kim init EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 metal
#=== BEGIN kim init ==========================================
units metal
neighbor 2.0 bin # Angstroms
timestep 1.0e-3 # picoseconds
This model has 6 mutable parameters.
No. | Parameter name | data type | extent
-----------------------------------------------------
1 | cutoff | "Double" | 1
2 | deltaRho | "Double" | 1
3 | deltaR | "Double" | 1
4 | embeddingData | "Double" | 10000
5 | rPhiData | "Double" | 10000
6 | densityData | "Double" | 10000
#=== END kim init ============================================
kim query latconst split get_lattice_constant_hexagonal crystal=["hcp"] species=["Zr"] units=["angstrom"]
#=== BEGIN kim-query =========================================
variable latconst_1 string 3.234055244384789
variable latconst_2 string 5.167650199630013
#=== END kim-query ===========================================
print "HCP lattice constants = ${latconst_1}, ${latconst_2}"
HCP lattice constants = 3.234055244384789, 5.167650199630013
clear
# -----------------------------------------------
# Query for KIM models from openkim.org
# Get all the EAM models that support Al
# -----------------------------------------------
kim query model index get_available_models species=[Al] potential_type=[eam]
#=== BEGIN kim-query =========================================
variable model index "EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002" "EAM_Dynamo_AngeloMoodyBaskes_1995_NiAlH__MO_418978237058_005" "EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_005" "EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005" "EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000" "EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000" "EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005" "EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_000" "EAM_Dynamo_LiuErcolessiAdams_2004_Al__MO_051157671505_000" "EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_000" "EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000" "EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_005" "EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000" "EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_005" "EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005" "EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005" "EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_005" "EAM_Dynamo_Mishin_2004_NiAl__MO_101214310689_005" "EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005" "EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000" "EAM_Dynamo_PunYamakovMishin_2013_NiAlCo__MO_826591359508_000" "EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_000" "EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005" "EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_005" "EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005" "EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000" "EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Al__MO_060567868558_000" "EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005" "EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000" "EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005" "EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005" "EAM_ErcolessiAdams_1994_Al__MO_324507536345_003" "EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003" "EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003" "EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_003" "EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002" "EAM_QuinticHermiteSpline_ErcolessiAdams_1994_Al__MO_781138671863_002" "EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001" "EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001"
#=== END kim-query ===========================================
label model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082748413087"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_002) = 4.032082748413087
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_AngeloMoodyBaskes_1995_NiAlH__MO_418978237058_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050000071525574"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_AngeloMoodyBaskes_1995_NiAlH__MO_418978237058_005) = 4.050000071525574
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049763545393944"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_005) = 4.049763545393944
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082033157349"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005) = 4.032082033157349
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000]
#=== BEGIN kim-query =========================================
variable latconst string "3.869337007403374"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000) = 3.869337007403374
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000]
#=== BEGIN kim-query =========================================
variable latconst string "3.987558534741402"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000) = 3.987558534741402
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.031036108732224"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005) = 4.031036108732224
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.03203821182251"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_000) = 4.03203821182251
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuErcolessiAdams_2004_Al__MO_051157671505_000]
#=== BEGIN kim-query =========================================
variable latconst string "9.5"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuErcolessiAdams_2004_Al__MO_051157671505_000) = 9.5
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.032073378562927"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_000) = 4.032073378562927
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000]
#=== BEGIN kim-query =========================================
variable latconst string "8.5"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000) = 8.5
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.045270472764969"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_005) = 4.045270472764969
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.040926471352577"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000) = 4.040926471352577
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.045259781181811"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevKramerBecker_2008_Al__MO_106969701023_005) = 4.045259781181811
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.03330184519291"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005) = 4.03330184519291
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050004702806472"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MishinFarkasMehl_1999_Al__MO_651801486679_005) = 4.050004702806472
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.051526293158533"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_MishinMehlPapaconstantopoulos_2002_NiAl__MO_109933561507_005) = 4.051526293158533
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_Mishin_2004_NiAl__MO_101214310689_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049999862909317"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_Mishin_2004_NiAl__MO_101214310689_005) = 4.049999862909317
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050000071525574"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005) = 4.050000071525574
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.05000014603138"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000) = 4.05000014603138
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_PunYamakovMishin_2013_NiAlCo__MO_826591359508_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.05000014603138"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_PunYamakovMishin_2013_NiAlCo__MO_826591359508_000) = 4.05000014603138
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.210718545317654"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_SchopfBrommerFrigan_2012_AlMnPd__MO_137572817842_000) = 4.210718545317654
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050010219216347"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_SturgeonLaird_2000_Al__MO_120808805541_005) = 4.050010219216347
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049696564674378"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_005) = 4.049696564674378
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.024845376610756"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_WineyKubotaGupta_2010_Al__MO_149316865608_005) = 4.024845376610756
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.031999975442885"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000) = 4.031999975442885
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Al__MO_060567868558_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.050199627876282"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Al__MO_060567868558_000) = 4.050199627876282
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050180745124819"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZhouJohnsonWadley_2004_Al__MO_131650261510_005) = 4.050180745124819
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000]
#=== BEGIN kim-query =========================================
variable latconst string "4.081654928624631"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZhouWadleyJohnson_2001_Al__MO_049243498555_000) = 4.081654928624631
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.050000011920929"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005) = 4.050000011920929
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005]
#=== BEGIN kim-query =========================================
variable latconst string "4.049999445676804"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005) = 4.049999445676804
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_ErcolessiAdams_1994_Al__MO_324507536345_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082714140415"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_ErcolessiAdams_1994_Al__MO_324507536345_003) = 4.032082714140415
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.128871455788613"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_IMD_BrommerGaehler_2006A_AlNiCo__MO_122703700223_003) = 4.128871455788613
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.073718130588532"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_IMD_BrommerGaehler_2006B_AlNiCo__MO_128037485276_003) = 4.073718130588532
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_003]
#=== BEGIN kim-query =========================================
variable latconst string "4.210700303316115"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_IMD_SchopfBrommerFrigan_2012_AlMnPd__MO_878712978062_003) = 4.210700303316115
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002]
#=== BEGIN kim-query =========================================
variable latconst string "4.032082897424699"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_002) = 4.032082897424699
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EAM_QuinticHermiteSpline_ErcolessiAdams_1994_Al__MO_781138671863_002]
#=== BEGIN kim-query =========================================
variable latconst string "4.03208246231079"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EAM_QuinticHermiteSpline_ErcolessiAdams_1994_Al__MO_781138671863_002) = 4.03208246231079
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001]
#=== BEGIN kim-query =========================================
variable latconst string "3.994616635143757"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_AlAgAuCuNiPdPt__MO_115316750986_001) = 3.994616635143757
next model
jump SELF model_loop
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[${model}]
kim query latconst get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom] model=[EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001]
#=== BEGIN kim-query =========================================
variable latconst string "3.994608342647553"
#=== END kim-query ===========================================
print "FCC lattice constant (${model}) = ${latconst}"
FCC lattice constant (EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001) = 3.994608342647553
next model
jump SELF model_loop
clear
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/MO_123629422045_005#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_123629422045_005a} is archived in OpenKIM~\cite{MO_123629422045_005, MD_120291908751_005, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_123629422045_005.bib}
\end{document}
}
@Misc{MO_123629422045_005,
author = {Ryan S. Elliott},
title = {{EAM} potential ({LAMMPS} cubic hermite tabulation) for {A}l developed by {E}rcolessi and {A}dams (1994) v005},
doi = {10.25950/7cd2a6ab},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7cd2a6ab}},
keywords = {OpenKIM, Model, MO_123629422045_005},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_120291908751_005,
author = {Ryan S. Elliott},
title = {{EAM} {M}odel {D}river for tabulated potentials with cubic {H}ermite spline interpolation as used in {LAMMPS} v005},
doi = {10.25950/68defa36},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7cd2a6ab}},
keywords = {OpenKIM, Model Driver, MD_120291908751_005},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_123629422045_005a,
author = {F. Ercolessi and J. B. Adams},
doi = {10.1209/0295-5075/26/8/005},
journal = {Europhysics Letters},
number = {8},
pages = {583},
title = {Interatomic Potentials from First-Principles Calculations: {T}he Force-Matching Method},
volume = {26},
year = {1994},
}
- OpenKIM query: https://doi.org/10.1063/5.0014267
@Article{karls:bierbaum:2020,
author = {D. S. Karls and M. Bierbaum and A. A. Alemi and R. S. Elliott and J. P. Sethna and E. B. Tadmor},
title = {The {O}pen{KIM} processing pipeline: {A} cloud-based automatic material property computation engine},
journal = {{T}he {J}ournal of {C}hemical {P}hysics},
year = 2020,
volume = 153,
number = 6,
pages = {064104},
doi = {10.1063/5.0014267}
}
- OpenKIM potential: https://openkim.org/cite/MO_004835508849_000#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Model originally published in \cite{MO_004835508849_000a} is archived in OpenKIM~\cite{MO_004835508849_000, MD_120291908751_005, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-MO_004835508849_000.bib}
\end{document}
}
@Misc{MO_004835508849_000,
author = {Ellad Tadmor},
title = {{F}innis-{S}inclair potential ({LAMMPS} cubic hermite tabulation) for {Z}r developed by {M}endelev and {A}ckland (2007); version 3 refitted for radiation studies v000},
doi = {10.25950/7b7b5ab5},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7b7b5ab5}},
keywords = {OpenKIM, Model, MO_004835508849_000},
publisher = {OpenKIM},
year = 2018,
}
@Misc{MD_120291908751_005,
author = {Ryan S. Elliott},
title = {{EAM} {M}odel {D}river for tabulated potentials with cubic {H}ermite spline interpolation as used in {LAMMPS} v005},
doi = {10.25950/68defa36},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/7b7b5ab5}},
keywords = {OpenKIM, Model Driver, MD_120291908751_005},
publisher = {OpenKIM},
year = 2018,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{MO_004835508849_000a,
author = {Mendelev, M. I. and Ackland, G. J.},
doi = {10.1080/09500830701191393},
journal = {Philosophical Magazine Letters},
number = {5},
pages = {349-359},
title = {Development of an interatomic potential for the simulation of phase transformations in zirconium},
volume = {87},
year = {2007},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Total wall time: 0:01:59

223
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LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# `Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000`
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
#=== BEGIN kim init ==========================================
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# For Simulator : LAMMPS 28 Feb 2019
# Running on : LAMMPS 10 Feb 2021
#
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
atom_style charge
neigh_modify one 4000
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003 seconds
kim interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/param.qeq
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/SM_107643900657_000#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Simulator Model originally published in \cite{SM_107643900657_000a} is archived in OpenKIM~\cite{SM_107643900657_000, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-SM_107643900657_000.bib}
\end{document}
}
@Misc{SM_107643900657_000,
author = {Ellad Tadmor},
title = {{LAMMPS} {R}eax{FF} potential for {RDX} ({C}-{H}-{N}-{O}) systems developed by {S}trachan et al. (2003) v000},
doi = {10.25950/acd3fc89},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/acd3fc89}},
keywords = {OpenKIM, Simulator Model, SM_107643900657_000},
publisher = {OpenKIM},
year = 2019,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{SM_107643900657_000a,
author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.},
doi = {10.1103/PhysRevLett.91.098301},
issue = {9},
journal = {Physical Review Letters},
month = {Aug},
numpages = {4},
pages = {098301},
publisher = {American Physical Society},
title = {Shock Waves in High-Energy Materials: {T}he Initial Chemical Events in Nitramine {RDX}},
volume = {91},
year = {2003},
}
- pair reax/c command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reax command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 4000, page size: 100000
master list distance cutoff = 10.3
ghost atom cutoff = 10.3
binsize = 5.15, bins = 18 18 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 1803.0 | 1803.0 | 1803.0 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661
Loop time of 38.6526 on 1 procs for 100 steps with 32000 atoms
Performance: 0.224 ns/day, 107.368 hours/ns, 2.587 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 23.493 | 23.493 | 23.493 | 0.0 | 60.78
Neigh | 0.4498 | 0.4498 | 0.4498 | 0.0 | 1.16
Comm | 0.020568 | 0.020568 | 0.020568 | 0.0 | 0.05
Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00
Modify | 14.677 | 14.677 | 14.677 | 0.0 | 37.97
Other | | 0.01223 | | | 0.03
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26825.0 ave 26825 max 26825 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3.73924e+06 ave 3.73924e+06 max 3.73924e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3739236
Ave neighs/atom = 116.85112
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:39

