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lammps
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Merge branch 'master' into viscosity

This commit is contained in:
Axel Kohlmeyer 2020-04-30 12:32:06 -04:00
parent 26321d49c4 c39b71cd1b
commit 5062d57ccb
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GPG Key ID: D9B44E93BF0C375A
60 changed files with 236 additions and 907 deletions
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35
cmake/CMakeLists.txt
View File

@ -160,9 +160,6 @@ else()
enable_language(C)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
@ -249,9 +246,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS linalg EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
@ -411,9 +405,6 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
@ -520,14 +511,15 @@ endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
add_dependencies(lammps ${_HEADER})
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
if(BUILD_SHARED_LIBS)
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
endif()
endforeach()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
add_library(LAMMPS::lammps ALIAS lammps)
@ -536,15 +528,18 @@ set(LAMMPS_API_DEFINES)
foreach(_DEF ${LAMMPS_DEFINES})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
endforeach()
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
include(CMakePackageConfigHelpers)
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
if(BUILD_SHARED_LIBS)
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
include(CMakePackageConfigHelpers)
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
endif()
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
if(BUILD_TOOLS)

78
cmake/LAMMPSConfig.cmake.in
View File

@ -1,4 +1,4 @@
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
include(CMakeFindDependencyMacro)
if(@BUILD_MPI@)
find_dependency(MPI REQUIRED CXX)
@ -8,80 +8,4 @@ if(@PKG_KSPACE@)
find_dependency(@FFTW@ REQUIRED MODULE)
endif()
endif()
if(NOT @BUILD_SHARED_LIBS@)
if(@BUILD_OMP@)
find_dependency(OpenMP REQUIRED)
endif()
if(@WITH_JPEG@)
find_dependency(JPEG REQUIRED)
endif()
if(@WITH_PNG@)
find_dependency(PNG REQUIRED)
find_dependency(ZLIB REQUIRED)
endif()
if(@PKG_KIM@)
find_dependency(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=@KIM-API_MIN_VERSION@)
if(@CURL_FOUND@)
find_dependency(CURL REQUIRED)
endif()
endif()
if(@PKG_USER-SMD@)
find_dependency(Eigen3 NO_MODULE REQUIRED)
endif()
if(@PKG_USER-SCAFACOS@)
find_dependency(PkgConfig REQUIRED)
find_ependency(GSL REQUIRED)
find_dependency(MPI REQUIRED C Fortran)
pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
endif()
if(@PKG_PYTHON@ AND NOT CMAKE_VERSION VERSION_LESS 3.12)
find_package(Python REQUIRED COMPONENTS Development)
endif()
if(@PKG_COMPRESS@)
find_dependency(ZLIB REQUIRED)
endif()
if(@PKG_KOKKOS@)
if(@EXTERNAL_KOKKOS@)
find_dependency(Kokkos 3 REQUIRED)
endif()
endif()
if(@PKG_VORONOI@)
find_dependency(VORO REQUIRED)
endif()
if(@PKG_USER-INTEL@)
if(@INTEL_LRT_MODE@ STREQUAL "THREADS")
find_dependency(Threads REQUIRED)
endif()
if(@TBB_MALLOC_FOUND@)
find_ependency(TBB_MALLOC REQUIRED)
endif()
endif()
if(@PKG_USER-ADIOS@)
find_ependency(ADIOS2 REQUIRED)
endif()
if(@PKG_LATTE@)
find_ependency(LATTE REQUIRED)
endif()
if(@PKG_MESSAGE@)
if(@MESSAGE_ZMQ@)
find_ependency(ZMQ REQUIRED)
endif()
endif()
if(@PKG_MSCG@)
find_ependency(GSL REQUIRED)
find_ependency(MSCG REQUIRED)
endif()
if(@USER-NETCDF@)
if(@NETCDF_FOUND@)
find_ependency(NetCDF REQUIRED)
endif()
if(@PNETCDF_FOUND@)
find_ependency(PNetCDF REQUIRED)
endif()
endif()
if(@PKG_QUIP@)
find_ependency(QUIP REQUIRED)
endif()
endif()
include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

3
cmake/Modules/Packages/GPU.cmake
View File

@ -365,9 +365,6 @@ if(NOT BUILD_MPI)
else()
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
endif()
if(NOT BUILD_SHARED_LIBS)
install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
target_sources(lammps PRIVATE ${GPU_SOURCES})

3
cmake/Modules/Packages/KIM.cmake
View File

@ -56,9 +56,6 @@ if(DOWNLOAD_KIM)
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
target_link_libraries(lammps PRIVATE LAMMPS::KIM)
add_dependencies(LAMMPS::KIM kim_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})

3
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -49,9 +49,6 @@ if(DOWNLOAD_KOKKOS)
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.1)
if(NOT Kokkos_FOUND)

3
cmake/Modules/Packages/LATTE.cmake
View File

@ -34,9 +34,6 @@ if(DOWNLOAD_LATTE)
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
add_dependencies(LAMMPS::LATTE latte_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(LATTE)
if(NOT LATTE_FOUND)

3
cmake/Modules/Packages/MESSAGE.cmake
View File

@ -7,9 +7,6 @@ file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
add_library(cslib STATIC ${cslib_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS cslib EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
if(BUILD_MPI)

3
cmake/Modules/Packages/MSCG.cmake
View File

@ -35,9 +35,6 @@ if(DOWNLOAD_MSCG)
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
add_dependencies(LAMMPS::MSCG mscg_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(MSCG)
if(NOT MSCG_FOUND)

6
cmake/Modules/Packages/USER-COLVARS.cmake
View File

@ -9,9 +9,6 @@ if(COLVARS_LEPTON)
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
add_library(lepton STATIC ${LEPTON_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS lepton EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
# Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
@ -19,9 +16,6 @@ if(COLVARS_LEPTON)
endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS colvars EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)

3
cmake/Modules/Packages/USER-MOLFILE.cmake
View File

@ -1,8 +1,5 @@
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
add_library(molfile INTERFACE)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS molfile EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
# no need to link with -ldl on windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")

3
cmake/Modules/Packages/USER-PLUMED.cmake
View File

@ -70,9 +70,6 @@ if(DOWNLOAD_PLUMED)
ExternalProject_get_property(plumed_build INSTALL_DIR)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")

