Merge branch 'master' into mliap_nn

cmake/CMakeLists.txt

@@ -26,7 +26,14 @@ find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
+option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
+if (LAMMPS_INSTALL_RPATH)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
@@ -156,8 +163,7 @@ if(BUILD_MPI)
     endif()
   endif()
 else()
-  enable_language(C)
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
-  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
   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 +784,7 @@ if(PKG_GPU)
   message(STATUS "<<< GPU package settings >>>
 -- GPU API:          ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
-    message(STATUS "GPU architecture: ${GPU_ARCH}")
+    message(STATUS "GPU default architecture: ${GPU_ARCH}")
-  elseif(GPU_API STREQUAL "OPENCL")
-    message(STATUS "OpenCL tuning:    ${OCL_TUNE}")
   elseif(GPU_API STREQUAL "HIP")
     message(STATUS "HIP platform:     ${HIP_PLATFORM}")
     message(STATUS "HIP architecture: ${HIP_ARCH}")

cmake/Modules/Documentation.cmake

@@ -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 $ENV{PIP_OPTIONS} install --upgrade pip
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} 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 -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
   # download mathjax distribution and unpack to folder "mathjax"

cmake/Modules/GTest.cmake

@@ -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${GTEST_LIB_POSTFIX}.a
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
+                                     <BINARY_DIR>/lib/libgmock_main${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(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
-set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
-set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
-set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
+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

cmake/Modules/OpenCLLoader.cmake

@@ -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}")
+
+

cmake/Modules/Packages/GPU.cmake

@@ -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(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
-    # download and unpack support binaries for compilation of windows binaries.
+  mark_as_advanced(USE_STATIC_OPENCL_LOADER)
-    set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
+  if (USE_STATIC_OPENCL_LOADER)
-    file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
+    include(OpenCLLoader)
-            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")
   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}")
-
+# detect styles which have a GPU version
-# detects styles which have GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
 

cmake/Modules/Packages/KIM.cmake

@@ -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()

cmake/Modules/Packages/MESSAGE.cmake

@@ -2,8 +2,7 @@ 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
+file(GLOB_RECURSE cslib_SOURCES
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
         ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
 add_library(cslib STATIC ${cslib_SOURCES})

cmake/Modules/YAML.cmake

@@ -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

doc/Makefile

@@ -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 $(PIP_OPTIONS) install --upgrade pip; \
-		pip install -r $(BUILDDIR)/utils/requirements.txt; \
+		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)
 	@( \

doc/src/Build_basics.rst

@@ -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
@@ -526,6 +526,20 @@ you want to copy files to is protected.
          make                        # perform make after CMake command
          make install                # perform the installation into prefix
 
+      During the installation process CMake will by default remove any runtime
+      path settings for loading shared libraries.  Because of this you may
+      have to set or modify the ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH``)
+      environment variable, if you are installing LAMMPS into a non-system
+      location and/or are linking to libraries in a non-system location that
+      depend on such runtime path settings.
+      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      to ``on`` and then the runtime paths for any linked shared libraries
+      and the library installation folder for the LAMMPS library will be
+      embedded and thus the requirement to set environment variables is avoided.
+      The ``off`` setting is usually preferred for packaged binaries or when
+      setting up environment modules, the ``on`` setting is more convenient
+      for installing software into a non-system or personal folder.
+
    .. tab:: Traditional make
 
       There is no "install" option in the ``src/Makefile`` for LAMMPS.

doc/src/Build_extras.rst

@@ -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
+also need to install the ``kim-property`` Python package, which can be easily
-*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
+done using *pip* as ``pip install kim-property``, or from the *conda-forge*
-``conda install kim-property`` if LAMMPS is built in Conda. More detailed
+channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
-information is available at:
+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.
 
@@ -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_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
-  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
+  ``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.

doc/src/Build_link.rst

@@ -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 the LAMMPS library unless LAMMPS is to be compiled without (real)
-   and uses definitions from it so those need to be available and
+   MPI support using the include STUBS MPI library.
-   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.
 