223
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LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# `Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000`
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See `https://openkim.org/doc/obtaining-models` for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
#=== BEGIN kim init ==========================================
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# For Simulator : LAMMPS 28 Feb 2019
# Running on : LAMMPS 10 Feb 2021
#
units real
neighbor 2.0 bin # Angstroms
timestep 1.0 # femtoseconds
atom_style charge
neigh_modify one 4000
#=== END kim init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
kim interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-hIWMxB258NXk/param.qeq
#=== END kim interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = 2011,
volume = 63,
number = 17,
pages = {17},
doi = {10.1007/s11837-011-0102-6}
}
- OpenKIM potential: https://openkim.org/cite/SM_107643900657_000#item-citation
@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Simulator Model originally published in \cite{SM_107643900657_000a} is archived in OpenKIM~\cite{SM_107643900657_000, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-SM_107643900657_000.bib}
\end{document}
}
@Misc{SM_107643900657_000,
author = {Ellad Tadmor},
title = {{LAMMPS} {R}eax{FF} potential for {RDX} ({C}-{H}-{N}-{O}) systems developed by {S}trachan et al. (2003) v000},
doi = {10.25950/acd3fc89},
howpublished = {OpenKIM, \url{https://doi.org/10.25950/acd3fc89}},
keywords = {OpenKIM, Simulator Model, SM_107643900657_000},
publisher = {OpenKIM},
year = 2019,
}
@Article{tadmor:elliott:2011,
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
journal = {{JOM}},
year = {2011},
volume = {63},
number = {7},
pages = {17},
doi = {10.1007/s11837-011-0102-6},
}
@Misc{elliott:tadmor:2011,
author = {Ryan S. Elliott and Ellad B. Tadmor},
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
howpublished = {\url{https://openkim.org/kim-api}},
publisher = {OpenKIM},
year = 2011,
doi = {10.25950/ff8f563a},
}
@Article{SM_107643900657_000a,
author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.},
doi = {10.1103/PhysRevLett.91.098301},
issue = {9},
journal = {Physical Review Letters},
month = {Aug},
numpages = {4},
pages = {098301},
publisher = {American Physical Society},
title = {Shock Waves in High-Energy Materials: {T}he Initial Chemical Events in Nitramine {RDX}},
volume = {91},
year = {2003},
}
- pair reax/c command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reax command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 4000, page size: 100000
master list distance cutoff = 10.3
ghost atom cutoff = 10.3
binsize = 5.15, bins = 18 18 18
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 630.2 | 630.2 | 630.2 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -39091.147 0 -20014.559 19501.107
100 63.198252 -26042.062 0 -20014.027 21497.661
Loop time of 14.1676 on 4 procs for 100 steps with 32000 atoms
Performance: 0.610 ns/day, 39.355 hours/ns, 7.058 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3935 | 9.3935 | 9.3936 | 0.0 | 66.30
Neigh | 0.15786 | 0.15879 | 0.16003 | 0.2 | 1.12
Comm | 0.025777 | 0.025906 | 0.025992 | 0.1 | 0.18
Output | 2.8e-05 | 3.35e-05 | 4.6e-05 | 0.0 | 0.00
Modify | 4.5801 | 4.5814 | 4.5823 | 0.0 | 32.34
Other | | 0.00801 | | | 0.06
Nlocal: 8000.00 ave 8010 max 7993 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 12605.0 ave 12612 max 12595 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1.00097e+06 ave 1.00187e+06 max 1.0006e+06 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 4003876
Ave neighs/atom = 125.12113
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:14

88
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LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units real
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.002 seconds
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453
Loop time of 1.87123 on 1 procs for 100 steps with 32000 atoms
Performance: 4.617 ns/day, 5.198 hours/ns, 53.441 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.686 | 1.686 | 1.686 | 0.0 | 90.10
Neigh | 0.14211 | 0.14211 | 0.14211 | 0.0 | 7.59
Comm | 0.01013 | 0.01013 | 0.01013 | 0.0 | 0.54
Output | 6.3e-05 | 6.3e-05 | 6.3e-05 | 0.0 | 0.00
Modify | 0.022686 | 0.022686 | 0.022686 | 0.0 | 1.21
Other | | 0.0102 | | | 0.55
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911.0 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.96027e+06 ave 1.96027e+06 max 1.96027e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1960266
Ave neighs/atom = 61.258313
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units real
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.633 | 7.633 | 7.633 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453
Loop time of 0.532082 on 4 procs for 100 steps with 32000 atoms
Performance: 16.238 ns/day, 1.478 hours/ns, 187.941 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.46077 | 0.46347 | 0.46621 | 0.3 | 87.10
Neigh | 0.038499 | 0.038599 | 0.038759 | 0.0 | 7.25
Comm | 0.01395 | 0.016623 | 0.019377 | 1.7 | 3.12
Output | 3.1e-05 | 3.675e-05 | 4.7e-05 | 0.0 | 0.01
Modify | 0.00787 | 0.007971 | 0.008083 | 0.1 | 1.50
Other | | 0.005382 | | | 1.01
Nlocal: 8000.00 ave 8012 max 7989 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 9131.00 ave 9142 max 9119 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 490066.0 ave 491443 max 489273 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1960266
Ave neighs/atom = 61.258313
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init LennardJones_Ar real
#=== BEGIN kim-init ==========================================
units real
#=== END kim-init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.004321 secs
kim_interactions Ar
#=== BEGIN kim_interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
pair_coeff * * Ar
#=== END kim_interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75
Loop time of 3.48256 on 1 procs for 100 steps with 32000 atoms
Performance: 2.481 ns/day, 9.674 hours/ns, 28.715 timesteps/s
98.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0502 | 3.0502 | 3.0502 | 0.0 | 87.59
Neigh | 0.3646 | 0.3646 | 0.3646 | 0.0 | 10.47
Comm | 0.01783 | 0.01783 | 0.01783 | 0.0 | 0.51
Output | 6.8e-05 | 6.8e-05 | 6.8e-05 | 0.0 | 0.00
Modify | 0.034349 | 0.034349 | 0.034349 | 0.0 | 0.99
Other | | 0.01547 | | | 0.44
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the example models provided with
# the kim-api package are installed. see the ./lib/kim/README or
# ./lib/kim/Install.py files for details on how to install these
# example models.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init LennardJones_Ar real
#=== BEGIN kim-init ==========================================
units real
#=== END kim-init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.000989 secs
kim_interactions Ar
#=== BEGIN kim_interactions ==================================
pair_style kim LennardJones_Ar
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
pair_coeff * * Ar
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
#=== END kim_interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:974)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:979)
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 9.791 | 9.791 | 9.791 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 145069.63 0 164146.22 128015.94
100 95.179703 154939.42 0 164017.94 131602.75
Loop time of 0.924494 on 4 procs for 100 steps with 32000 atoms
Performance: 9.346 ns/day, 2.568 hours/ns, 108.167 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.76434 | 0.76847 | 0.77207 | 0.3 | 83.12
Neigh | 0.09089 | 0.094446 | 0.099911 | 1.1 | 10.22
Comm | 0.038599 | 0.044759 | 0.051381 | 2.1 | 4.84
Output | 3.5e-05 | 4e-05 | 4.9e-05 | 0.0 | 0.00
Modify | 0.009396 | 0.009685 | 0.009941 | 0.2 | 1.05
Other | | 0.00709 | | | 0.77
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim-init ==========================================
units real
#=== END kim-init ============================================
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
#=== BEGIN kim-query =========================================
variable a0 string 4.146581932902336
#=== END kim-query ===========================================
lattice fcc ${a0}
lattice fcc 4.146581932902336
Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.005415 secs
kim_interactions Si
#=== BEGIN kim_interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim_interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 41 41 41
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 10.36 | 10.36 | 10.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685
Loop time of 74.6055 on 1 procs for 100 steps with 32000 atoms
Performance: 0.116 ns/day, 207.238 hours/ns, 1.340 timesteps/s
98.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 74.446 | 74.446 | 74.446 | 0.0 | 99.79
Neigh | 0.096611 | 0.096611 | 0.096611 | 0.0 | 0.13
Comm | 0.014594 | 0.014594 | 0.014594 | 0.0 | 0.02
Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00
Modify | 0.03454 | 0.03454 | 0.03454 | 0.0 | 0.05
Other | | 0.01396 | | | 0.02
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9667 ave 9667 max 9667 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 450192 ave 450192 max 450192 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 450192
Ave neighs/atom = 14.0685
Neighbor list builds = 3
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:16

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LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim-init ==========================================
units real
#=== END kim-init ============================================
kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
#=== BEGIN kim-query =========================================
variable a0 string 4.146581932902336
#=== END kim-query ===========================================
lattice fcc ${a0}
lattice fcc 4.146581932902336
Lattice spacing in x,y,z = 4.14658 4.14658 4.14658
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (82.9316 82.9316 82.9316)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.000946 secs
kim_interactions Si
#=== BEGIN kim_interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim_interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 41 41 41
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -126084.25 0 -107007.66 1528.8768
100 94.450495 -116016.03 0 -107007.07 2282.2685
Loop time of 19.0792 on 4 procs for 100 steps with 32000 atoms
Performance: 0.453 ns/day, 52.998 hours/ns, 5.241 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.78 | 18.855 | 18.937 | 1.5 | 98.83
Neigh | 0.026047 | 0.026274 | 0.0266 | 0.1 | 0.14
Comm | 0.09039 | 0.17196 | 0.24675 | 15.9 | 0.90
Output | 3.9e-05 | 4.975e-05 | 6.1e-05 | 0.0 | 0.00
Modify | 0.015667 | 0.015819 | 0.016008 | 0.1 | 0.08
Other | | 0.01008 | | | 0.05
Nlocal: 8000 ave 8029 max 7968 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 4259 ave 4303 max 4202 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 112548 ave 113091 max 111995 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 450192
Ave neighs/atom = 14.0685
Neighbor list builds = 3
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:20

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LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim-init ==========================================
units real
#=== END kim-init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003591 secs
kim_interactions Si
#=== BEGIN kim_interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim_interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698
Loop time of 74.248 on 1 procs for 100 steps with 32000 atoms
Performance: 0.116 ns/day, 206.244 hours/ns, 1.347 timesteps/s
98.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 74.118 | 74.118 | 74.118 | 0.0 | 99.83
Neigh | 0.069623 | 0.069623 | 0.069623 | 0.0 | 0.09
Comm | 0.0137 | 0.0137 | 0.0137 | 0.0 | 0.02
Output | 7.6e-05 | 7.6e-05 | 7.6e-05 | 0.0 | 0.00
Modify | 0.031883 | 0.031883 | 0.031883 | 0.0 | 0.04
Other | | 0.01433 | | | 0.02
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7760 ave 7760 max 7760 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 402352 ave 402352 max 402352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 402352
Ave neighs/atom = 12.5735
Neighbor list builds = 4
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:14

118
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@ -1,118 +0,0 @@
LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed. This can be done with the command
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# Or, see https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim-init ==========================================
units real
#=== END kim-init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.000997 secs
kim_interactions Si
#=== BEGIN kim_interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si
#=== END kim_interactions ====================================
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.07118
ghost atom cutoff = 4.07118
binsize = 2.03559, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 4.07118
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -85249.847 0 -66173.259 -33302.387
100 253.43357 -90346.68 0 -66173.441 -14888.698
Loop time of 19.0287 on 4 procs for 100 steps with 32000 atoms
Performance: 0.454 ns/day, 52.857 hours/ns, 5.255 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.81 | 18.838 | 18.883 | 0.6 | 99.00
Neigh | 0.018598 | 0.01914 | 0.020732 | 0.7 | 0.10
Comm | 0.10341 | 0.1475 | 0.17393 | 7.1 | 0.78
Output | 6e-05 | 6.225e-05 | 6.7e-05 | 0.0 | 0.00
Modify | 0.014839 | 0.014925 | 0.015047 | 0.1 | 0.08
Other | | 0.008997 | | | 0.05
Nlocal: 8000 ave 8014 max 7988 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 3374.75 ave 3389 max 3361 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 100588 ave 100856 max 100392 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 402352
Ave neighs/atom = 12.5735
Neighbor list builds = 4
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:19

71
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@ -1,71 +0,0 @@
LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
#=== BEGIN kim-init ==========================================
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# For Simulator : LAMMPS 28 Feb 2019
# Running on : LAMMPS 7 Aug 2019
#
units real
atom_style charge
neigh_modify one 4000
#=== END kim-init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003447 secs
kim_interactions O
#=== BEGIN kim_interactions ==================================
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6Acs1QDbXgBx/lmp_control safezone 2.0 mincap 100
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[33054,1],0]
Exit code: 1
--------------------------------------------------------------------------

60
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@ -1,60 +0,0 @@
LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# is installed. This can be done with the command
# kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
# source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See https://openkim.org/doc/obtaining-models for alternative options.
#
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
#=== BEGIN kim-init ==========================================
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# For Simulator : LAMMPS 28 Feb 2019
# Running on : LAMMPS 7 Aug 2019
#
units real
atom_style charge
neigh_modify one 4000
#=== END kim-init ============================================
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001307 secs
kim_interactions O
#=== BEGIN kim_interactions ==================================
pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100
ERROR: Unrecognized pair style 'reax/c' is part of the USER-REAXC package which is not enabled in this LAMMPS binary. (../force.cpp:262)
Last command: pair_style reax/c /var/tmp/kim-simulator-model-parameter-file-directory-6tmKtZEXzhgv/lmp_control safezone 2.0 mincap 100