6
cmake/Modules/Packages/USER-QMMM.cmake
View File

@ -1,12 +1,6 @@
enable_language(C)
if(NOT BUILD_SHARED_LIBS)
message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
endif()
add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS qmmm EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(qmmm PROPERTIES OUTPUT_NAME lammps_qmmm${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE qmmm)
target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)

3
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -52,9 +52,6 @@ if(DOWNLOAD_SCAFACOS)
INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libfcs.a;${INSTALL_DIR}/lib/libfcs_direct.a;${INSTALL_DIR}/lib/libfcs_ewald.a;${INSTALL_DIR}/lib/libfcs_fmm.a;${INSTALL_DIR}/lib/libfcs_p2nfft.a;${INSTALL_DIR}/lib/libfcs_p3m.a;GSL::gsl;${INSTALL_DIR}/lib/libfcs_near.a;${INSTALL_DIR}/lib/libfcs_gridsort.a;${INSTALL_DIR}/lib/libfcs_resort.a;${INSTALL_DIR}/lib/libfcs_redist.a;${INSTALL_DIR}/lib/libfcs_common.a;${INSTALL_DIR}/lib/libfcs_pnfft.a;${INSTALL_DIR}/lib/libfcs_pfft.a;${INSTALL_DIR}/lib/libfcs_fftw3_mpi.a;${INSTALL_DIR}/lib/libfcs_fftw3.a;MPI::MPI_Fortran;MPI::MPI_C")
target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
add_dependencies(LAMMPS::SCAFACOS scafacos_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)

3
cmake/Modules/Packages/USER-SMD.cmake
View File

@ -18,9 +18,6 @@ if(DOWNLOAD_EIGEN3)
set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)

3
cmake/Modules/Packages/VORONOI.cmake
View File

@ -35,9 +35,6 @@ if(DOWNLOAD_VORO)
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
target_link_libraries(lammps PRIVATE LAMMPS::VORO)
add_dependencies(LAMMPS::VORO voro_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(VORO)
if(NOT VORO_FOUND)

2
doc/src/Commands_compute.rst
View File

@ -87,7 +87,7 @@ KOKKOS, o = USER-OMP, t = OPT.
* :doc:`msd/chunk <compute_msd_chunk>`
* :doc:`msd/nongauss <compute_msd_nongauss>`
* :doc:`omega/chunk <compute_omega_chunk>`
* :doc:`orientorder/atom <compute_orientorder_atom>`
* :doc:`orientorder/atom (k) <compute_orientorder_atom>`
* :doc:`pair <compute_pair>`
* :doc:`pair/local <compute_pair_local>`
* :doc:`pe <compute_pe>`

8
doc/src/Howto_cmake.rst
View File

@ -378,9 +378,9 @@ change some variables later with additional *-D* flags. A few examples:
.. code-block:: bash
cmake -C ../cmake/preset/minimal.cmake -D PKG_MISC=on ../cmake
cmake -C ../cmake/preset/clang.cmake -C ../cmake/preset/most.cmake ../cmake
cmake -C ../cmake/preset/minimal.cmake -D BUILD_MPI=off ../cmake
cmake -C ../cmake/presets/minimal.cmake -D PKG_MISC=on ../cmake
cmake -C ../cmake/presets/clang.cmake -C ../cmake/presets/most.cmake ../cmake
cmake -C ../cmake/presets/minimal.cmake -D BUILD_MPI=off ../cmake
The first command will install the packages ``KSPACE``, ``MANYBODY``,
``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset
@ -396,7 +396,7 @@ It is also possible to do this incrementally.
.. code-block:: bash
cmake -C ../cmake/preset/minimal.cmake ../cmake
cmake -C ../cmake/presets/minimal.cmake ../cmake
cmake -D PKG_MISC=on .
will achieve the same configuration like in the first example above. In

68
doc/src/Install_linux.rst
View File

@ -24,12 +24,13 @@ allows you to install LAMMPS with a single command, and stay
up-to-date with the current version of LAMMPS by simply updating your
operating system.
To install the appropriate personal-package archive (PPA), do the
To install the appropriate personal-package archives (PPAs), do the
following once:
.. code-block:: bash
$ sudo add-apt-repository ppa:gladky-anton/lammps
$ sudo add-apt-repository ppa:openkim/latest
$ sudo apt-get update
To install LAMMPS do the following once:
@ -38,7 +39,7 @@ To install LAMMPS do the following once:
$ sudo apt-get install lammps-daily
This downloads an executable named "lmp_daily" to your box, which
This downloads an executable named ``lmp_daily`` to your box, which
can then be used in the usual way to run input scripts:
.. code-block:: bash
@ -60,11 +61,29 @@ To get a copy of the current documentation and examples:
$ sudo apt-get install lammps-daily-doc
which will download the doc files in
/usr/share/doc/lammps-daily-doc/doc and example problems in
/usr/share/doc/lammps-doc/examples.
``/usr/share/doc/lammps-daily-doc/doc`` and example problems in
``/usr/share/doc/lammps-doc/examples``.
Note that you may still wish to download the tarball to get potential
files and auxiliary tools.
To get a copy of the current potentials files:
.. code-block:: bash
$ sudo apt-get install lammps-daily-data
which will download the potentials files to
``/usr/share/lammps-daily/potentials``. The ``lmp_daily`` binary is
hard-coded to look for potential files in this directory (it does not
use the `LAMMPS_POTENTIALS` environment variable, as described
in :doc:`pair_coeff <pair_coeff>` command).
The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which
results in the above command also installing the `kim-api` binaries when LAMMPS
is installed. In order to use potentials from `openkim.org <openkim_>`_, you
can install the `openkim-models` package
.. code-block:: bash
$ sudo apt-get install openkim-models
To un-install LAMMPS, do the following:
@ -72,17 +91,8 @@ To un-install LAMMPS, do the following:
$ sudo apt-get remove lammps-daily
Note that the lammps-daily executable is built with the following
sequence of make commands, as if you had done the same with the
unpacked tarball files in the src directory:
.. code-block:: bash
$ make yes-all
$ make no-lib
$ make mpi
Thus it builds with FFTW3 and OpenMPI.
Please use ``lmp_daily -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
Ubuntu package capability.
@ -103,14 +113,14 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
lammps-openmpi-devel), the header for compiling programs using
the C library interface (lammps-headers), and the LAMMPS python
module for Python 3. All packages can be installed at the same
time and the name of the LAMMPS executable is *lmp* and *lmp_openmpi*
or *lmp_mpich* respectively. By default, *lmp* will refer to the
time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``
or ``lmp_mpich`` respectively. By default, ``lmp`` will refer to the
serial executable, unless one of the MPI environment modules is loaded
("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).
Then the corresponding parallel LAMMPS executable can be used.
The same mechanism applies when loading the LAMMPS python module.
To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
.. code-block:: bash
@ -118,10 +128,10 @@ To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
$ module load mpi/openmpi-x86_64
$ mpirun -np 2 lmp -in in.lj
The "dnf install" command is needed only once. In case of a new LAMMPS
stable release, "dnf update" will automatically update to the newer
The ``dnf install`` command is needed only once. In case of a new LAMMPS
stable release, ``dnf update`` will automatically update to the newer
version as soon at the RPM files are built and uploaded to the download
mirrors. The "module load" command is needed once per (shell) session
mirrors. The ``module load`` command is needed once per (shell) session
or shell terminal instance, unless it is automatically loaded from the
shell profile.
@ -134,7 +144,7 @@ can install the `openkim-models` package
$ dnf install openkim-models
Please use "lmp -help" to see which compilation options, packages,
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
@ -153,10 +163,10 @@ in the `Extra Packages for Enterprise Linux (EPEL) repository <https://fedorapro
for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
and compatible Linux distributions. Names of packages, executable,
and content are the same as described above for Fedora Linux.
But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
But RHEL/CentOS 7.x uses the ``yum`` package manager instead of ``dnf``
in Fedora 28.
Please use "lmp -help" to see which compilation options, packages,
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
@ -176,13 +186,13 @@ in OpenSuse as of Leap 15.0. You can install the package with:
$ zypper install lammps
This includes support for OpenMPI. The name of the LAMMPS executable
is *lmp*\ . Thus to run an input in parallel on 2 CPUs you would do:
is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do:
.. code-block:: bash
$ mpirun -np 2 lmp -in in.lj
Please use "lmp -help" to see which compilation options, packages,
Please use ``lmp -help`` to see which compilation options, packages,
and styles are included in the binary.
The LAMMPS binary is built with the :ref:`KIM package <kim>` which