 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

doc/src/Build_manual.rst

@@ -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
 

doc/src/Commands_all.rst

@@ -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 <kim_commands>`
-   * :doc:`kim_interactions <kim_commands>`
-   * :doc:`kim_param <kim_commands>`
-   * :doc:`kim_property <kim_commands>`
-   * :doc:`kim_query <kim_commands>`
    * :doc:`kspace_modify <kspace_modify>`
    * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`

doc/src/Commands_fix.rst

@@ -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 (giko) <fix_nve>`
-   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :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>`

doc/src/Commands_pair.rst

@@ -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>`

doc/src/Developer_utils.rst

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

doc/src/Howto_cmake.rst

@@ -296,6 +296,8 @@ Some common CMake variables
      - Description
    * - ``CMAKE_INSTALL_PREFIX``
      - root directory of install location for ``make install``  (default: ``$HOME/.local``)
+   * - ``LAMMPS_INSTALL_RPATH``
+     - set or remove runtime path setting from binaries for ``make install`` (default: ``off``)
    * - ``CMAKE_BUILD_TYPE``
      - controls compilation options:
        one of ``RelWithDebInfo`` (default), ``Release``, ``Debug``, ``MinSizeRel``

doc/src/Install_tarball.rst

@@ -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
+You can also download a compressed tar or zip archives from the
-the `LAMMPS GitHub site <git_>`_.  The file name will be lammps-master.zip
+"Assets" sections of the `LAMMPS GitHub releases site <git_>`_.
-which can be unzipped with the following command, to create
+The file name will be lammps-<version>.zip which can be unzipped
-a lammps-master dir:
+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
+This version corresponds to the selected LAMMPS patch or stable
-will have the date of the most recent patch release (see the file
+release.
-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.
 
-.. _git: https://github.com/lammps/lammps
+.. _git: https://github.com/lammps/lammps/releases
 
 ----------
 

doc/src/Intro_features.rst

@@ -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
 

doc/src/Packages_details.rst

@@ -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
+This includes :doc:`kim init <kim_commands>`, and
-instantiate the IM, a :doc:`kim_query <kim_commands>` command to perform web
+: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
+:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
-LAMMPS, and a :doc:`kim_property <kim_commands>` command to write material
+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
+   The command *pair_style kim* is called by *kim interactions* and is not
-   is not recommended to be directly used in input scripts.
+   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

doc/src/Python_atoms.rst

@@ -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
 

doc/src/Python_formats.rst

@@ -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:

doc/src/Python_head.rst

@@ -13,6 +13,7 @@ together.
    Python_module
    Python_ext
    Python_call
+   Python_formats
    Python_examples
    Python_error
    Python_trouble

doc/src/Python_module.rst

@@ -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_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
+   :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_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
+   :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:

doc/src/Python_neighbor.rst

@@ -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() <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.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)
+* :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)

doc/src/Python_objects.rst

@@ -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_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
-      :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`, and
+      :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
-      :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>` are
+      :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_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.extract_fix()>`: extract value(s) from a fix, 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.extract_variable()>`: extract value(s) from a variable, 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

doc/src/Speed_gpu.rst

@@ -1,11 +1,14 @@
 GPU package
 ===========
 
-The GPU package was developed by Mike Brown while at SNL and ORNL
+The GPU package was developed by Mike Brown while at SNL and ORNL (now
-and his collaborators, particularly Trung Nguyen (now at Northwestern).
+at Intel Corp.) and his collaborators, particularly Trung Nguyen (now at
-It provides GPU versions of many pair styles and for parts of the
+Northwestern).  Support for AMD GPUs via HIP was added by Vsevolod Nikolskiy
-:doc:`kspace_style pppm <kspace_style>` for long-range Coulombics.
+and coworkers at HSE University.
-It has the following general features:
+
+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
+  either Nvidia support, AMD support, or more general OpenCL support
-  same functionality is supported on a variety of hardware.
+  (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,
+as 'platforms'.  The GPU library will try to auto-select the best suitable platform,
-but this can be overridden using the device option of the :doc:`package <package>`
+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
+:doc:`package gpu 0 <package>` command, which will result in
-GPUs/node to 1.
+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

doc/src/Speed_packages.rst

@@ -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
+  on Intel, NVIDIA, or AMD GPUs.  The speed-up on a GPU depends on a
-  factors, discussed in the accelerator sections.
+  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,

doc/src/compute_fep.rst

@@ -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 |
 +------------------------------------------------------------------------------+-------------------------+------------+

doc/src/compute_temp_chunk.rst

@@ -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
 
 ----------
 

doc/src/create_box.rst

@@ -13,7 +13,7 @@ Syntax
 * N = # of atom types to use in this simulation
 * region-ID = ID of region to use as simulation domain
 * zero or more keyword/value pairs may be appended
-* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
+* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom*
 