92
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@ -1,92 +0,0 @@
LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units real
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.003037 secs
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453
Loop time of 2.43768 on 1 procs for 100 steps with 32000 atoms
Performance: 3.544 ns/day, 6.771 hours/ns, 41.023 timesteps/s
97.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1895 | 2.1895 | 2.1895 | 0.0 | 89.82
Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 7.20
Comm | 0.021001 | 0.021001 | 0.021001 | 0.0 | 0.86
Output | 7.9e-05 | 7.9e-05 | 7.9e-05 | 0.0 | 0.00
Modify | 0.034253 | 0.034253 | 0.034253 | 0.0 | 1.41
Other | | 0.01735 | | | 0.71
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.96027e+06 ave 1.96027e+06 max 1.96027e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1960266
Ave neighs/atom = 61.2583
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02

92
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@ -1,92 +0,0 @@
LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable xx equal 20*1
variable yy equal 20*$y
variable yy equal 20*1
variable zz equal 20*$z
variable zz equal 20*1
units real
lattice fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 20 0 ${yy} 0 ${zz}
region box block 0 20 0 20 0 ${zz}
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001194 secs
pair_style lj/cut 8.1500
pair_coeff 1 1 0.0104 3.4000
#pair_style kim LennardJones_Ar
#pair_coeff * * Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 7.633 | 7.633 | 7.633 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 25367.408 6750.7421
100 98.747096 15900.676 0 25319.465 10184.453
Loop time of 0.726239 on 4 procs for 100 steps with 32000 atoms
Performance: 11.897 ns/day, 2.017 hours/ns, 137.696 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.57617 | 0.5835 | 0.59084 | 0.9 | 80.34
Neigh | 0.046682 | 0.047783 | 0.048641 | 0.3 | 6.58
Comm | 0.065469 | 0.071509 | 0.07899 | 2.3 | 9.85
Output | 3.9e-05 | 4.6e-05 | 6.1e-05 | 0.0 | 0.01
Modify | 0.013205 | 0.01363 | 0.014044 | 0.3 | 1.88
Other | | 0.009775 | | | 1.35
Nlocal: 8000 ave 8012 max 7989 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 9131 ave 9142 max 9119 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 490066 ave 491443 max 489273 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1960266
Ave neighs/atom = 61.2583
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

2
lib/gpu/Makefile.cuda_mps
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@ -51,7 +51,7 @@ BIN2C = $(CUDA_HOME)/bin/bin2c
# host code compiler and settings
CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
CUDR_CPP = mpicxx -fopenmp -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
CUDR_OPTS = -O2 $(LMP_INC)
CUDR = $(CUDR_CPP) $(CUDR_OPTS) $(CUDA_PROXY) $(CUDA_PRECISION) $(CUDA_INCLUDE) \
$(CUDPP_OPT)

2
lib/gpu/Makefile.hip
View File

@ -17,7 +17,7 @@ LMP_INC = -DLAMMPS_SMALLBIG
HIP_PRECISION = -D_SINGLE_DOUBLE
HIP_OPTS = -O3
HIP_HOST_OPTS = -Wno-deprecated-declarations
HIP_HOST_OPTS = -Wno-deprecated-declarations -fopenmp
HIP_HOST_INCLUDE =
# use device sort

2
lib/gpu/Makefile.lammps.mac_ocl
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@ -1,5 +1,5 @@
# Settings that the LAMMPS build will import when this package library is used
gpu_SYSINC =
gpu_SYSINC = -DFFT_SINGLE
gpu_SYSLIB = -framework OpenCL
gpu_SYSPATH =

15
lib/gpu/Makefile.linux_opencl
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@ -1,25 +1,21 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for OpenCL
# Generic Linux Makefile for OpenCL - Mixed precision
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.opencl
# OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi
# OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler
# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress
OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
OCL_INC = -I/usr/local/cuda/include # Path to CL directory
OCL_CPP = mpic++ $(DEFAULT_DEVICE) -O3 -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC) -std=c++11
OCL_LINK = -L/usr/local/cuda/lib64 -lOpenCL
OCL_INC =
OCL_CPP = mpic++ -std=c++11 -O3 -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
OCL_LINK = -lOpenCL
OCL_PREC = -D_SINGLE_DOUBLE
OCL_TUNE = -fopenmp -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT
BIN_DIR = ./
OBJ_DIR = ./
@ -28,4 +24,3 @@ AR = ar
BSH = /bin/sh
include Opencl.makefile

10
lib/gpu/Makefile.mac_opencl
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@ -1,19 +1,17 @@
# /* ----------------------------------------------------------------------
# Generic Mac Makefile for OpenCL
# Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.mac_ocl
OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi
# OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler
# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress
# OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
LMP_INC = -DLAMMPS_SMALLBIG
OCL_CPP = mpic++ -O3 -DMPI_GERYON -DUCL_NO_EXIT
OCL_CPP = clang++ -std=c++11 -O3 -I../../src/STUBS
OCL_LINK = -framework OpenCL
OCL_PREC = -D_SINGLE_SINGLE
OCL_TUNE = -DUCL_NO_EXIT
BIN_DIR = ./
OBJ_DIR = ./

23
lib/gpu/Makefile.mac_opencl_mpi Normal file
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@ -0,0 +1,23 @@
# /* ----------------------------------------------------------------------
# Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.mac_ocl
LMP_INC = -DLAMMPS_SMALLBIG
OCL_CPP = mpicxx -std=c++11 -O3 -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
OCL_LINK = -framework OpenCL
OCL_PREC = -D_SINGLE_SINGLE
OCL_TUNE = -DUCL_NO_EXIT -DMPI_GERYON
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
include Opencl.makefile

26
lib/gpu/Makefile.oneapi Normal file
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@ -0,0 +1,26 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for OpenCL
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.opencl
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
OCL_INC =
OCL_CPP = mpiicpc -std=c++11 -xHost -O2 -qopenmp -qopenmp-simd -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
OCL_LINK = -lOpenCL
OCL_PREC = -D_SINGLE_DOUBLE
OCL_TUNE = -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT -fp-model fast=2 -no-prec-div
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
include Opencl.makefile

92
lib/gpu/Makefile.opencl
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@ -1,92 +0,0 @@
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for OpenCL
# ------------------------------------------------------------------------- */
# which file will be copied to Makefile.lammps
EXTRAMAKE = Makefile.lammps.opencl
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
LMP_INC = -DLAMMPS_SMALLBIG
# precision for GPU calculations
# -D_SINGLE_SINGLE # Single precision for all calculations
# -D_DOUBLE_DOUBLE # Double precision for all calculations
# -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
OCL_PREC = -D_SINGLE_DOUBLE
BIN_DIR = ./
OBJ_DIR = ./
LIB_DIR = ./
AR = ar
BSH = /bin/sh
# Compiler and linker settings
# OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi
# OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler
# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress
OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
OCL_INC = -I/usr/local/cuda/include # Path to CL directory
OCL_CPP = mpic++ $(DEFAULT_DEVICE) -g -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
OCL_LINK = -lOpenCL
OCL = $(OCL_CPP) $(OCL_PREC) $(OCL_TUNE) -DUSE_OPENCL
# Headers for Geryon
UCL_H = $(wildcard ./geryon/ucl*.h)
OCL_H = $(wildcard ./geryon/ocl*.h) $(UCL_H) lal_preprocessor.h
PRE1_H = lal_preprocessor.h lal_aux_fun1.h
ALL_H = $(OCL_H) $(wildcard ./lal_*.h)
# Source files
SRCS := $(wildcard ./lal_*.cpp)
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
CUS := $(wildcard lal_*.cu)
KERS := $(subst ./,$(OBJ_DIR)/,$(CUS:lal_%.cu=%_cl.h))
KERS := $(addprefix $(OBJ_DIR)/, $(KERS))
# targets
GPU_LIB = $(LIB_DIR)/libgpu.a
EXECS = $(BIN_DIR)/ocl_get_devices
all: $(OBJ_DIR) $(KERS) $(GPU_LIB) $(EXECS)
$(OBJ_DIR):
mkdir -p $@
# device code compilation
$(OBJ_DIR)/%_cl.h: lal_%.cu $(PRE1_H)
$(BSH) ./geryon/file_to_cstr.sh $* $(PRE1_H) $< $@;
# host code compilation
$(OBJ_DIR)/lal_%.o: lal_%.cpp $(KERS)
$(OCL) -o $@ -c $< -I$(OBJ_DIR)
# build libgpu.a
$(GPU_LIB): $(OBJS)
$(AR) -crusv $(GPU_LIB) $(OBJS)
@cp $(EXTRAMAKE) Makefile.lammps
# test app for querying device info
$(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp $(OCL_H)
$(OCL) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_OPENCL $(OCL_LINK)
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(KERS) *.linkinfo
veryclean: clean
-rm -rf *~ *.linkinfo
cleanlib:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(KERS) *.linkinfo

13
lib/gpu/Nvidia.makefile
View File

@ -1,6 +1,7 @@
# Headers for Geryon
UCL_H = $(wildcard ./geryon/ucl*.h)
NVD_H = $(wildcard ./geryon/nvd*.h) $(UCL_H) lal_preprocessor.h
NVD_H = $(wildcard ./geryon/nvd*.h) $(UCL_H) lal_preprocessor.h \
lal_pre_cuda_hip.h
ALL_H = $(NVD_H) $(wildcard ./lal_*.h)
# Source files
@ -39,17 +40,21 @@ BIN2C = $(CUDA_HOME)/bin/bin2c
# device code compilation
$(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
$(OBJ_DIR)/pppm_f.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \
lal_pre_cuda_hip.h
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=float -Dgrdtyp4=float4 -o $@ lal_pppm.cu
$(OBJ_DIR)/pppm_f_cubin.h: $(OBJ_DIR)/pppm_f.cubin
$(BIN2C) -c -n pppm_f $(OBJ_DIR)/pppm_f.cubin > $(OBJ_DIR)/pppm_f_cubin.h
rm $(OBJ_DIR)/pppm_f.cubin
$(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h
$(OBJ_DIR)/pppm_d.cubin: lal_pppm.cu lal_precision.h lal_preprocessor.h \
lal_pre_cuda_hip.h
$(CUDA) --fatbin -DNV_KERNEL -Dgrdtyp=double -Dgrdtyp4=double4 -o $@ lal_pppm.cu
$(OBJ_DIR)/pppm_d_cubin.h: $(OBJ_DIR)/pppm_d.cubin
$(BIN2C) -c -n pppm_d $(OBJ_DIR)/pppm_d.cubin > $(OBJ_DIR)/pppm_d_cubin.h
rm $(OBJ_DIR)/pppm_d.cubin
$(OBJ_DIR)/%_cubin.h: lal_%.cu $(ALL_H)
$(CUDA) --fatbin -DNV_KERNEL -o $(OBJ_DIR)/$*.cubin $(OBJ_DIR)/lal_$*.cu
@ -93,7 +98,7 @@ $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.cubin *.linkinfo
veryclean: clean
-rm -rf *~ *.linkinfo