2
doc/src/compute_orientorder_atom.rst
View File

@ -4,7 +4,7 @@ compute orientorder/atom command
================================
compute orientorder/atom/kk command
=======================
===================================
Syntax
""""""

22
src/KOKKOS/angle_charmm_kokkos.cpp
View File

@ -72,21 +72,21 @@ void AngleCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//if(k_eatom.extent(0)<maxeatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
d_eatom = k_eatom.template view<KKDeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.extent(0)<maxvatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
d_vatom = k_vatom.template view<KKDeviceType>();
//}
}
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
neighborKK->k_anglelist.template sync<DeviceType>();
anglelist = neighborKK->k_anglelist.view<DeviceType>();
anglelist = neighborKK->k_anglelist.view<KKDeviceType>();
int nanglelist = neighborKK->nanglelist;
nlocal = atom->nlocal;
newton_bond = force->newton_bond;
@ -265,10 +265,10 @@ void AngleCharmmKokkos<DeviceType>::coeff(int narg, char **arg)
AngleCharmm::coeff(narg, arg);
int n = atom->nangletypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k("AngleCharmm::k",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_theta0("AngleCharmm::theta0",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_k_ub("AngleCharmm::k_ub",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_r_ub("AngleCharmm::r_ub",n+1);
typename AT::tdual_ffloat_1d k_k("AngleCharmm::k",n+1);
typename AT::tdual_ffloat_1d k_theta0("AngleCharmm::theta0",n+1);
typename AT::tdual_ffloat_1d k_k_ub("AngleCharmm::k_ub",n+1);
typename AT::tdual_ffloat_1d k_r_ub("AngleCharmm::r_ub",n+1);
d_k = k_k.template view<DeviceType>();
d_theta0 = k_theta0.template view<DeviceType>();
@ -303,10 +303,10 @@ void AngleCharmmKokkos<DeviceType>::read_restart(FILE *fp)
AngleCharmm::read_restart(fp);
int n = atom->nangletypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k("AngleCharmm::k",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_theta0("AngleCharmm::theta0",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_k_ub("AngleCharmm::k_ub",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_r_ub("AngleCharmm::r_ub",n+1);
typename AT::tdual_ffloat_1d k_k("AngleCharmm::k",n+1);
typename AT::tdual_ffloat_1d k_theta0("AngleCharmm::theta0",n+1);
typename AT::tdual_ffloat_1d k_k_ub("AngleCharmm::k_ub",n+1);
typename AT::tdual_ffloat_1d k_r_ub("AngleCharmm::r_ub",n+1);
d_k = k_k.template view<DeviceType>();
d_theta0 = k_theta0.template view<DeviceType>();

8
src/KOKKOS/angle_charmm_kokkos.h
View File

@ -63,11 +63,13 @@ class AngleCharmmKokkos : public AngleCharmm {
typedef ArrayTypes<DeviceType> AT;
typename AT::t_x_array_randomread x;
typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
typedef typename KKDevice<DeviceType>::value KKDeviceType;
typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
typename AT::t_int_2d anglelist;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType> k_vatom;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;

21
src/KOKKOS/atom_vec_kokkos.h
View File

@ -153,15 +153,7 @@ class AtomVecKokkos : public AtomVec {
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.span());
buffer_size = src.span();
}
return mirror_type( buffer ,
src.extent(0) ,
src.extent(1) ,
src.extent(2) ,
src.extent(3) ,
src.extent(4) ,
src.extent(5) ,
src.extent(6) ,
src.extent(7) );
return mirror_type(buffer, src.d_view.layout());
}
template<class ViewType>
@ -179,15 +171,8 @@ class AtomVecKokkos : public AtomVec {
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.span()*sizeof(typename ViewType::value_type));
buffer_size = src.span();
}
mirror_type tmp_view( (typename ViewType::value_type*)buffer ,
src.extent(0) ,
src.extent(1) ,
src.extent(2) ,
src.extent(3) ,
src.extent(4) ,
src.extent(5) ,
src.extent(6) ,
src.extent(7) );
mirror_type tmp_view((typename ViewType::value_type*)buffer, src.d_view.layout());
if(space == Device) {
Kokkos::deep_copy(LMPHostType(),tmp_view,src.h_view),
Kokkos::deep_copy(LMPHostType(),src.d_view,tmp_view);