   .. parsed-literal::
 

doc/src/fix_adapt.rst

@@ -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  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+

doc/src/fix_adapt_fep.rst

@@ -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 |
 +------------------------------------------------------------------------------+-------------------------+------------+

doc/src/fix_nh.rst

@@ -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
 ===============

doc/src/fix_nve.rst

@@ -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
 """"""

doc/src/fix_nve_asphere.rst

@@ -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
 """"""

doc/src/fix_wall_body_polygon.rst

@@ -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::

doc/src/fix_wall_gran.rst

@@ -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 |
 +-------+----------------------------------------------------+----------------+

doc/src/fix_wall_gran_region.rst

@@ -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 |
 +-------+----------------------------------------------------+----------------+

doc/src/package.rst

@@ -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
+           *tpa* value = Nlanes
-             first = ID of first GPU to be used on each node
+             Nlanes = # of GPU vector lanes (CUDA threads) used per atom
-             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)
            *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 0 omp 2 device_type intelgpu
-   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 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
+The *Ngpu* argument sets the number of GPUs per node. If *Ngpu* is 0
-at least as many MPI tasks per node as GPUs, as set by the mpirun or
+and no other keywords are specified, GPU or accelerator devices are
-mpiexec command.  If there are more MPI tasks (per node)
+auto-selected. In this process, all platforms are searched for
-than GPUs, multiple MPI tasks will share each GPU.
+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
+If *binsize* is set to 0.0 (the default), then the binsize is set
-pairwise cutoff + neighbor skin distance.  This is 2x larger than the
+automatically using heuristics in the GPU package.
-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.
 
 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
+The *gpuID* keyword is used to specify the first ID for the GPU or
-be used for a simulation.  The *first* and *last* values specify the
+other accelerator that LAMMPS will use. For example, if the ID is
-GPU IDs to use (from 0 to Ngpu-1).  By default, first = 0 and last =
+1 and *Ngpu* is 3, GPUs 1-3 will be used. Device IDs should be
-Ngpu-1, so that all GPUs are used, assuming Ngpu is set to the number
+determined from the output of nvc_get_devices, ocl_get_devices,
-of physical GPUs.  If you only wish to use a subset, set Ngpu to a
+or hip_get_devices
-smaller number and first/last to a sub-range of the available GPUs.
+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
+the value can improve performance. The number of lanes per atom must
-be a power of 2 and currently cannot be greater than 32.
+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
-The *device* keyword can be used to tune parameters optimized for a
+will automatically be decreased to meet the restriction.
-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 *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
+The *Nthreads* value for the *omp* keyword sets the number of OpenMP
-for each MPI task when any portion of the interactions computed by a
+threads allocated for each MPI task. This setting controls OpenMP
-USER-INTEL pair style are run on the CPU.  This can be the case even
+parallelism only for routines run on the CPUs. For more details on
-if LAMMPS was built with co-processor support; see the *balance*
+setting the number of OpenMP threads, see the discussion of the
-keyword discussion below.  If you are running with less MPI tasks/node
+*Nthreads* setting on this doc page for the "package omp" command.
-than there are CPUs, it can be advantageous to use OpenMP threading on
+The meaning of *Nthreads* is exactly the same for the GPU, USER-INTEL,
-the CPUs.
+and GPU packages.
-
-.. 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 *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>`.

doc/src/pair_adp.rst

@@ -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.
 
 ----------
 

doc/src/pair_charmm.rst

@@ -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
 =================================================

doc/src/pair_eam.rst

@@ -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.
 