78
lib/gpu/Opencl.makefile
View File

@ -1,8 +1,15 @@
# Common headers for kernels
PRE1_H = lal_preprocessor.h lal_aux_fun1.h
# Headers for Geryon
UCL_H = $(wildcard ./geryon/ucl*.h)
OCL_H = $(wildcard ./geryon/ocl*.h) $(UCL_H) lal_preprocessor.h
PRE1_H = lal_preprocessor.h lal_aux_fun1.h
ALL_H = $(OCL_H) $(wildcard ./lal_*.h)
OCL_H = $(wildcard ./geryon/ocl*.h) $(UCL_H) lal_precision.h
# Headers for Host files
HOST_H = lal_answer.h lal_atom.h lal_balance.h lal_base_atomic.h \
lal_base_charge.h lal_base_dipole.h lal_base_dpd.h \
lal_base_ellipsoid.h lal_base_three.h lal_device.h lal_neighbor.h \
lal_neighbor_shared.h lal_pre_ocl_config.h $(OCL_H)
# Source files
SRCS := $(wildcard ./lal_*.cpp)
@ -28,12 +35,75 @@ OCL = $(OCL_CPP) $(OCL_PREC) $(OCL_TUNE) -DUSE_OPENCL
# device code compilation
$(OBJ_DIR)/atom_cl.h: lal_atom.cu lal_preprocessor.h
$(BSH) ./geryon/file_to_cstr.sh atom lal_preprocessor.h lal_atom.cu $(OBJ_DIR)/atom_cl.h
$(OBJ_DIR)/neighbor_cpu_cl.h: lal_neighbor_cpu.cu lal_preprocessor.h
$(BSH) ./geryon/file_to_cstr.sh neighbor_cpu lal_preprocessor.h lal_neighbor_cpu.cu $(OBJ_DIR)/neighbor_cpu_cl.h
$(OBJ_DIR)/neighbor_gpu_cl.h: lal_neighbor_gpu.cu lal_preprocessor.h
$(BSH) ./geryon/file_to_cstr.sh neighbor_gpu lal_preprocessor.h lal_neighbor_gpu.cu $(OBJ_DIR)/neighbor_gpu_cl.h
$(OBJ_DIR)/device_cl.h: lal_device.cu lal_preprocessor.h
$(BSH) ./geryon/file_to_cstr.sh device lal_preprocessor.h lal_device.cu $(OBJ_DIR)/device_cl.h
$(OBJ_DIR)/pppm_cl.h: lal_pppm.cu lal_preprocessor.h
$(BSH) ./geryon/file_to_cstr.sh pppm lal_preprocessor.h lal_pppm.cu $(OBJ_DIR)/pppm_cl.h;
$(OBJ_DIR)/ellipsoid_nbor_cl.h: lal_ellipsoid_nbor.cu lal_preprocessor.h
$(BSH) ./geryon/file_to_cstr.sh ellipsoid_nbor lal_preprocessor.h lal_ellipsoid_nbor.cu $(OBJ_DIR)/ellipsoid_nbor_cl.h
$(OBJ_DIR)/gayberne_cl.h: lal_gayberne.cu $(PRE1_H) lal_ellipsoid_extra.h
$(BSH) ./geryon/file_to_cstr.sh gayberne $(PRE1_H) lal_ellipsoid_extra.h lal_gayberne.cu $(OBJ_DIR)/gayberne_cl.h;
$(OBJ_DIR)/gayberne_lj_cl.h: lal_gayberne_lj.cu $(PRE1_H) lal_ellipsoid_extra.h
$(BSH) ./geryon/file_to_cstr.sh gayberne_lj $(PRE1_H) lal_ellipsoid_extra.h lal_gayberne_lj.cu $(OBJ_DIR)/gayberne_lj_cl.h;
$(OBJ_DIR)/re_squared_cl.h: lal_re_squared.cu $(PRE1_H) lal_ellipsoid_extra.h
$(BSH) ./geryon/file_to_cstr.sh re_squared $(PRE1_H) lal_ellipsoid_extra.h lal_re_squared.cu $(OBJ_DIR)/re_squared_cl.h;
$(OBJ_DIR)/re_squared_lj_cl.h: lal_re_squared_lj.cu $(PRE1_H) lal_ellipsoid_extra.h
$(BSH) ./geryon/file_to_cstr.sh re_squared_lj $(PRE1_H) lal_ellipsoid_extra.h lal_re_squared_lj.cu $(OBJ_DIR)/re_squared_lj_cl.h;
$(OBJ_DIR)/tersoff_cl.h: lal_tersoff.cu $(PRE1_H) lal_tersoff_extra.h
$(BSH) ./geryon/file_to_cstr.sh tersoff $(PRE1_H) lal_tersoff_extra.h lal_tersoff.cu $(OBJ_DIR)/tersoff_cl.h;
$(OBJ_DIR)/tersoff_mod_cl.h: lal_tersoff_mod.cu $(PRE1_H) lal_tersoff_mod_extra.h
$(BSH) ./geryon/file_to_cstr.sh tersoff_mod $(PRE1_H) lal_tersoff_mod_extra.h lal_tersoff_mod.cu $(OBJ_DIR)/tersoff_mod_cl.h;
$(OBJ_DIR)/tersoff_zbl_cl.h: lal_tersoff_zbl.cu $(PRE1_H) lal_tersoff_zbl_extra.h
$(BSH) ./geryon/file_to_cstr.sh tersoff_zbl $(PRE1_H) lal_tersoff_zbl_extra.h lal_tersoff_zbl.cu $(OBJ_DIR)/tersoff_zbl_cl.h;
$(OBJ_DIR)/%_cl.h: lal_%.cu $(PRE1_H)
$(BSH) ./geryon/file_to_cstr.sh $* $(PRE1_H) $< $@;
# host code compilation
$(OBJ_DIR)/lal_%.o: lal_%.cpp $(KERS)
$(OBJ_DIR)/lal_answer.o: lal_answer.cpp $(HOST_H)
$(OCL) -o $@ -c lal_answer.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lal_dpd_tstat_ext.o: lal_dpd_tstat_ext.cpp lal_dpd.h $(HOST_H)
$(OCL) -o $@ -c lal_dpd_tstat_ext.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lal_eam_alloy_ext.o: lal_eam_alloy_ext.cpp lal_eam.h $(HOST_H)
$(OCL) -o $@ -c lal_eam_alloy_ext.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lal_eam_fs_ext.o: lal_eam_fs_ext.cpp lal_eam.h $(HOST_H)
$(OCL) -o $@ -c lal_eam_fs_ext.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lal_neighbor.o: lal_neighbor.cpp $(HOST_H)
$(OCL) -o $@ -c lal_neighbor.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lal_neighbor_shared.o: lal_neighbor_shared.cpp $(HOST_H)
$(OCL) -o $@ -c lal_neighbor_shared.cpp -I$(OBJ_DIR)
$(OBJ_DIR)/lal_%_ext.o: lal_%_ext.cpp lal_%.h $(HOST_H)
$(OCL) -o $@ -c $< -I$(OBJ_DIR)
$(OBJ_DIR)/lal_base_%.o: lal_base_%.cpp $(HOST_H)
$(OCL) -o $@ -c $< -I$(OBJ_DIR)
$(OBJ_DIR)/lal_%.o: lal_%.cpp %_cl.h $(HOST_H)
$(OCL) -o $@ -c $< -I$(OBJ_DIR)
$(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp $(OCL_H)