12
src/KOKKOS/bond_harmonic_kokkos.cpp
View File

@ -69,14 +69,14 @@ void BondHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//if(k_eatom.extent(0)<maxeatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
d_eatom = k_eatom.template view<KKDeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.extent(0)<maxvatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
d_vatom = k_vatom.template view<KKDeviceType>();
//}
}
@ -204,8 +204,8 @@ void BondHarmonicKokkos<DeviceType>::coeff(int narg, char **arg)
BondHarmonic::coeff(narg, arg);
int n = atom->nbondtypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k("BondHarmonic::k",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_r0("BondHarmonic::r0",n+1);
typename AT::tdual_ffloat_1d k_k("BondHarmonic::k",n+1);
typename AT::tdual_ffloat_1d k_r0("BondHarmonic::r0",n+1);
d_k = k_k.template view<DeviceType>();
d_r0 = k_r0.template view<DeviceType>();
@ -231,8 +231,8 @@ void BondHarmonicKokkos<DeviceType>::read_restart(FILE *fp)
BondHarmonic::read_restart(fp);
int n = atom->nbondtypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k("BondHarmonic::k",n+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_r0("BondHarmonic::r0",n+1);
typename AT::tdual_ffloat_1d k_k("BondHarmonic::k",n+1);
typename AT::tdual_ffloat_1d k_r0("BondHarmonic::r0",n+1);
d_k = k_k.template view<DeviceType>();
d_r0 = k_r0.template view<DeviceType>();

9
src/KOKKOS/bond_harmonic_kokkos.h
View File

@ -66,10 +66,11 @@ class BondHarmonicKokkos : public BondHarmonic {
typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
typename AT::t_int_2d bondlist;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
typedef typename KKDevice<DeviceType>::value KKDeviceType;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
int nlocal,newton_bond;
int eflag,vflag;

48
src/KOKKOS/dihedral_charmm_kokkos.cpp
View File

@ -28,6 +28,7 @@
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "kokkos.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -69,6 +70,9 @@ void DihedralCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
if (lmp->kokkos->neighflag == FULL)
error->all(FLERR,"Dihedral_style charmm/kk requires half neighbor list");
ev_init(eflag,vflag,0);
// insure pair->ev_tally() will use 1-4 virial contribution
@ -82,18 +86,18 @@ void DihedralCharmmKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//if(k_eatom.extent(0)<maxeatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"dihedral:eatom");
d_eatom = k_eatom.template view<DeviceType>();
k_eatom_pair = Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType>("dihedral:eatom_pair",maxeatom);
d_eatom_pair = k_eatom.template view<DeviceType>();
d_eatom = k_eatom.template view<KKDeviceType>();
k_eatom_pair = Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType>("dihedral:eatom_pair",maxeatom);
d_eatom_pair = k_eatom_pair.template view<KKDeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.extent(0)<maxvatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"dihedral:vatom");
d_vatom = k_vatom.template view<DeviceType>();
k_vatom_pair = Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType>("dihedral:vatom_pair",maxvatom);
d_vatom_pair = k_vatom.template view<DeviceType>();
d_vatom = k_vatom.template view<KKDeviceType>();
k_vatom_pair = Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType>("dihedral:vatom_pair",maxvatom);
d_vatom_pair = k_vatom_pair.template view<KKDeviceType>();
//}
}
@ -424,12 +428,12 @@ void DihedralCharmmKokkos<DeviceType>::coeff(int narg, char **arg)
DihedralCharmm::coeff(narg, arg);
int nd = atom->ndihedraltypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k("DihedralCharmm::k",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_multiplicity("DihedralCharmm::multiplicity",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_shift("DihedralCharmm::shift",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_cos_shift("DihedralCharmm::cos_shift",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_sin_shift("DihedralCharmm::sin_shift",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_weight("DihedralCharmm::weight",nd+1);
typename AT::tdual_ffloat_1d k_k("DihedralCharmm::k",nd+1);
typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmm::multiplicity",nd+1);
typename AT::tdual_ffloat_1d k_shift("DihedralCharmm::shift",nd+1);
typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmm::cos_shift",nd+1);
typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmm::sin_shift",nd+1);
typename AT::tdual_ffloat_1d k_weight("DihedralCharmm::weight",nd+1);
d_k = k_k.template view<DeviceType>();
d_multiplicity = k_multiplicity.template view<DeviceType>();
@ -473,10 +477,10 @@ void DihedralCharmmKokkos<DeviceType>::init_style()
DihedralCharmm::init_style();
int n = atom->ntypes;
Kokkos::DualView<F_FLOAT**,Kokkos::LayoutRight,DeviceType> k_lj14_1("DihedralCharmm:lj14_1",n+1,n+1);
Kokkos::DualView<F_FLOAT**,Kokkos::LayoutRight,DeviceType> k_lj14_2("DihedralCharmm:lj14_2",n+1,n+1);
Kokkos::DualView<F_FLOAT**,Kokkos::LayoutRight,DeviceType> k_lj14_3("DihedralCharmm:lj14_3",n+1,n+1);
Kokkos::DualView<F_FLOAT**,Kokkos::LayoutRight,DeviceType> k_lj14_4("DihedralCharmm:lj14_4",n+1,n+1);
DAT::tdual_ffloat_2d k_lj14_1("DihedralCharmm:lj14_1",n+1,n+1);
DAT::tdual_ffloat_2d k_lj14_2("DihedralCharmm:lj14_2",n+1,n+1);
DAT::tdual_ffloat_2d k_lj14_3("DihedralCharmm:lj14_3",n+1,n+1);
DAT::tdual_ffloat_2d k_lj14_4("DihedralCharmm:lj14_4",n+1,n+1);
d_lj14_1 = k_lj14_1.template view<DeviceType>();
d_lj14_2 = k_lj14_2.template view<DeviceType>();
@ -517,12 +521,12 @@ void DihedralCharmmKokkos<DeviceType>::read_restart(FILE *fp)
DihedralCharmm::read_restart(fp);
int nd = atom->ndihedraltypes;
Kokkos::DualView<F_FLOAT*,DeviceType> k_k("DihedralCharmm::k",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_multiplicity("DihedralCharmm::multiplicity",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_shift("DihedralCharmm::shift",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_cos_shift("DihedralCharmm::cos_shift",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_sin_shift("DihedralCharmm::sin_shift",nd+1);
Kokkos::DualView<F_FLOAT*,DeviceType> k_weight("DihedralCharmm::weight",nd+1);
typename AT::tdual_ffloat_1d k_k("DihedralCharmm::k",nd+1);
typename AT::tdual_ffloat_1d k_multiplicity("DihedralCharmm::multiplicity",nd+1);
typename AT::tdual_ffloat_1d k_shift("DihedralCharmm::shift",nd+1);
typename AT::tdual_ffloat_1d k_cos_shift("DihedralCharmm::cos_shift",nd+1);
typename AT::tdual_ffloat_1d k_sin_shift("DihedralCharmm::sin_shift",nd+1);
typename AT::tdual_ffloat_1d k_weight("DihedralCharmm::weight",nd+1);
d_k = k_k.template view<DeviceType>();
d_multiplicity = k_multiplicity.template view<DeviceType>();