 ----------
 

doc/src/pair_kim.rst

@@ -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
+This pair style is a wrapper on the
-potentials to enable their use in LAMMPS scripts.
+`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,
+   Since *pair_style kim* is called by *kim interactions* as needed,
-   is not recommended to be directly used in input scripts.
+   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
 """""""

doc/utils/requirements.txt

@@ -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

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -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",
+"improper_style", "include", "info", "jump", "kim",
-"kim_param", "kim_query", "kspace_modify", "kspace_style", "label", "lattice",
+"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",

doc/utils/sphinx-config/false_positives.txt

@@ -2300,6 +2300,7 @@ omegaz
 Omelyan
 omp
 OMP
+oneAPI
 onelevel
 oneway
 onn
@@ -2369,6 +2370,7 @@ parmin
 Parrinello
 Partay
 Particuology
+Pascuet
 pastewka
 Pastewka
 pathangle
@@ -2531,6 +2533,7 @@ ptm
 PTM
 ptol
 ptr
+PTX
 pu
 purdue
 Purohit

examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane

@@ -26,7 +26,7 @@ Masses
 7 12.0112
 8 1.00797
 
-Pair Coeffs # lj/class2/coul/long
+Pair Coeffs # hybrid
 
 1 lj/class2/coul/long 0.054 4.01
 2 lj/class2/coul/long 0.054 4.01

examples/USER/fep/C7inEthanol/fep01/in.insertion

@@ -12,7 +12,7 @@ improper_style  class2
 pair_modify     mix sixthpower tail yes
 special_bonds   lj/coul 0 0 1
 
-read_data       data.init_conf_without_heptane
+read_data       data.init_conf_with_heptane
 
 pair_coeff    1    6  lj/class2/coul/long/soft   0.054 4.01 0.0
 pair_coeff    2    6  lj/class2/coul/long/soft   0.054 4.01 0.0
@@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
   atom charge 8 v_q3 &
   after yes
 
-thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
 thermo_modify line one
 thermo          100
 

examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane

@@ -26,7 +26,7 @@ Masses
 7 12.0112
 8 1.00797
 
-Pair Coeffs # lj/class2/coul/long
+Pair Coeffs # hybrid
 
 1 lj/class2/coul/long 0.054 4.01
 2 lj/class2/coul/long 0.054 4.01

examples/USER/fep/C7inEthanol/fep10/in.deletion

@@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
   atom charge 8 v_q3 &
   after yes
 
-thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
+thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
 thermo_modify line one
 thermo          100
 

examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability

@@ -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

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

@@ -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

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

@@ -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

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

@@ -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

examples/kim/in.kim-ex.melt

@@ -1,8 +1,8 @@
 # 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
+# the kim-api package are installed.  see the `./lib/kim/README` or
-# ./lib/kim/Install.py files for details on how to install these
+# `./lib/kim/Install.py` files for details on how to install these
 # example models.
 #
 
@@ -14,14 +14,14 @@ 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
 
-kim_interactions Ar
+kim          interactions Ar
 
 mass         1 39.95
 velocity     all create 200.0 232345 loop geom

examples/kim/in.kim-pm-property

@@ -1,7 +1,7 @@
-# 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:
 #
@@ -10,10 +10,10 @@
 # `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://openkim.org/doc/schema/properties-framework/` and
-# https://lammps.sandia.gov/doc/kim_commands.html for further details).
+# `https://lammps.sandia.gov/doc/kim_commands.html` for further details).
-# Then the created property instance is written to a file named results.edn 
+# Then the created property instance is written to a file named `results.edn`
-# using the `kim_property dump` commands.  
+# 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
@@ -62,7 +62,7 @@ create_atoms 1 box
 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"

examples/kim/in.kim-pm-query.melt

@@ -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.
@@ -13,7 +13,7 @@
 #   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
@@ -24,15 +24,15 @@ 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
-kim_query       a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
+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
 
-kim_interactions Si
+kim          interactions Si
 
 mass         1 39.95
 velocity     all create 200.0 232345 loop geom

examples/kim/in.kim-pm.melt

@@ -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.
@@ -13,7 +13,7 @@
 #   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
@@ -24,14 +24,14 @@ 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
 