363
lib/gpu/README
View File

@ -4,18 +4,109 @@
W. Michael Brown (ORNL)
Trung Dac Nguyen (ORNL/Northwestern)
Peng Wang (NVIDIA)
Nitin Dhamankar (Intel)
Axel Kohlmeyer (Temple)
Peng Wang (NVIDIA)
Anders Hafreager (UiO)
V. Nikolskiy (HSE)
Maurice de Koning (Unicamp/Brazil)
Rodolfo Paula Leite (Unicamp/Brazil)
Steve Plimpton (SNL)
Inderaj Bains (NVIDIA)
-------------------------------------------------------------------
This directory has source files to build a library that LAMMPS
links against when using the GPU package.
------------------------------------------------------------------------------
This library must be built with a C++ compiler, before LAMMPS is
built, so LAMMPS can link against it.
This directory has source files to build a library that LAMMPS links against
when using the GPU package.
This library must be built with a C++ compiler along with CUDA, HIP, or OpenCL
before LAMMPS is built, so LAMMPS can link against it.
This library, libgpu.a, provides routines for acceleration of certain
LAMMPS styles and neighbor list builds using CUDA, OpenCL, or ROCm HIP.
Pair styles supported by this library are marked in the list of Pair style
potentials with a "g". See the online version at:
https://lammps.sandia.gov/doc/Commands_pair.html
In addition the (plain) pppm kspace style is supported as well.
------------------------------------------------------------------------------
DEVICE QUERY
------------------------------------------------------------------------------
The gpu library includes binaries to check for available GPUs and their
properties. It is a good idea to run this on first use to make sure the
system and build is setup properly. Additionally, the GPU numbering for
specific selection of devices should be taking from this output. The GPU
library may split some accelerators into separate virtual accelerators for
efficient use with MPI.
After building the GPU library, for OpenCL:
./ocl_get_devices
for CUDA:
./nvc_get_devices
and for ROCm HIP:
./hip_get_devices
------------------------------------------------------------------------------
QUICK START
------------------------------------------------------------------------------
OpenCL: Mac without MPI:
make -f Makefile.mac_opencl -j; cd ../../src/; make mpi-stubs
make g++_serial -j
./lmp_g++_serial -in ../bench/in.lj -log none -sf gpu
OpenCL: Mac with MPI:
make -f Makefile.mac_opencl_mpi -j; cd ../../src/; make g++_openmpi -j
mpirun -np $NUM_MPI ./lmp_g++_openmpi -in ../bench/in.lj -log none -sf gpu
OpenCL: Linux with Intel oneAPI:
make -f Makefile.oneapi -j; cd ../../src; make oneapi -j
export OMP_NUM_THREADS=$NUM_THREADS
mpirun -np $NUM_MPI ./lmp_oneapi -in ../bench/in.lj -log none -sf gpu
OpenCL: Linux with MPI:
make -f Makefile.linux_opencl -j; cd ../../src; make omp -j
export OMP_NUM_THREADS=$NUM_THREADS
mpirun -np $NUM_MPI ./lmp_omp -in ../bench/in.lj -log none -sf gpu
NVIDIA CUDA:
make -f Makefile.cuda_mps -j; cd ../../src; make omp -j
export CUDA_MPS_LOG_DIRECTORY=/tmp; export CUDA_MPS_PIPE_DIRECTORY=/tmp
nvidia-smi -i 0 -c EXCLUSIVE_PROCESS
export OMP_NUM_THREADS=$NUM_THREADS
mpirun -np $NUM_MPI ./lmp_omp -in ../bench/in.lj -log none -sf gpu
echo quit | /usr/bin/nvidia-cuda-mps-control
AMD HIP:
make -f Makefile.hip -j; cd ../../src; make omp -j
export OMP_NUM_THREADS=$NUM_THREADS
mpirun -np $NUM_MPI ./lmp_omp -in ../bench/in.lj -log none -sf gpu
------------------------------------------------------------------------------
Installing oneAPI, OpenCl, CUDA, or ROCm
------------------------------------------------------------------------------
The easiest approach is to use the linux package manger to perform the
installation from Intel, NVIDIA, etc. repositories. All are available for
free. The oneAPI installation includes Intel optimized MPI and C++ compilers,
along with many libraries. Alternatively, Intel OpenCL can also be installed
separately from the Intel repository.
NOTE: Installation of the CUDA SDK is not required, only the CUDA toolkit.
See:
https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html
https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html
https://github.com/RadeonOpenCompute/ROCm
------------------------------------------------------------------------------
Build Intro
------------------------------------------------------------------------------
You can type "make lib-gpu" from the src directory to see help on how
to build this library via make commands, or you can do the same thing
@ -25,13 +116,13 @@ do it manually by following the instructions below.
Build the library using one of the provided Makefile.* files or create
your own, specific to your compiler and system. For example:
make -f Makefile.linux
make -f Makefile.linux_opencl
When you are done building this library, two files should
exist in this directory:
libgpu.a the library LAMMPS will link against
Makefile.lammps settings the LAMMPS Makefile will import
libgpu.a the library LAMMPS will link against
Makefile.lammps settings the LAMMPS Makefile will import
Makefile.lammps is created by the make command, by copying one of the
Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
@ -45,33 +136,132 @@ IMPORTANT: If you re-build the library, e.g. for a different precision
Makefile.linux clean, to insure all previous derived files are removed
before the new build is done.
Makefile.lammps has settings for 3 variables:
NOTE: The system-specific setting LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG,
or LAMMPS_SMALLSMALL if specified when building LAMMPS (i.e. in
src/MAKE/Makefile.foo) should be consistent with that specified
when building libgpu.a (i.e. by LMP_INC in the lib/gpu/Makefile.bar).
user-gpu_SYSINC = leave blank for this package
user-gpu_SYSLIB = CUDA libraries needed by this package
user-gpu_SYSPATH = path(s) to where those libraries are
Because you have the CUDA compilers on your system, you should have
the needed libraries. If the CUDA development tools were installed
in the standard manner, the settings in the Makefile.lammps.standard
file should work.
------------------------------------------------------------------------------
PRECISION MODES
------------------------------------------------------------------------------
The GPU library supports 3 precision modes: single, double, and mixed, with
the latter being the default for most Makefiles aside from Mac specific
Makefiles due to the more restrictive nature of the Apple OpenCL for some
devices.
-------------------------------------------------------------------
To specify the precision mode (output to the screen before LAMMPS runs for
verification), set either CUDA_PRECISION, OCL_PREC, or HIP_PRECISION to one
of -D_SINGLE_SINGLE, -D_DOUBLE_DOUBLE, or -D_SINGLE_DOUBLE.
GENERAL NOTES
--------------------------------
Some accelerators or OpenCL implementations only support single precision.
This mode should be used with care and appropriate validation as the errors
can scale with system size in this implementation. This can be useful for
accelerating test runs when setting up a simulation for production runs on
another machine. In the case where only single precision is supported, either
LAMMPS must be compiled with -DFFT_SINGLE to use PPPM with GPU acceleration
or GPU acceleration should be disabled for PPPM (e.g. suffix off or pair/only
as described in the LAMMPS documentation).
This library, libgpu.a, provides routines for GPU acceleration
of certain LAMMPS styles and neighbor list builds. Compilation of this
library requires installing the CUDA GPU driver and CUDA toolkit for
your operating system. Installation of the CUDA SDK is not necessary.
In addition to the LAMMPS library, the binary nvc_get_devices will also
be built. This can be used to query the names and properties of GPU
devices on your system. A Makefile for OpenCL and ROCm HIP compilation
is provided, but support for it is not currently provided by the developers.
Details of the implementation are provided in:
----
------------------------------------------------------------------------------
CUDA BUILD NOTES
------------------------------------------------------------------------------
NOTE: when compiling with CMake, all of the considerations listed below
are considered within the CMake configuration process, so no separate
compilation of the gpu library is required. Also this will build in support
for all compute architecture that are supported by the CUDA toolkit version
used to build the gpu library.
If you do not want to use a fat binary, that supports multiple CUDA
architectures, the CUDA_ARCH must be set to match the GPU architecture. This
is reported by nvc_get_devices executable created by the build process and
a detailed list of GPU architectures and CUDA compatible GPUs can be found
e.g. here: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
The CUDA_HOME variable should be set to the location of the CUDA toolkit.
To build, edit the CUDA_ARCH, CUDA_PRECISION, CUDA_HOME variables in one of
the Makefiles. CUDA_ARCH should be set based on the compute capability of
your GPU. This can be verified by running the nvc_get_devices executable after
the build is complete. Additionally, the GPU package must be installed and
compiled for LAMMPS. This may require editing the gpu_SYSPATH variable in the
LAMMPS makefile.
Please note that the GPU library accesses the CUDA driver library directly,
so it needs to be linked with the CUDA driver library (libcuda.so) that ships
with the Nvidia driver. If you are compiling LAMMPS on the head node of a GPU
cluster, this library may not be installed, so you may need to copy it over
from one of the compute nodes (best into this directory). Recent CUDA toolkits
starting from CUDA 9 provide a dummy libcuda.so library (typically under
$(CUDA_HOME)/lib64/stubs), that can be used for linking.
Best performance with the GPU library is typically with multiple MPI processes
sharing the same GPU cards. For NVIDIA, this is most efficient with CUDA
MPS enabled. To prevent runtime errors for GPUs configured in exclusive process
mode with MPS, the GPU library should be build with either of the equivalent
-DCUDA_MPS_SUPPORT or -DCUDA_PROXY flags.
------------------------------------------------------------------------------
HIP BUILD NOTES
------------------------------------------------------------------------------
1. GPU sorting requires installing hipcub
(https://github.com/ROCmSoftwarePlatform/hipCUB). The HIP CUDA-backend
additionally requires cub (https://nvlabs.github.io/cub). Download and
extract the cub directory to lammps/lib/gpu/ or specify an appropriate
path in lammps/lib/gpu/Makefile.hip.
2. In Makefile.hip it is possible to specify the target platform via
export HIP_PLATFORM=hcc or HIP_PLATFORM=nvcc as well as the target
architecture (gfx803, gfx900, gfx906 etc.)
3. If your MPI implementation does not support `mpicxx --showme` command,
it is required to specify the corresponding MPI compiler and linker flags
in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip.
------------------------------------------------------------------------------
OPENCL BUILD NOTES
------------------------------------------------------------------------------
If GERYON_NUMA_FISSION is defined at build time, LAMMPS will consider separate
NUMA nodes on GPUs or accelerators as separate devices. For example, a 2-socket
CPU would appear as two separate devices for OpenCL (and LAMMPS would require
two MPI processes to use both sockets with the GPU library - each with its
own device ID as output by ocl_get_devices).
For a debug build, use "-DUCL_DEBUG -DGERYON_KERNEL_DUMP" and remove
"-DUCL_NO_EXIT" and "-DMPI_GERYON" from the build options.
------------------------------------------------------------------------------
ALL PREPROCESSOR OPTIONS (For Advanced Users)
------------------------------------------------------------------------------
_SINGLE_SINGLE Build library for single precision mode
_SINGLE_DOUBLE Build library for mixed precision mode
_DOUBLE_DOUBLE Build library for double precision mode
CUDA_MPS_SUPPORT Do not generate errors for exclusive mode for CUDA
CUDA_PROXY Same as above
MPI_GERYON Library should use MPI_Abort for unhandled errors
GERYON_NUMA_FISSION Accelerators with main memory NUMA are split into
multiple virtual accelerators for each NUMA node
LAL_USE_OMP=0 Disable OpenMP in lib, regardless of compiler setting
LAL_USE_OMP_SIMD=0 Disable OpenMP SIMD in lib, regardless of compiler set
GERYON_OCL_FLUSH For OpenCL, flush queue after every enqueue
LAL_NO_OCL_EV_JIT Turn off JIT specialization for kernels in OpenCL
LAL_USE_OLD_NEIGHBOR Use old neighbor list algorithm
USE_CUDPP Enable GPU binning in neighbor builds (not recommended)
USE_HIP_DEVICE_SORT Enable GPU binning for HIP builds
(only w/ LAL_USE_OLD_NEIGHBOR)
LAL_NO_BLOCK_REDUCE Use host for energy/virial accumulation
LAL_OCL_EXTRA_ARGS Supply extra args for OpenCL compiler delimited with :
UCL_NO_EXIT LAMMPS should handle errors instead of Geryon lib
UCL_DEBUG Debug build for Geryon
GERYON_KERNEL_DUMP Dump all compiled OpenCL programs with compiler
flags and build logs
GPU_CAST Casting performed on GPU, untested recently
THREE_CONCURRENT Concurrent 3-body calcs in separate queues, untested
------------------------------------------------------------------------------
References for Details
------------------------------------------------------------------------------
Brown, W.M., Wang, P. Plimpton, S.J., Tharrington, A.N. Implementing
Molecular Dynamics on Hybrid High Performance Computers - Short Range
@ -89,116 +279,3 @@ Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High
Performance Computers - Three-Body Potentials. Computer Physics Communications.
2013. 184: p. 2785–2793.
----
NOTE: Installation of the CUDA SDK is not required, only the CUDA
toolkit itself or an OpenCL 1.2 compatible header and library.
Pair styles supporting GPU acceleration this this library
are marked in the list of Pair style potentials with a "g".
See the online version at: https://lammps.sandia.gov/doc/Commands_pair.html
In addition the (plain) pppm kspace style is supported as well.
MULTIPLE LAMMPS PROCESSES
--------------------------------
Multiple LAMMPS MPI processes can share GPUs on the system, but multiple
GPUs cannot be utilized by a single MPI process. In many cases, the
best performance will be obtained by running as many MPI processes as
CPU cores available with the condition that the number of MPI processes
is an integer multiple of the number of GPUs being used. See the
LAMMPS user manual for details on running with GPU acceleration.
BUILDING AND PRECISION MODES
--------------------------------
To build, edit the CUDA_ARCH, CUDA_PRECISION, CUDA_HOME variables in one of
the Makefiles. CUDA_ARCH should be set based on the compute capability of
your GPU. This can be verified by running the nvc_get_devices executable after
the build is complete. Additionally, the GPU package must be installed and
compiled for LAMMPS. This may require editing the gpu_SYSPATH variable in the
LAMMPS makefile.
Please note that the GPU library accesses the CUDA driver library directly,
so it needs to be linked not only to the CUDA runtime library (libcudart.so)
that ships with the CUDA toolkit, but also with the CUDA driver library
(libcuda.so) that ships with the Nvidia driver. If you are compiling LAMMPS
on the head node of a GPU cluster, this library may not be installed,
so you may need to copy it over from one of the compute nodes (best into
this directory). Recent CUDA toolkits starting from CUDA 9 provide a dummy
libcuda.so library (typically under $(CUDA_HOME)/lib64/stubs), that can be used for
linking.
The gpu library supports 3 precision modes as determined by
the CUDA_PRECISION variable:
CUDA_PRECISION = -D_SINGLE_SINGLE # Single precision for all calculations
CUDA_PRECISION = -D_DOUBLE_DOUBLE # Double precision for all calculations
CUDA_PRECISION = -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double
As of CUDA 7.5 only GPUs with compute capability 2.0 (Fermi) or newer are
supported and as of CUDA 9.0 only compute capability 3.0 (Kepler) or newer
are supported. There are some limitations of this library for GPUs older
than that, which require additional preprocessor flag, and limit features,
but they are kept for historical reasons. There is no value in trying to
use those GPUs for production calculations.
You have to make sure that you set a CUDA_ARCH line suitable for your
hardware and CUDA toolkit version: e.g. -arch=sm_35 for Tesla K20 or K40
or -arch=sm_52 GeForce GTX Titan X. A detailed list of GPU architectures
and CUDA compatible GPUs can be found e.g. here:
https://en.wikipedia.org/wiki/CUDA#GPUs_supported
NOTE: when compiling with CMake, all of the considerations listed below
are considered within the CMake configuration process, so no separate
compilation of the gpu library is required. Also this will build in support
for all compute architecture that are supported by the CUDA toolkit version
used to build the gpu library.
Please note the CUDA_CODE settings in Makefile.linux_multi, which allows
to compile this library with support for multiple GPUs. This list can be
extended for newer GPUs with newer CUDA toolkits and should allow to build
a single GPU library compatible with all GPUs that are worth using for
GPU acceleration and supported by the current CUDA toolkits and drivers.
NOTE: The system-specific setting LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG,
or LAMMPS_SMALLSMALL if specified when building LAMMPS (i.e. in
src/MAKE/Makefile.foo) should be consistent with that specified
when building libgpu.a (i.e. by LMP_INC in the lib/gpu/Makefile.bar).
BUILDING FOR HIP FRAMEWORK
--------------------------------
1. Install the latest ROCm framework (https://github.com/RadeonOpenCompute/ROCm).
2. GPU sorting requires installing hipcub
(https://github.com/ROCmSoftwarePlatform/hipCUB). The HIP CUDA-backend
additionally requires cub (https://nvlabs.github.io/cub). Download and
extract the cub directory to lammps/lib/gpu/ or specify an appropriate
path in lammps/lib/gpu/Makefile.hip.
3. In Makefile.hip it is possible to specify the target platform via
export HIP_PLATFORM=hcc or HIP_PLATFORM=nvcc as well as the target
architecture (gfx803, gfx900, gfx906 etc.)
4. If your MPI implementation does not support `mpicxx --showme` command,
it is required to specify the corresponding MPI compiler and linker flags
in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip.
5. Building the GPU library (libgpu.a):
cd lammps/lib/gpu; make -f Makefile.hip -j
6. Building the LAMMPS executable (lmp_hip):
cd ../../src; make hip -j
EXAMPLE CONVENTIONAL BUILD PROCESS
--------------------------------
cd ~/lammps/lib/gpu
emacs Makefile.linux
make -f Makefile.linux
./nvc_get_devices
cd ../../src
emacs ./MAKE/Makefile.linux
make yes-asphere
make yes-kspace
make yes-gpu
make linux