17
src/KOKKOS/dihedral_charmm_kokkos.h
View File

@ -132,15 +132,16 @@ class DihedralCharmmKokkos : public DihedralCharmm {
typename AT::t_f_array f;
typename AT::t_int_2d dihedrallist;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
typedef typename KKDevice<DeviceType>::value KKDeviceType;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType> k_eatom_pair;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType> k_vatom_pair;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom_pair;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom_pair;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom_pair;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom_pair;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom_pair;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom_pair;
int nlocal,newton_bond;
int eflag,vflag;

10
src/KOKKOS/fix_qeq_reax_kokkos.cpp
View File

@ -39,8 +39,6 @@ using namespace FixConst;
#define SMALL 0.0001
#define EV_TO_KCAL_PER_MOL 14.4
#define TEAMSIZE 128
/* ---------------------------------------------------------------------- */
template<class DeviceType>
@ -726,7 +724,9 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve1()
const int inum = list->inum;
F_FLOAT tmp, sig_old, b_norm;
const int teamsize = TEAMSIZE;
int teamsize;
if (execution_space == Host) teamsize = 1;
else teamsize = 128;
// sparse_matvec( &H, x, q );
FixQEqReaxKokkosSparse12Functor<DeviceType> sparse12_functor(this);
@ -861,7 +861,9 @@ void FixQEqReaxKokkos<DeviceType>::cg_solve2()
const int inum = list->inum;
F_FLOAT tmp, sig_old, b_norm;
const int teamsize = TEAMSIZE;
int teamsize;
if (execution_space == Host) teamsize = 1;
else teamsize = 128;
// sparse_matvec( &H, x, q );
FixQEqReaxKokkosSparse32Functor<DeviceType> sparse32_functor(this);

4
src/KOKKOS/improper_harmonic_kokkos.cpp
View File

@ -73,14 +73,14 @@ void ImproperHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
//if(k_eatom.extent(0)<maxeatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_eatom,eatom);
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
d_eatom = k_eatom.template view<DeviceType>();
d_eatom = k_eatom.template view<KKDeviceType>();
//}
}
if (vflag_atom) {
//if(k_vatom.extent(0)<maxvatom) { // won't work without adding zero functor
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"improper:vatom");
d_vatom = k_vatom.template view<DeviceType>();
d_vatom = k_vatom.template view<KKDeviceType>();
//}
}

11
src/KOKKOS/improper_harmonic_kokkos.h
View File

@ -63,14 +63,15 @@ class ImproperHarmonicKokkos : public ImproperHarmonic {
class NeighborKokkos *neighborKK;
typedef typename KKDevice<DeviceType>::value KKDeviceType;
typename AT::t_x_array_randomread x;
typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
typename AT::t_int_2d improperlist;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,DeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,DeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom;
Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom;
Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
int nlocal,newton_bond;
int eflag,vflag;

4
src/KOKKOS/kokkos.cpp
View File

@ -306,7 +306,7 @@ void KokkosLMP::accelerator(int narg, char **arg)
neighflag = HALFTHREAD;
else
neighflag = HALF;
} else if (strcmp(arg[iarg+1],"n2") == 0) neighflag = N2;
}
else error->all(FLERR,"Illegal package kokkos command");
if (!neighflag_qeq_set) neighflag_qeq = neighflag;
iarg += 2;
@ -318,7 +318,7 @@ void KokkosLMP::accelerator(int narg, char **arg)
neighflag_qeq = HALFTHREAD;
else
neighflag_qeq = HALF;
} else if (strcmp(arg[iarg+1],"n2") == 0) neighflag_qeq = N2;
}
else error->all(FLERR,"Illegal package kokkos command");
neighflag_qeq_set = 1;
iarg += 2;

2
src/KOKKOS/kokkos_type.h
View File

@ -22,7 +22,7 @@
#include <Kokkos_Vectorization.hpp>
#include <Kokkos_ScatterView.hpp>
enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u};
enum{FULL=1u,HALFTHREAD=2u,HALF=4u};
#if defined(KOKKOS_ENABLE_CXX11)
#undef ISFINITE

3
src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
View File

@ -307,9 +307,6 @@ void PairBuckCoulCutKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with buck/coul/cut/kk");
}

3
src/KOKKOS/pair_buck_kokkos.cpp
View File

@ -229,9 +229,6 @@ void PairBuckKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with buck/kk");
}

5
src/KOKKOS/pair_buck_kokkos.h
View File

@ -31,7 +31,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairBuckKokkos : public PairBuck {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
@ -98,15 +98,12 @@ class PairBuckKokkos : public PairBuck {
friend class PairComputeFunctor<PairBuckKokkos,FULL,true>;
friend class PairComputeFunctor<PairBuckKokkos,HALF,true>;
friend class PairComputeFunctor<PairBuckKokkos,HALFTHREAD,true>;
friend class PairComputeFunctor<PairBuckKokkos,N2,true>;
friend class PairComputeFunctor<PairBuckKokkos,FULL,false>;
friend class PairComputeFunctor<PairBuckKokkos,HALF,false>;
friend class PairComputeFunctor<PairBuckKokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairBuckKokkos,N2,false>;
friend EV_FLOAT pair_compute_neighlist<PairBuckKokkos,FULL,void>(PairBuckKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairBuckKokkos,HALF,void>(PairBuckKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairBuckKokkos,HALFTHREAD,void>(PairBuckKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairBuckKokkos,N2,void>(PairBuckKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairBuckKokkos,void>(PairBuckKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairBuckKokkos>(PairBuckKokkos*);
};

3
src/KOKKOS/pair_coul_debye_kokkos.cpp
View File

@ -276,9 +276,6 @@ void PairCoulDebyeKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with coul/debye/kk");
}