-kim_interactions Si
+kim          interactions Si
 
 mass         1 39.95
 velocity     all create 200.0 232345 loop geom

examples/kim/in.kim-query

@@ -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
+

examples/kim/in.kim-sm.melt

@@ -1,7 +1,7 @@
 # 3d Lennard-Jones melt
 #
 # This example requires that the KIM Simulator Model (PM)
-# Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
+# `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.
@@ -13,7 +13,7 @@
 #   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
@@ -24,14 +24,14 @@ 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
 
-kim_interactions O
+kim          interactions O
 
 mass         1 39.95
 velocity     all create 200.0 232345 loop geom

examples/kim/log.10Feb21.in.kim-ex.melt.clang.1

@@ -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

examples/kim/log.10Feb21.in.kim-ex.melt.clang.4

@@ -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

examples/kim/log.10Feb21.in.kim-pm-property.clang.1

@@ -0,0 +1,238 @@
+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

examples/kim/log.10Feb21.in.kim-pm-property.clang.4

@@ -0,0 +1,238 @@
+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

examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.1

@@ -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 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

examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.4

@@ -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

examples/kim/log.10Feb21.in.kim-pm.melt.clang.1

@@ -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

examples/kim/log.10Feb21.in.kim-pm.melt.clang.4

@@ -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 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

examples/kim/log.10Feb21.in.kim-query.clang.1

@@ -0,0 +1,685 @@
+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

examples/kim/log.10Feb21.in.kim-sm.melt.clang.1

@@ -0,0 +1,223 @@
+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

examples/kim/log.10Feb21.in.kim-sm.melt.clang.4

@@ -0,0 +1,223 @@
+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

examples/kim/log.10Feb21.in.lammps.melt.clang.1

@@ -0,0 +1,88 @@
+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

examples/kim/log.10Feb21.in.lammps.melt.clang.4

@@ -0,0 +1,88 @@
+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

examples/kim/log.7Aug19.in.kim-ex.melt.clang.1

@@ -1,107 +0,0 @@
-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

examples/kim/log.7Aug19.in.kim-ex.melt.clang.4

@@ -1,113 +0,0 @@
-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

examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.1

@@ -1,124 +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 ============================================
-
-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

examples/kim/log.7Aug19.in.kim-pm-query.melt.clang.4

@@ -1,124 +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 ============================================
-
-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

examples/kim/log.7Aug19.in.kim-pm.melt.clang.1

@@ -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 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

examples/kim/log.7Aug19.in.kim-pm.melt.clang.4

@@ -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

examples/kim/log.7Aug19.in.kim-sm.melt.clang.1

@@ -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
---------------------------------------------------------------------------

examples/kim/log.7Aug19.in.kim-sm.melt.clang.4

@@ -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

examples/kim/log.7Aug19.in.lammps.melt.clang.1

@@ -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

examples/kim/log.7Aug19.in.lammps.melt.clang.4

@@ -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

lib/gpu/Makefile.cuda_mps

@@ -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)

lib/gpu/Makefile.hip

@@ -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

lib/gpu/Makefile.lammps.mac_ocl

@@ -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 = 

lib/gpu/Makefile.linux_opencl

@@ -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_INC = 
-OCL_CPP = mpic++ $(DEFAULT_DEVICE) -O3 -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC) -std=c++11
+OCL_CPP = mpic++ -std=c++11 -O3 -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
-OCL_LINK = -L/usr/local/cuda/lib64 -lOpenCL
+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
-

lib/gpu/Makefile.mac_opencl

@@ -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
+LMP_INC = -DLAMMPS_SMALLBIG
-# 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_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 = ./

lib/gpu/Makefile.mac_opencl_mpi

@@ -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
+

lib/gpu/Makefile.oneapi

@@ -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

lib/gpu/Makefile.opencl

@@ -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
-

lib/gpu/Nvidia.makefile

@@ -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

lib/gpu/Opencl.makefile

@@ -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
+OCL_H  = $(wildcard ./geryon/ocl*.h) $(UCL_H) lal_precision.h
-PRE1_H = lal_preprocessor.h lal_aux_fun1.h
+
-ALL_H  =  $(OCL_H) $(wildcard ./lal_*.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)