84
lib/gpu/geryon/hip_device.h
View File

@ -8,6 +8,9 @@
#ifndef HIP_DEVICE
#define HIP_DEVICE
// workaround after GPU package Feb2021 update
// todo: make new neighbor code work with HIP
#define LAL_USE_OLD_NEIGHBOR
#include <hip/hip_runtime.h>
#include <unordered_map>
@ -24,6 +27,8 @@ namespace ucl_hip {
// --------------------------------------------------------------------------
typedef hipStream_t command_queue;
inline void ucl_flush(command_queue &cq) {}
inline void ucl_sync(hipStream_t &stream) {
CU_SAFE_CALL(hipStreamSynchronize(stream));
}
@ -39,8 +44,8 @@ struct NVDProperties {
int maxThreadsPerBlock;
int maxThreadsDim[3];
int maxGridSize[3];
int sharedMemPerBlock;
int totalConstantMemory;
CUDA_INT_TYPE sharedMemPerBlock;
CUDA_INT_TYPE totalConstantMemory;
int SIMDWidth;
int memPitch;
int regsPerBlock;
@ -143,15 +148,26 @@ class UCL_Device {
inline std::string device_type_name(const int i) { return "GPU"; }
/// Get current device type (UCL_CPU, UCL_GPU, UCL_ACCELERATOR, UCL_DEFAULT)
inline int device_type() { return device_type(_device); }
inline enum UCL_DEVICE_TYPE device_type() { return device_type(_device); }
/// Get device type (UCL_CPU, UCL_GPU, UCL_ACCELERATOR, UCL_DEFAULT)
inline int device_type(const int i) { return UCL_GPU; }
inline enum UCL_DEVICE_TYPE device_type(const int i) { return UCL_GPU; }
/// Returns true if host memory is efficiently addressable from device
inline bool shared_memory() { return shared_memory(_device); }
/// Returns true if host memory is efficiently addressable from device
inline bool shared_memory(const int i) { return device_type(i)==UCL_CPU; }
/// Returns preferred vector width
inline int preferred_fp32_width() { return preferred_fp32_width(_device); }
/// Returns preferred vector width
inline int preferred_fp32_width(const int i)
{return _properties[i].SIMDWidth;}
/// Returns preferred vector width
inline int preferred_fp64_width() { return preferred_fp64_width(_device); }
/// Returns preferred vector width
inline int preferred_fp64_width(const int i)
{return _properties[i].SIMDWidth;}
/// Returns true if double precision is support for the current device
inline bool double_precision() { return double_precision(_device); }
/// Returns true if double precision is support for the device
@ -215,6 +231,18 @@ class UCL_Device {
/// Get the maximum number of threads per block
inline size_t group_size(const int i)
{ return _properties[i].maxThreadsPerBlock; }
/// Get the maximum number of threads per block in dimension 'dim'
inline size_t group_size_dim(const int dim)
{ return group_size_dim(_device, dim); }
/// Get the maximum number of threads per block in dimension 'dim'
inline size_t group_size_dim(const int i, const int dim)
{ return _properties[i].maxThreadsDim[dim];}
/// Get the shared local memory size in bytes
inline size_t slm_size() { return slm_size(_device); }
/// Get the shared local memory size in bytes
inline size_t slm_size(const int i)
{ return _properties[i].sharedMemPerBlock; }
/// Return the maximum memory pitch in bytes for current device
inline size_t max_pitch() { return max_pitch(_device); }
@ -255,11 +283,20 @@ class UCL_Device {
inline int max_sub_devices(const int i)
{ return 0; }
/// True if the device supports shuffle intrinsics
inline bool has_shuffle_support()
{ return has_shuffle_support(_device); }
/// True if the device supports shuffle intrinsics
inline bool has_shuffle_support(const int i)
{ return arch(i)>=3.0; }
/// List all devices along with all properties
inline void print_all(std::ostream &out);
/// Select the platform that has accelerators (for compatibility with OpenCL)
inline int set_platform_accelerator(int pid=-1) { return UCL_SUCCESS; }
/// For compatability with OCL API
inline int auto_set_platform(const enum UCL_DEVICE_TYPE type=UCL_GPU,
const std::string vendor="")
{ return set_platform(0); }
inline int load_module(const void* program, hipModule_t& module, std::string *log=nullptr){
auto it = _loaded_modules.emplace(program, hipModule_t());
@ -328,32 +365,35 @@ UCL_Device::UCL_Device() {
CU_SAFE_CALL_NS(hipDeviceGetName(namecstr,1024,dev));
prop.name=namecstr;
CU_SAFE_CALL_NS(hipDeviceTotalMem(&prop.totalGlobalMem,dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.multiProcessorCount, hipDeviceAttributeMultiprocessorCount, dev));
hipDeviceProp_t hip_prop;
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.maxThreadsPerBlock, hipDeviceAttributeMaxThreadsPerBlock, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.maxThreadsDim[0], hipDeviceAttributeMaxBlockDimX, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.maxThreadsDim[1], hipDeviceAttributeMaxBlockDimY, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.maxThreadsDim[2], hipDeviceAttributeMaxBlockDimZ, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.maxGridSize[0], hipDeviceAttributeMaxGridDimX, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.maxGridSize[1], hipDeviceAttributeMaxGridDimY, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.maxGridSize[2], hipDeviceAttributeMaxGridDimZ, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.sharedMemPerBlock, hipDeviceAttributeMaxSharedMemoryPerBlock, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.totalConstantMemory, hipDeviceAttributeTotalConstantMemory, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.SIMDWidth, hipDeviceAttributeWarpSize, dev));
CU_SAFE_CALL_NS(hipGetDeviceProperties(&hip_prop,dev));
prop.totalGlobalMem = hip_prop.totalGlobalMem;
prop.multiProcessorCount = hip_prop.multiProcessorCount;
prop.maxThreadsPerBlock = hip_prop.maxThreadsPerBlock;
prop.maxThreadsDim[0] = hip_prop.maxThreadsDim[0];
prop.maxThreadsDim[1] = hip_prop.maxThreadsDim[1];
prop.maxThreadsDim[2] = hip_prop.maxThreadsDim[2];
prop.maxGridSize[0] = hip_prop.maxGridSize[0];
prop.maxGridSize[1] = hip_prop.maxGridSize[1];
prop.maxGridSize[2] = hip_prop.maxGridSize[2];
prop.sharedMemPerBlock = hip_prop.sharedMemPerBlock;
prop.totalConstantMemory = hip_prop.totalConstMem;
prop.SIMDWidth = hip_prop.warpSize;
prop.regsPerBlock = hip_prop.regsPerBlock;
prop.clockRate = hip_prop.clockRate;
prop.computeMode = hip_prop.computeMode;
//CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.memPitch, CU_DEVICE_ATTRIBUTE_MAX_PITCH, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.regsPerBlock, hipDeviceAttributeMaxRegistersPerBlock, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.clockRate, hipDeviceAttributeClockRate, dev));
//CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.textureAlign, CU_DEVICE_ATTRIBUTE_TEXTURE_ALIGNMENT, dev));
//#if CUDA_VERSION >= 2020
//CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.kernelExecTimeoutEnabled, CU_DEVICE_ATTRIBUTE_KERNEL_EXEC_TIMEOUT,dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.integrated, hipDeviceAttributeIntegrated, dev));
//CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.canMapHostMemory, CU_DEVICE_ATTRIBUTE_CAN_MAP_HOST_MEMORY, dev));
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.computeMode, hipDeviceAttributeComputeMode,dev));
//#endif
//#if CUDA_VERSION >= 3010
CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.concurrentKernels, hipDeviceAttributeConcurrentKernels, dev));
prop.concurrentKernels = hip_prop.concurrentKernels;
//CU_SAFE_CALL_NS(hipDeviceGetAttribute(&prop.ECCEnabled, CU_DEVICE_ATTRIBUTE_ECC_ENABLED, dev));
//#endif

7
lib/gpu/geryon/hip_kernel.h
View File

@ -14,6 +14,7 @@
#include <fstream>
#include <string>
#include <iostream>
#include <cstdio>
namespace ucl_hip {
@ -64,15 +65,19 @@ class UCL_Program {
}
/// Load a program from a string and compile with flags
inline int load_string(const void *program, const char *flags="", std::string *log=nullptr) {
inline int load_string(const void *program, const char *flags="", std::string *log=nullptr, FILE* foutput=nullptr) {
return _device_ptr->load_module(program, _module, log);
}
/// Return the default command queue/stream associated with this data
inline hipStream_t & cq() { return _cq; }
friend class UCL_Kernel;
private:
hipModule_t _module;
hipStream_t _cq;
friend class UCL_Texture;
friend class UCL_Const;
};
/// Class for dealing with CUDA Driver kernels

31
lib/gpu/geryon/hip_texture.h
View File

@ -107,6 +107,37 @@ class UCL_Texture {
}
};
/// Class storing a const global memory reference
class UCL_Const {
public:
UCL_Const() {}
~UCL_Const() {}
/// Construct with a specified global reference
inline UCL_Const(UCL_Program &prog, const char *global_name)
{ get_global(prog,global_name); }
/// Set the global reference for this object
inline void get_global(UCL_Program &prog, const char *global_name) {
_cq=prog.cq();
CU_SAFE_CALL(hipModuleGetGlobal(&_global, &_global_bytes, prog._module,
global_name));
}
/// Copy from array on host to const memory
template <class numtyp>
inline void update_device(UCL_H_Vec<numtyp> &src, const int numel) {
CU_SAFE_CALL(hipMemcpyHtoDAsync(_global, src.begin(), numel*sizeof(numtyp),
_cq));
}
/// Get device ptr associated with object
inline const void* begin() const { return &_global; }
inline void clear() {}
private:
hipStream_t _cq;
void* _global;
size_t _global_bytes;
friend class UCL_Kernel;
};
} // namespace
#endif

44
lib/gpu/geryon/nvd_device.h
View File

@ -37,6 +37,8 @@ namespace ucl_cudadr {
// --------------------------------------------------------------------------
typedef CUstream command_queue;
inline void ucl_flush(command_queue &cq) {}
inline void ucl_sync(CUstream &stream) {
CU_SAFE_CALL(cuStreamSynchronize(stream));
}
@ -156,15 +158,26 @@ class UCL_Device {
inline std::string device_type_name(const int i) { return "GPU"; }
/// Get current device type (UCL_CPU, UCL_GPU, UCL_ACCELERATOR, UCL_DEFAULT)
inline int device_type() { return device_type(_device); }
inline enum UCL_DEVICE_TYPE device_type() { return device_type(_device); }
/// Get device type (UCL_CPU, UCL_GPU, UCL_ACCELERATOR, UCL_DEFAULT)
inline int device_type(const int i) { return UCL_GPU; }
inline enum UCL_DEVICE_TYPE device_type(const int i) { return UCL_GPU; }
/// Returns true if host memory is efficiently addressable from device
inline bool shared_memory() { return shared_memory(_device); }
/// Returns true if host memory is efficiently addressable from device
inline bool shared_memory(const int i) { return device_type(i)==UCL_CPU; }
/// Returns preferred vector width
inline int preferred_fp32_width() { return preferred_fp32_width(_device); }
/// Returns preferred vector width
inline int preferred_fp32_width(const int i)
{return _properties[i].SIMDWidth;}
/// Returns preferred vector width
inline int preferred_fp64_width() { return preferred_fp64_width(_device); }
/// Returns preferred vector width
inline int preferred_fp64_width(const int i)
{return _properties[i].SIMDWidth;}
/// Returns true if double precision is support for the current device
inline bool double_precision() { return double_precision(_device); }
/// Returns true if double precision is support for the device
@ -228,6 +241,18 @@ class UCL_Device {
/// Get the maximum number of threads per block
inline size_t group_size(const int i)
{ return _properties[i].maxThreadsPerBlock; }
/// Get the maximum number of threads per block in dimension 'dim'
inline size_t group_size_dim(const int dim)
{ return group_size_dim(_device, dim); }
/// Get the maximum number of threads per block in dimension 'dim'
inline size_t group_size_dim(const int i, const int dim)
{ return _properties[i].maxThreadsDim[dim]; }
/// Get the shared local memory size in bytes
inline size_t slm_size() { return slm_size(_device); }
/// Get the shared local memory size in bytes
inline size_t slm_size(const int i)
{ return _properties[i].sharedMemPerBlock; }
/// Return the maximum memory pitch in bytes for current device
inline size_t max_pitch() { return max_pitch(_device); }
@ -268,11 +293,22 @@ class UCL_Device {
inline int max_sub_devices(const int i)
{ return 0; }
/// True if the device supports shuffle intrinsics
inline bool has_shuffle_support()
{ return has_shuffle_support(_device); }
/// True if the device supports shuffle intrinsics
inline bool has_shuffle_support(const int i)
{ return arch(i)>=3.0; }
/// List all devices along with all properties
inline void print_all(std::ostream &out);
/// Select the platform that has accelerators (for compatibility with OpenCL)
inline int set_platform_accelerator(int pid=-1) { return UCL_SUCCESS; }
/// For compatability with OCL API
inline int auto_set_platform(const enum UCL_DEVICE_TYPE type=UCL_GPU,
const std::string vendor="",
const int ndevices=-1,
const int first_device=-1)
{ return set_platform(0); }
private:
int _device, _num_devices;

24
lib/gpu/geryon/nvd_kernel.h
View File

@ -26,6 +26,7 @@
#include "nvd_device.h"
#include <fstream>
#include <cstdio>
namespace ucl_cudadr {
@ -77,7 +78,7 @@ class UCL_Program {
/// Load a program from a string and compile with flags
inline int load_string(const void *program, const char *flags="",
std::string *log=nullptr) {
std::string *log=nullptr, FILE* foutput=nullptr) {
if (std::string(flags)=="BINARY")
return load_binary((const char *)program);
const unsigned int num_opts=2;
@ -100,12 +101,25 @@ class UCL_Program {
if (err != CUDA_SUCCESS) {
#ifndef UCL_NO_EXIT
std::cerr << std::endl
std::cerr << std::endl << std::endl
<< "----------------------------------------------------------\n"
<< " UCL Error: Error compiling PTX Program...\n"
<< "----------------------------------------------------------\n";
std::cerr << log << std::endl;
std::cerr << log << std::endl
<< "----------------------------------------------------------\n\n";
#endif
if (foutput != NULL) {
fprintf(foutput,"\n\n");
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput," UCL Error: Error compiling PTX Program...\n");
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,"%s\n",log);
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,"\n\n");
}
return UCL_COMPILE_ERROR;
}
@ -139,11 +153,15 @@ class UCL_Program {
return UCL_SUCCESS;
}
/// Return the default command queue/stream associated with this data
inline command_queue & cq() { return _cq; }
friend class UCL_Kernel;
private:
CUmodule _module;
CUstream _cq;
friend class UCL_Texture;
friend class UCL_Const;
};
/// Class for dealing with CUDA Driver kernels

42
lib/gpu/geryon/nvd_texture.h
View File

@ -38,8 +38,11 @@ class UCL_Texture {
inline UCL_Texture(UCL_Program &prog, const char *texture_name)
{ get_texture(prog,texture_name); }
/// Set the texture reference for this object
inline void get_texture(UCL_Program &prog, const char *texture_name)
{ CU_SAFE_CALL(cuModuleGetTexRef(&_tex, prog._module, texture_name)); }
inline void get_texture(UCL_Program &prog, const char *texture_name) {
#if (CUDA_VERSION < 11000)
CU_SAFE_CALL(cuModuleGetTexRef(&_tex, prog._module, texture_name));
#endif
}
/// Bind a float array where each fetch grabs a vector of length numel
template<class numtyp>
@ -72,11 +75,14 @@ class UCL_Texture {
}
private:
#if (CUDA_VERSION < 11000)
CUtexref _tex;
#endif
friend class UCL_Kernel;
template<class mat_typ>
inline void _bind_float(mat_typ &vec, const unsigned numel) {
#if (CUDA_VERSION < 11000)
#ifdef UCL_DEBUG
assert(numel!=0 && numel<5);
#endif
@ -90,10 +96,42 @@ class UCL_Texture {
else
CU_SAFE_CALL(cuTexRefSetFormat(_tex,CU_AD_FORMAT_SIGNED_INT32,numel*2));
}
#endif
}
};
/// Class storing a const global memory reference
class UCL_Const {
public:
UCL_Const() {}
~UCL_Const() {}
/// Construct with a specified global reference
inline UCL_Const(UCL_Program &prog, const char *global_name)
{ get_global(prog,global_name); }
/// Set the global reference for this object
inline void get_global(UCL_Program &prog, const char *global_name) {
_cq=prog.cq();
CU_SAFE_CALL(cuModuleGetGlobal(&_global, &_global_bytes, prog._module,
global_name));
}
/// Copy from array on host to const memory
template <class numtyp>
inline void update_device(UCL_H_Vec<numtyp> &src, const int numel) {
CU_SAFE_CALL(cuMemcpyHtoDAsync(_global, src.begin(), numel*sizeof(numtyp),
_cq));
}
/// Get device ptr associated with object
inline const CUdeviceptr * begin() const { return &_global; }
inline void clear() {}
private:
CUstream _cq;
CUdeviceptr _global;
size_t _global_bytes;
friend class UCL_Kernel;
};
} // namespace
#endif