191
src/KOKKOS/pair_kokkos.h
View File

@ -87,6 +87,8 @@ struct PairComputeFunctor {
c(*c_ptr),list(*list_ptr) {
// allocate duplicated memory
f = c.f;
d_eatom = c.d_eatom;
d_vatom = c.d_vatom;
dup_f = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, NeedDup<NEIGHFLAG,device_type>::value >(c.f);
dup_eatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, NeedDup<NEIGHFLAG,device_type>::value >(c.d_eatom);
dup_vatom = Kokkos::Experimental::create_scatter_view<Kokkos::Experimental::ScatterSum, NeedDup<NEIGHFLAG,device_type>::value >(c.d_vatom);
@ -422,15 +424,15 @@ struct PairComputeFunctor {
F_FLOAT evdwl = 0.0;
if (c.eflag) {
evdwl = factor_lj * c.template compute_evdwl<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
fev.evdwl += 0.5*evdwl;
fev_tmp.evdwl += 0.5*evdwl;
}
if (c.vflag_either) {
fev.v[0] += 0.5*delx*delx*fpair;
fev.v[1] += 0.5*dely*dely*fpair;
fev.v[2] += 0.5*delz*delz*fpair;
fev.v[3] += 0.5*delx*dely*fpair;
fev.v[4] += 0.5*delx*delz*fpair;
fev.v[5] += 0.5*dely*delz*fpair;
fev_tmp.v[0] += 0.5*delx*delx*fpair;
fev_tmp.v[1] += 0.5*dely*dely*fpair;
fev_tmp.v[2] += 0.5*delz*delz*fpair;
fev_tmp.v[3] += 0.5*delx*dely*fpair;
fev_tmp.v[4] += 0.5*delx*delz*fpair;
fev_tmp.v[5] += 0.5*dely*delz*fpair;
}
}
},fev);
@ -479,8 +481,8 @@ struct PairComputeFunctor {
const int inum = team.league_size();
const int atoms_per_team = team.team_size();
int firstatom = team.league_rank()*atoms_per_team;
int lastatom = firstatom + atoms_per_team < inum ? firstatom + atoms_per_team : inum;
const int firstatom = team.league_rank()*atoms_per_team;
const int lastatom = firstatom + atoms_per_team < inum ? firstatom + atoms_per_team : inum;
Kokkos::parallel_for(Kokkos::TeamThreadRange(team, firstatom, lastatom), [&] (const int &ii) {
const int i = list.d_ilist[ii];
@ -497,6 +499,7 @@ struct PairComputeFunctor {
Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team,jnum),
[&] (const int jj, FEV_FLOAT& fev_tmp) {
int j = neighbors_i(jj);
const F_FLOAT factor_lj = c.special_lj[sbmask(j)];
const F_FLOAT factor_coul = c.special_coul[sbmask(j)];
@ -516,29 +519,29 @@ struct PairComputeFunctor {
if(rsq < (STACKPARAMS?c.m_cut_coulsq[itype][jtype]:c.d_cut_coulsq(itype,jtype)))
fpair+=c.template compute_fcoul<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype,factor_coul,qtmp);
fev.f[0] += delx*fpair;
fev.f[1] += dely*fpair;
fev.f[2] += delz*fpair;
fev_tmp.f[0] += delx*fpair;
fev_tmp.f[1] += dely*fpair;
fev_tmp.f[2] += delz*fpair;
F_FLOAT evdwl = 0.0;
F_FLOAT ecoul = 0.0;
if (c.eflag) {
if(rsq < (STACKPARAMS?c.m_cut_ljsq[itype][jtype]:c.d_cut_ljsq(itype,jtype))) {
evdwl = factor_lj * c.template compute_evdwl<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
ev.evdwl += 0.5*evdwl;
fev_tmp.evdwl += 0.5*evdwl;
}
if(rsq < (STACKPARAMS?c.m_cut_coulsq[itype][jtype]:c.d_cut_coulsq(itype,jtype))) {
ecoul = c.template compute_ecoul<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype,factor_coul,qtmp);
ev.ecoul += 0.5*ecoul;
fev_tmp.ecoul += 0.5*ecoul;
}
}
if (c.vflag) {
fev.v[0] += 0.5*delx*delx*fpair;
fev.v[1] += 0.5*dely*dely*fpair;
fev.v[2] += 0.5*delz*delz*fpair;
fev.v[3] += 0.5*delx*dely*fpair;
fev.v[4] += 0.5*delx*delz*fpair;
fev.v[5] += 0.5*dely*delz*fpair;
if (c.vflag_either) {
fev_tmp.v[0] += 0.5*delx*delx*fpair;
fev_tmp.v[1] += 0.5*dely*dely*fpair;
fev_tmp.v[2] += 0.5*delz*delz*fpair;
fev_tmp.v[3] += 0.5*delx*dely*fpair;
fev_tmp.v[4] += 0.5*delx*delz*fpair;
fev_tmp.v[5] += 0.5*dely*delz*fpair;
}
}
},fev);
@ -690,148 +693,6 @@ struct PairComputeFunctor {
}
};
template <class PairStyle, bool STACKPARAMS, class Specialisation>
struct PairComputeFunctor<PairStyle,N2,STACKPARAMS,Specialisation> {
typedef typename PairStyle::device_type device_type ;
typedef EV_FLOAT value_type;
PairStyle c;
NeighListKokkos<device_type> list;
PairComputeFunctor(PairStyle* c_ptr,
NeighListKokkos<device_type>* list_ptr):
c(*c_ptr),list(*list_ptr) {};
~PairComputeFunctor() {c.cleanup_copy();list.copymode = 1;};
KOKKOS_INLINE_FUNCTION int sbmask(const int& j) const {
return j >> SBBITS & 3;
}
void contribute() {}
template<int EVFLAG, int NEWTON_PAIR>
KOKKOS_FUNCTION
EV_FLOAT compute_item(const int& ii,
const NeighListKokkos<device_type> &list, const NoCoulTag&) const {
(void) list;
EV_FLOAT ev;
const int i = ii;//list.d_ilist[ii];
const X_FLOAT xtmp = c.x(i,0);
const X_FLOAT ytmp = c.x(i,1);
const X_FLOAT ztmp = c.x(i,2);
const int itype = c.type(i);
//const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
const int jnum = c.nall;
F_FLOAT fxtmp = 0.0;
F_FLOAT fytmp = 0.0;
F_FLOAT fztmp = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = jj;//neighbors_i(jj);
if(i==j) continue;
const F_FLOAT factor_lj = c.special_lj[sbmask(j)];
j &= NEIGHMASK;
const X_FLOAT delx = xtmp - c.x(j,0);
const X_FLOAT dely = ytmp - c.x(j,1);
const X_FLOAT delz = ztmp - c.x(j,2);
const int jtype = c.type(j);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if(rsq < (STACKPARAMS?c.m_cutsq[itype][jtype]:c.d_cutsq(itype,jtype))) {
const F_FLOAT fpair = factor_lj*c.template compute_fpair<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (EVFLAG) {
F_FLOAT evdwl = 0.0;
if (c.eflag) {
evdwl = 0.5*
factor_lj * c.template compute_evdwl<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
ev.evdwl += evdwl;
}
if (c.vflag_either || c.eflag_atom) ev_tally(ev,i,j,evdwl,fpair,delx,dely,delz);
}
}
}
c.f(i,0) += fxtmp;
c.f(i,1) += fytmp;
c.f(i,2) += fztmp;
return ev;
}
KOKKOS_INLINE_FUNCTION
void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
const F_FLOAT &dely, const F_FLOAT &delz) const
{
const int EFLAG = c.eflag;
const int VFLAG = c.vflag_either;
if (EFLAG) {
if (c.eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
if (i < c.nlocal) c.d_eatom[i] += epairhalf;
if (j < c.nlocal) c.d_eatom[j] += epairhalf;
}
}
if (VFLAG) {
const E_FLOAT v0 = delx*delx*fpair;
const E_FLOAT v1 = dely*dely*fpair;
const E_FLOAT v2 = delz*delz*fpair;
const E_FLOAT v3 = delx*dely*fpair;
const E_FLOAT v4 = delx*delz*fpair;
const E_FLOAT v5 = dely*delz*fpair;
if (c.vflag_global) {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
if (c.vflag_atom) {
if (i < c.nlocal) {
c.d_vatom(i,0) += 0.5*v0;
c.d_vatom(i,1) += 0.5*v1;
c.d_vatom(i,2) += 0.5*v2;
c.d_vatom(i,3) += 0.5*v3;
c.d_vatom(i,4) += 0.5*v4;
c.d_vatom(i,5) += 0.5*v5;
}
}
}
}
KOKKOS_INLINE_FUNCTION
void operator()(const int i) const {
compute_item<0,0>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
KOKKOS_INLINE_FUNCTION
void operator()(const int i, value_type &energy_virial) const {
energy_virial += compute_item<1,0>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
KOKKOS_INLINE_FUNCTION
void operator()(const typename Kokkos::TeamPolicy<>::member_type& team) const
{}
KOKKOS_INLINE_FUNCTION
void operator()(const typename Kokkos::TeamPolicy<>::member_type& team, value_type &energy_virial) const
{}
};
// Filter out Neighflags which are not supported for PairStyle
// The enable_if clause will invalidate the last parameter of the function, so that
@ -867,7 +728,7 @@ int GetTeamSize(FunctorStyle& functor, int inum, int reduce_flag, int team_size,
return team_size;
}
// Submit ParallelFor for NEIGHFLAG=HALF,HALFTHREAD,FULL,N2
// Submit ParallelFor for NEIGHFLAG=HALF,HALFTHREAD,FULL
template<class PairStyle, unsigned NEIGHFLAG, class Specialisation>
EV_FLOAT pair_compute_neighlist (PairStyle* fpair, typename std::enable_if<(NEIGHFLAG&PairStyle::EnabledNeighFlags) != 0, NeighListKokkos<typename PairStyle::device_type>*>::type list) {
EV_FLOAT ev;
@ -918,8 +779,6 @@ EV_FLOAT pair_compute (PairStyle* fpair, NeighListKokkos<typename PairStyle::dev
ev = pair_compute_neighlist<PairStyle,HALFTHREAD,Specialisation> (fpair,list);
} else if (fpair->neighflag == HALF) {
ev = pair_compute_neighlist<PairStyle,HALF,Specialisation> (fpair,list);
} else if (fpair->neighflag == N2) {
ev = pair_compute_neighlist<PairStyle,N2,Specialisation> (fpair,list);
}
return ev;
}