322
lib/gpu/geryon/ocl_device.h
View File

@ -28,12 +28,8 @@
#include <vector>
#include <iostream>
/* We default to OpenCL 1.2 as target version for now as
* there are known issues with OpenCL 2.0 and later.
* This is also to silence warnings from generic OpenCL headers */
#if !defined(CL_TARGET_OPENCL_VERSION)
#define CL_TARGET_OPENCL_VERSION 120
#ifndef CL_TARGET_OPENCL_VERSION
#define CL_TARGET_OPENCL_VERSION 210
#endif
#ifdef __APPLE__
@ -55,17 +51,36 @@ namespace ucl_opencl {
typedef cl_command_queue command_queue;
typedef cl_context context_type;
inline void ucl_flush(command_queue &cq) { CL_SAFE_CALL(clFlush(cq)); }
inline void ucl_sync(cl_command_queue &cq) {
CL_SAFE_CALL(clFinish(cq));
}
inline bool _shared_mem_device(cl_device_type &device_type) {
#if defined(GERYON_FORCE_SHARED_MAIN_MEM_ON)
inline bool _shared_mem_device(cl_device_id &device) { return true; }
#elif defined(GERYON_FORCE_SHARED_MAIN_MEM_OFF)
inline bool _shared_mem_device(cl_device_id &device) { return false; }
#else
inline bool _shared_mem_device(cl_device_id &device) {
#ifdef CL_VERSION_1_2
cl_bool br;
CL_SAFE_CALL(clGetDeviceInfo(device, CL_DEVICE_HOST_UNIFIED_MEMORY,
sizeof(cl_bool), &br,NULL));
return (br == CL_TRUE);
#else
cl_device_type device_type;
CL_SAFE_CALL(clGetDeviceInfo(device,CL_DEVICE_TYPE,
sizeof(device_type),&device_type,NULL));
return (device_type==CL_DEVICE_TYPE_CPU);
#endif
}
#endif
struct OCLProperties {
std::string name;
cl_device_type device_type;
bool is_subdevice;
cl_ulong global_mem;
cl_ulong shared_mem;
cl_ulong const_mem;
@ -74,12 +89,16 @@ struct OCLProperties {
size_t work_group_size;
size_t work_item_size[3];
bool double_precision;
int preferred_vector_width32, preferred_vector_width64;
int alignment;
size_t timer_resolution;
bool ecc_support;
std::string c_version;
bool partition_equal, partition_counts, partition_affinity;
cl_uint max_sub_devices;
int cl_device_version;
bool has_subgroup_support;
bool has_shuffle_support;
};
/// Class for looking at data parallel device properties
@ -182,15 +201,26 @@ class UCL_Device {
inline std::string device_type_name(const int i);
/// Get current device type (UCL_CPU, UCL_GPU, UCL_ACCELERATOR, UCL_DEFAULT)
inline int device_type() { return device_type(_device); }
inline enum UCL_DEVICE_TYPE device_type() { return device_type(_device); }
/// Get device type (UCL_CPU, UCL_GPU, UCL_ACCELERATOR, UCL_DEFAULT)
inline int device_type(const int i);
inline enum UCL_DEVICE_TYPE device_type(const int i);
/// Returns true if host memory is efficiently addressable from device
inline bool shared_memory() { return shared_memory(_device); }
/// Returns true if host memory is efficiently addressable from device
inline bool shared_memory(const int i)
{ return _shared_mem_device(_properties[i].device_type); }
{ return _shared_mem_device(_cl_devices[i]); }
/// Returns preferred vector width
inline int preferred_fp32_width() { return preferred_fp32_width(_device); }
/// Returns preferred vector width
inline int preferred_fp32_width(const int i)
{return _properties[i].preferred_vector_width32;}
/// Returns preferred vector width
inline int preferred_fp64_width() { return preferred_fp64_width(_device); }
/// Returns preferred vector width
inline int preferred_fp64_width(const int i)
{return _properties[i].preferred_vector_width64;}
/// Returns true if double precision is support for the current device
inline bool double_precision() { return double_precision(_device); }
@ -242,6 +272,18 @@ class UCL_Device {
/// Get the maximum number of threads per block
inline size_t group_size(const int i)
{ return _properties[i].work_group_size; }
/// Get the maximum number of threads per block in dimension 'dim'
inline size_t group_size_dim(const int dim)
{ return group_size_dim(_device, dim); }
/// Get the maximum number of threads per block in dimension 'dim'
inline size_t group_size_dim(const int i, const int dim)
{ return _properties[i].work_item_size[dim]; }
/// Get the shared local memory size in bytes
inline size_t slm_size() { return slm_size(_device); }
/// Get the shared local memory size in bytes
inline size_t slm_size(const int i)
{ return _properties[i].shared_mem; }
/// Return the maximum memory pitch in bytes for current device
inline size_t max_pitch() { return max_pitch(_device); }
@ -256,6 +298,12 @@ class UCL_Device {
inline bool sharing_supported(const int i)
{ return true; }
/// True if the device is a sub-device
inline bool is_subdevice()
{ return is_subdevice(_device); }
/// True if the device is a sub-device
inline bool is_subdevice(const int i)
{ return _properties[i].is_subdevice; }
/// True if splitting device into equal subdevices supported
inline bool fission_equal()
{ return fission_equal(_device); }
@ -274,6 +322,18 @@ class UCL_Device {
/// True if splitting device into subdevices by affinity domains supported
inline bool fission_by_affinity(const int i)
{ return _properties[i].partition_affinity; }
/// True if the device has subgroup support
inline bool has_subgroup_support()
{ return has_subgroup_support(_device); }
/// True if the device has subgroup support
inline bool has_subgroup_support(const int i)
{ return _properties[i].has_subgroup_support; }
/// True if the device supports shuffle intrinsics
inline bool has_shuffle_support()
{ return has_shuffle_support(_device); }
/// True if the device supports shuffle intrinsics
inline bool has_shuffle_support(const int i)
{ return _properties[i].has_shuffle_support; }
/// Maximum number of subdevices allowed from device fission
inline int max_sub_devices()
@ -281,6 +341,12 @@ class UCL_Device {
/// Maximum number of subdevices allowed from device fission
inline int max_sub_devices(const int i)
{ return _properties[i].max_sub_devices; }
/// OpenCL version supported by the device
inline int cl_device_version()
{ return cl_device_version(_device); }
/// OpenCL version supported by the device
inline int cl_device_version(const int i)
{ return _properties[i].cl_device_version; }
/// List all devices along with all properties
inline void print_all(std::ostream &out);
@ -288,8 +354,14 @@ class UCL_Device {
/// Return the OpenCL type for the device
inline cl_device_id & cl_device() { return _cl_device; }
/// Select the platform that has accelerators
inline int set_platform_accelerator(int pid=-1);
/// Automatically set the platform by type, vendor, and/or CU count
/** If first_device is positive, search restricted to platforms containing
* this device IDs. If ndevices is positive, search is restricted
* to platforms with at least that many devices **/
inline int auto_set_platform(const enum UCL_DEVICE_TYPE type=UCL_GPU,
const std::string vendor="",
const int ndevices=-1,
const int first_device=-1);
private:
int _num_platforms; // Number of platforms
@ -322,8 +394,7 @@ UCL_Device::UCL_Device() {
return;
} else
_num_platforms=static_cast<int>(nplatforms);
// note that platform 0 may not necessarily be associated with accelerators
set_platform_accelerator();
set_platform(0);
}
UCL_Device::~UCL_Device() {
@ -332,6 +403,14 @@ UCL_Device::~UCL_Device() {
void UCL_Device::clear() {
_properties.clear();
#ifdef GERYON_NUMA_FISSION
#ifdef CL_VERSION_1_2
for (int i=0; i<_cl_devices.size(); i++)
CL_DESTRUCT_CALL(clReleaseDevice(_cl_devices[i]));
#endif
#endif
_cl_devices.clear();
if (_device>-1) {
for (size_t i=0; i<_cq.size(); i++) {
@ -341,6 +420,7 @@ void UCL_Device::clear() {
CL_DESTRUCT_CALL(clReleaseContext(_context));
}
_device=-1;
_num_devices=0;
}
int UCL_Device::set_platform(int pid) {
@ -370,11 +450,51 @@ int UCL_Device::set_platform(int pid) {
CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,n,device_list,
&n));
#ifndef GERYON_NUMA_FISSION
// --- Store properties for each device
for (int i=0; i<_num_devices; i++) {
_cl_devices.push_back(device_list[i]);
add_properties(device_list[i]);
}
#else
// --- Create sub-devices for anything partitionable by NUMA and store props
int num_unpart = _num_devices;
_num_devices = 0;
for (int i=0; i<num_unpart; i++) {
cl_uint num_subdevices = 1;
cl_device_id *subdevice_list = device_list + i;
#ifdef CL_VERSION_1_2
cl_device_affinity_domain adomain;
CL_SAFE_CALL(clGetDeviceInfo(device_list[i],
CL_DEVICE_PARTITION_AFFINITY_DOMAIN,
sizeof(cl_device_affinity_domain),
&adomain,NULL));
cl_device_partition_property props[3];
props[0]=CL_DEVICE_PARTITION_BY_AFFINITY_DOMAIN;
props[1]=CL_DEVICE_AFFINITY_DOMAIN_NUMA;
props[2]=0;
if (adomain & CL_DEVICE_AFFINITY_DOMAIN_NUMA)
CL_SAFE_CALL(clCreateSubDevices(device_list[i], props, 0, NULL,
&num_subdevices));
if (num_subdevices > 1) {
subdevice_list = new cl_device_id[num_subdevices];
CL_SAFE_CALL(clCreateSubDevices(device_list[i], props, num_subdevices,
subdevice_list, &num_subdevices));
}
#endif
for (int j=0; j<num_subdevices; j++) {
_num_devices++;
_cl_devices.push_back(subdevice_list[j]);
add_properties(subdevice_list[j]);
}
if (num_subdevices > 1) delete[] subdevice_list;
} // for i
#endif
delete[] device_list;
return UCL_SUCCESS;
}
@ -429,11 +549,18 @@ void UCL_Device::add_properties(cl_device_id device_list) {
sizeof(cl_uint),&op.alignment,nullptr));
op.alignment/=8;
cl_uint float_width;
CL_SAFE_CALL(clGetDeviceInfo(device_list,
CL_DEVICE_PREFERRED_VECTOR_WIDTH_FLOAT,
sizeof(float_width),&float_width,nullptr));
op.preferred_vector_width32=float_width;
// Determine if double precision is supported
cl_uint double_width;
CL_SAFE_CALL(clGetDeviceInfo(device_list,
CL_DEVICE_PREFERRED_VECTOR_WIDTH_DOUBLE,
sizeof(double_width),&double_width,nullptr));
op.preferred_vector_width64=double_width;
if (double_width==0)
op.double_precision=false;
else
@ -452,9 +579,14 @@ void UCL_Device::add_properties(cl_device_id device_list) {
op.ecc_support=true;
op.c_version="";
op.is_subdevice=false;
op.partition_equal=false;
op.partition_counts=false;
op.partition_affinity=false;
op.max_sub_devices=1;
op.cl_device_version=0;
op.has_subgroup_support=false;
op.has_shuffle_support=false;
#ifdef CL_VERSION_1_2
size_t return_bytes;
@ -463,6 +595,13 @@ void UCL_Device::add_properties(cl_device_id device_list) {
op.c_version=buffer;
cl_device_partition_property pinfo[4];
CL_SAFE_CALL(clGetDeviceInfo(device_list, CL_DEVICE_PARTITION_TYPE,
4*sizeof(cl_device_partition_property),
&pinfo, &return_bytes));
if (return_bytes == 0) op.is_subdevice=false;
else if (pinfo[0]) op.is_subdevice=true;
else op.is_subdevice=false;
CL_SAFE_CALL(clGetDeviceInfo(device_list,
CL_DEVICE_PARTITION_PROPERTIES,
4*sizeof(cl_device_partition_property),
@ -480,6 +619,46 @@ void UCL_Device::add_properties(cl_device_id device_list) {
CL_SAFE_CALL(clGetDeviceInfo(device_list,
CL_DEVICE_PARTITION_MAX_SUB_DEVICES,
sizeof(cl_uint),&op.max_sub_devices,nullptr));
CL_SAFE_CALL(clGetDeviceInfo(device_list,CL_DEVICE_VERSION,1024,buffer,nullptr));
int cl_version_maj = buffer[7] - '0';
int cl_version_min = buffer[9] - '0';
op.cl_device_version = cl_version_maj * 100 + cl_version_min * 10;
size_t ext_str_size_ret;
CL_SAFE_CALL(clGetDeviceInfo(device_list, CL_DEVICE_EXTENSIONS, 0, nullptr,
&ext_str_size_ret));
char buffer2[ext_str_size_ret];
CL_SAFE_CALL(clGetDeviceInfo(device_list, CL_DEVICE_EXTENSIONS,
ext_str_size_ret, buffer2, nullptr));
#if defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)
if (op.cl_device_version >= 210) {
if ((std::string(buffer2).find("cl_khr_subgroups") != std::string::npos) ||
(std::string(buffer2).find("cl_intel_subgroups") != std::string::npos))
op.has_subgroup_support=true;
if (std::string(buffer2).find("cl_intel_subgroups") != std::string::npos)
op.has_shuffle_support=true;
}
#endif
if (std::string(buffer2).find("cl_nv_device_attribute_query") !=
std::string::npos) {
#ifndef CL_DEVICE_COMPUTE_CAPABILITY_MAJOR_NV
#define CL_DEVICE_COMPUTE_CAPABILITY_MAJOR_NV 0x4000
#endif
#ifndef CL_DEVICE_COMPUTE_CAPABILITY_MINOR_NV
#define CL_DEVICE_COMPUTE_CAPABILITY_MINOR_NV 0x4001
#endif
cl_uint major, minor;
CL_SAFE_CALL(clGetDeviceInfo(device_list,
CL_DEVICE_COMPUTE_CAPABILITY_MAJOR_NV,
sizeof(cl_uint), &major, nullptr));
CL_SAFE_CALL(clGetDeviceInfo(device_list,
CL_DEVICE_COMPUTE_CAPABILITY_MINOR_NV,
sizeof(cl_uint), &minor, nullptr));
double arch = static_cast<double>(minor)/10+major;
if (arch >= 3.0)
op.has_shuffle_support=true;
}
#endif
_properties.push_back(op);
@ -516,7 +695,7 @@ std::string UCL_Device::device_type_name(const int i) {
}
// Get a string telling the type of the device
int UCL_Device::device_type(const int i) {
enum UCL_DEVICE_TYPE UCL_Device::device_type(const int i) {
if (_properties[i].device_type==CL_DEVICE_TYPE_CPU)
return UCL_CPU;
else if (_properties[i].device_type==CL_DEVICE_TYPE_GPU)
@ -529,14 +708,8 @@ int UCL_Device::device_type(const int i) {
// Set the CUDA device to the specified device number
int UCL_Device::set(int num) {
cl_device_id *device_list = new cl_device_id[_num_devices];
cl_uint n;
CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,_num_devices,
device_list,&n));
_device=num;
_cl_device=device_list[_device];
delete[] device_list;
_cl_device=_cl_devices[_device];
return create_context();
}
@ -555,6 +728,11 @@ void UCL_Device::print_all(std::ostream &out) {
out << "\nDevice " << i << ": \"" << name(i).c_str() << "\"\n";
out << " Type of device: "
<< device_type_name(i).c_str() << std::endl;
out << " Is a subdevice: ";
if (is_subdevice(i))
out << "Yes\n";
else
out << "No\n";
out << " Double precision support: ";
if (double_precision(i))
out << "Yes\n";
@ -613,31 +791,91 @@ void UCL_Device::print_all(std::ostream &out) {
out << "No\n";
out << " Maximum subdevices from fission: "
<< max_sub_devices(i) << std::endl;
out << " Shared memory system: ";
if (shared_memory(i))
out << "Yes\n";
else
out << "No\n";
}
}
}
// Select the platform that is associated with accelerators
// if pid < 0, select the first platform
int UCL_Device::set_platform_accelerator(int pid) {
if (pid < 0) {
int found = 0;
for (int n=0; n<_num_platforms; n++) {
set_platform(n);
for (int i=0; i<num_devices(); i++) {
if ((_properties[i].device_type & CL_DEVICE_TYPE_CPU) ||
(_properties[i].device_type & CL_DEVICE_TYPE_GPU) ||
(_properties[i].device_type & CL_DEVICE_TYPE_ACCELERATOR)) {
found = 1;
break;
}
}
if (found) return UCL_SUCCESS;
}
return UCL_ERROR;
} else {
return set_platform(pid);
int UCL_Device::auto_set_platform(const enum UCL_DEVICE_TYPE type,
const std::string vendor,
const int ndevices,
const int first_device) {
if (_num_platforms < 2) return set_platform(0);
int last_device = -1;
if (first_device > -1) {
if (ndevices)
last_device = first_device + ndevices - 1;
else
last_device = first_device;
}
bool vendor_match=false;
bool type_match=false;
int max_cus=0;
int best_platform=0;
std::string vendor_upper=vendor;
for (int i=0; i<vendor.length(); i++)
if (vendor_upper[i]<='z' && vendor_upper[i]>='a')
vendor_upper[i]=toupper(vendor_upper[i]);
for (int n=0; n<_num_platforms; n++) {
set_platform(n);
if (last_device > -1 && last_device >= num_devices()) continue;
if (ndevices > num_devices()) continue;
int first_id=0;
int last_id=num_devices()-1;
if (last_device > -1) {
first_id=first_device;
last_id=last_device;
}
if (vendor_upper!="") {
std::string pname = platform_name();
for (int i=0; i<pname.length(); i++)
if (pname[i]<='z' && pname[i]>='a')
pname[i]=toupper(pname[i]);
if (pname.find(vendor_upper)!=std::string::npos) {
if (vendor_match == false) {
best_platform=n;
max_cus=0;
vendor_match=true;
}
} else if (vendor_match)
continue;
}
if (type != UCL_DEFAULT) {
bool ptype_matched=false;
for (int d=first_id; d<=last_id; d++) {
if (type==device_type(d)) {
if (type_match == false) {
best_platform=n;
max_cus=0;
type_match=true;
ptype_matched=true;
}
}
}
if (type_match==true && ptype_matched==false)
continue;
}
for (int d=first_id; d<=last_id; d++) {
if (cus(d) > max_cus) {
best_platform=n;
max_cus=cus(d);
}
}
}
return set_platform(best_platform);
}
} // namespace ucl_opencl