3
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
View File

@ -309,9 +309,6 @@ void PairLJClass2CoulCutKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/class2/coul/cut/kk");
}

3
src/KOKKOS/pair_lj_class2_kokkos.cpp
View File

@ -247,9 +247,6 @@ void PairLJClass2Kokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/class2/kk");
}

5
src/KOKKOS/pair_lj_class2_kokkos.h
View File

@ -31,7 +31,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairLJClass2Kokkos : public PairLJClass2 {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
@ -104,15 +104,12 @@ class PairLJClass2Kokkos : public PairLJClass2 {
friend class PairComputeFunctor<PairLJClass2Kokkos,FULL,true>;
friend class PairComputeFunctor<PairLJClass2Kokkos,HALF,true>;
friend class PairComputeFunctor<PairLJClass2Kokkos,HALFTHREAD,true>;
friend class PairComputeFunctor<PairLJClass2Kokkos,N2,true>;
friend class PairComputeFunctor<PairLJClass2Kokkos,FULL,false>;
friend class PairComputeFunctor<PairLJClass2Kokkos,HALF,false>;
friend class PairComputeFunctor<PairLJClass2Kokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairLJClass2Kokkos,N2,false>;
friend EV_FLOAT pair_compute_neighlist<PairLJClass2Kokkos,FULL,void>(PairLJClass2Kokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJClass2Kokkos,HALF,void>(PairLJClass2Kokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJClass2Kokkos,HALFTHREAD,void>(PairLJClass2Kokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJClass2Kokkos,N2,void>(PairLJClass2Kokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairLJClass2Kokkos,void>(PairLJClass2Kokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairLJClass2Kokkos>(PairLJClass2Kokkos*);
};

3
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
View File

@ -300,9 +300,6 @@ void PairLJCutCoulCutKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/coul/cut/kk");
}

3
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
View File

@ -329,9 +329,6 @@ void PairLJCutCoulDebyeKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/coul/debye/kk");
}

3
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
View File

@ -322,9 +322,6 @@ void PairLJCutCoulDSFKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/coul/cut/kk");
}

3
src/KOKKOS/pair_lj_cut_kokkos.cpp
View File

@ -241,9 +241,6 @@ void PairLJCutKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/kk");
}