115
lib/gpu/geryon/ocl_kernel.h
View File

@ -2,6 +2,7 @@
ocl_kernel.h
-------------------
W. Michael Brown
Nitin Dhamankar (Intel)
Utilities for dealing with OpenCL kernels
@ -26,6 +27,7 @@
#include "ocl_device.h"
#include <fstream>
#include <cstdio>
namespace ucl_opencl {
@ -93,7 +95,7 @@ class UCL_Program {
/// Load a program from a string and compile with flags
inline int load_string(const void *program, const char *flags="",
std::string *log=nullptr) {
std::string *log=nullptr, FILE* foutput=nullptr) {
cl_int error_flag;
const char *prog=(const char *)program;
_program=clCreateProgramWithSource(_context,1,&prog,nullptr,&error_flag);
@ -107,27 +109,66 @@ class UCL_Program {
sizeof(cl_build_status),&build_status,
nullptr));
if (build_status != CL_SUCCESS || log!=nullptr) {
#ifdef GERYON_KERNEL_DUMP
{
size_t ms;
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,0,
nullptr, &ms));
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,
0,NULL,&ms));
char *build_log = new char[ms];
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,ms,
build_log, nullptr));
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,
ms,build_log, NULL));
std::cout << std::endl << std::endl
<< "--------------------------------------------------------\n"
<< " UCL PROGRAM DUMP\n"
<< "--------------------------------------------------------\n"
<< flags << std::endl
<< "--------------------------------------------------------\n"
<< prog << std::endl
<< "--------------------------------------------------------\n"
<< build_log
<< "--------------------------------------------------------\n"
<< std::endl << std::endl;
}
#endif
if (build_status != CL_SUCCESS || log!=NULL) {
size_t ms;
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,
0,NULL,&ms));
char *build_log = new char[ms];
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,
ms,build_log, NULL));
if (log!=nullptr)
*log=std::string(build_log);
if (build_status != CL_SUCCESS) {
#ifndef UCL_NO_EXIT
std::cerr << std::endl
<< "----------------------------------------------------------\n"
<< " UCL Error: Error compiling OpenCL Program ("
<< build_status << ") ...\n"
<< "----------------------------------------------------------\n";
std::cerr << std::endl << std::endl
<< "----------------------------------------------------------\n"
<< " UCL Error: Error compiling OpenCL Program ("
<< build_status << ") ...\n"
<< "----------------------------------------------------------\n";
std::cerr << build_log << std::endl;
std::cerr <<
"----------------------------------------------------------\n"
<< std::endl << std::endl;
#endif
delete[] build_log;
if (foutput != NULL) {
fprintf(foutput,"\n\n");
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,
" UCL Error: Error compiling OpenCL Program (%d) ...\n",
build_status);
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,"%s\n",build_log);
fprintf(foutput,
"----------------------------------------------------------\n");
fprintf(foutput,"\n\n");
}
delete[] build_log;
return UCL_COMPILE_ERROR;
} else delete[] build_log;
}
@ -141,6 +182,7 @@ class UCL_Program {
inline void cq(command_queue &cq_in) { _cq=cq_in; }
friend class UCL_Kernel;
friend class UCL_Const;
private:
bool _init_done;
cl_program _program;
@ -322,9 +364,45 @@ class UCL_Kernel {
inline void cq(command_queue &cq_in) { _cq=cq_in; }
#include "ucl_arg_kludge.h"
#if defined(CL_VERSION_2_1) || defined(CL_VERSION_3_0)
inline size_t max_subgroup_size(const size_t block_size_x) {
size_t block_size = block_size_x;
CL_SAFE_CALL(clGetKernelSubGroupInfo(_kernel, _device,
CL_KERNEL_MAX_SUB_GROUP_SIZE_FOR_NDRANGE,
sizeof(block_size), (void *) &block_size,
sizeof(size_t), (void *) &_mx_subgroup_sz,
NULL));
return _mx_subgroup_sz;
}
inline size_t max_subgroup_size(const size_t block_size_x,
const size_t block_size_y) {
size_t block_size[2] { block_size_x, block_size_y };
CL_SAFE_CALL(clGetKernelSubGroupInfo(_kernel, _device,
CL_KERNEL_MAX_SUB_GROUP_SIZE_FOR_NDRANGE,
sizeof(block_size), (void *) &block_size,
sizeof(size_t), (void *) &_mx_subgroup_sz,
NULL));
return _mx_subgroup_sz;
}
inline size_t max_subgroup_size(const size_t block_size_x,
const size_t block_size_y,
const size_t block_size_z) {
size_t block_size[3] { block_size_x, block_size_y, block_size_z };
CL_SAFE_CALL(clGetKernelSubGroupInfo(_kernel, _device,
CL_KERNEL_MAX_SUB_GROUP_SIZE_FOR_NDRANGE,
sizeof(block_size), (void *) &block_size,
sizeof(size_t), (void *) &_mx_subgroup_sz,
NULL));
return _mx_subgroup_sz;
}
#endif
private:
cl_kernel _kernel;
cl_program _program;
cl_device_id _device;
cl_uint _dimensions;
size_t _block_size[3];
size_t _num_blocks[3];
@ -338,6 +416,11 @@ class UCL_Kernel {
unsigned _kernel_info_nargs;
//std::string _kernel_info_args[256];
#endif
#ifdef CL_VERSION_2_1
size_t _mx_subgroup_sz; // Maximum sub-group size for this kernel
#endif
};
inline int UCL_Kernel::set_function(UCL_Program &program, const char *function) {
@ -347,6 +430,7 @@ inline int UCL_Kernel::set_function(UCL_Program &program, const char *function)
CL_SAFE_CALL(clRetainCommandQueue(_cq));
_program=program._program;
CL_SAFE_CALL(clRetainProgram(_program));
_device=program._device;
cl_int error_flag;
_kernel=clCreateKernel(program._program,function,&error_flag);
@ -380,8 +464,11 @@ inline int UCL_Kernel::set_function(UCL_Program &program, const char *function)
}
void UCL_Kernel::run() {
CL_SAFE_CALL(clEnqueueNDRangeKernel(_cq,_kernel,_dimensions,nullptr,
_num_blocks,_block_size,0,nullptr,nullptr));
CL_SAFE_CALL(clEnqueueNDRangeKernel(_cq,_kernel,_dimensions,NULL,
_num_blocks,_block_size,0,NULL,NULL));
#ifdef GERYON_OCL_FLUSH
ucl_flush(_cq);
#endif
}
} // namespace

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