5
src/KOKKOS/pair_lj_cut_kokkos.h
View File

@ -31,7 +31,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairLJCutKokkos : public PairLJCut {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
@ -99,15 +99,12 @@ class PairLJCutKokkos : public PairLJCut {
friend class PairComputeFunctor<PairLJCutKokkos,FULL,true>;
friend class PairComputeFunctor<PairLJCutKokkos,HALF,true>;
friend class PairComputeFunctor<PairLJCutKokkos,HALFTHREAD,true>;
friend class PairComputeFunctor<PairLJCutKokkos,N2,true>;
friend class PairComputeFunctor<PairLJCutKokkos,FULL,false>;
friend class PairComputeFunctor<PairLJCutKokkos,HALF,false>;
friend class PairComputeFunctor<PairLJCutKokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairLJCutKokkos,N2,false>;
friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,FULL,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,HALF,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,HALFTHREAD,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,N2,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairLJCutKokkos,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairLJCutKokkos>(PairLJCutKokkos*);
};

3
src/KOKKOS/pair_lj_expand_kokkos.cpp
View File

@ -249,9 +249,6 @@ void PairLJExpandKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/expand/kk");
}

5
src/KOKKOS/pair_lj_expand_kokkos.h
View File

@ -31,7 +31,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairLJExpandKokkos : public PairLJExpand {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
@ -105,15 +105,12 @@ class PairLJExpandKokkos : public PairLJExpand {
friend class PairComputeFunctor<PairLJExpandKokkos,FULL,true>;
friend class PairComputeFunctor<PairLJExpandKokkos,HALF,true>;
friend class PairComputeFunctor<PairLJExpandKokkos,HALFTHREAD,true>;
friend class PairComputeFunctor<PairLJExpandKokkos,N2,true>;
friend class PairComputeFunctor<PairLJExpandKokkos,FULL,false>;
friend class PairComputeFunctor<PairLJExpandKokkos,HALF,false>;
friend class PairComputeFunctor<PairLJExpandKokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairLJExpandKokkos,N2,false>;
friend EV_FLOAT pair_compute_neighlist<PairLJExpandKokkos,FULL,void>(PairLJExpandKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJExpandKokkos,HALF,void>(PairLJExpandKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJExpandKokkos,HALFTHREAD,void>(PairLJExpandKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJExpandKokkos,N2,void>(PairLJExpandKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairLJExpandKokkos,void>(PairLJExpandKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairLJExpandKokkos>(PairLJExpandKokkos*);
};

3
src/KOKKOS/pair_lj_sdk_kokkos.cpp
View File

@ -279,9 +279,6 @@ void PairLJSDKKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/sdk/kk");
}

5
src/KOKKOS/pair_lj_sdk_kokkos.h
View File

@ -31,7 +31,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairLJSDKKokkos : public PairLJSDK {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
@ -100,15 +100,12 @@ class PairLJSDKKokkos : public PairLJSDK {
friend class PairComputeFunctor<PairLJSDKKokkos,FULL,true>;
friend class PairComputeFunctor<PairLJSDKKokkos,HALF,true>;
friend class PairComputeFunctor<PairLJSDKKokkos,HALFTHREAD,true>;
friend class PairComputeFunctor<PairLJSDKKokkos,N2,true>;
friend class PairComputeFunctor<PairLJSDKKokkos,FULL,false>;
friend class PairComputeFunctor<PairLJSDKKokkos,HALF,false>;
friend class PairComputeFunctor<PairLJSDKKokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairLJSDKKokkos,N2,false>;
friend EV_FLOAT pair_compute_neighlist<PairLJSDKKokkos,FULL,void>(PairLJSDKKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJSDKKokkos,HALF,void>(PairLJSDKKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJSDKKokkos,HALFTHREAD,void>(PairLJSDKKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairLJSDKKokkos,N2,void>(PairLJSDKKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairLJSDKKokkos,void>(PairLJSDKKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairLJSDKKokkos>(PairLJSDKKokkos*);
};

3
src/KOKKOS/pair_morse_kokkos.cpp
View File

@ -258,9 +258,6 @@ void PairMorseKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with morse/kk");
}

5
src/KOKKOS/pair_morse_kokkos.h
View File

@ -31,7 +31,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairMorseKokkos : public PairMorse {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
PairMorseKokkos(class LAMMPS *);
@ -98,15 +98,12 @@ class PairMorseKokkos : public PairMorse {
friend class PairComputeFunctor<PairMorseKokkos,FULL,true>;
friend class PairComputeFunctor<PairMorseKokkos,HALF,true>;
friend class PairComputeFunctor<PairMorseKokkos,HALFTHREAD,true>;
friend class PairComputeFunctor<PairMorseKokkos,N2,true>;
friend class PairComputeFunctor<PairMorseKokkos,FULL,false>;
friend class PairComputeFunctor<PairMorseKokkos,HALF,false>;
friend class PairComputeFunctor<PairMorseKokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairMorseKokkos,N2,false>;
friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,FULL,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,HALF,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,HALFTHREAD,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,N2,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairMorseKokkos,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairMorseKokkos>(PairMorseKokkos*);
};

409
src/KOKKOS/pair_reaxc_kokkos.cpp
View File

@ -152,16 +152,12 @@ void PairReaxCKokkos<DeviceType>::init_style()
neighbor->requests[irequest]->
kokkos_device = std::is_same<DeviceType,LMPDeviceType>::value;
if (neighflag == FULL) {
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->ghost = 1;
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->ghost = 1;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with reax/c/kk");
error->all(FLERR,"Must use half neighbor list with pair style reax/c/kk");
}
allocate();
@ -665,8 +661,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
eflag = eflag_in;
vflag = vflag_in;
if (neighflag == FULL) no_virial_fdotr_compute = 1;
ev_init(eflag,vflag);
atomKK->sync(execution_space,datamask_read);
@ -743,11 +737,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeTabulatedLJCoulomb<HALFTHREAD,1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxComputeTabulatedLJCoulomb<HALFTHREAD,0> >(0,inum),*this);
} else if (neighflag == FULL) {
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeTabulatedLJCoulomb<FULL,1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxComputeTabulatedLJCoulomb<FULL,0> >(0,inum),*this);
}
} else {
if (neighflag == HALF) {
@ -760,11 +749,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeLJCoulomb<HALFTHREAD,1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxComputeLJCoulomb<HALFTHREAD,0> >(0,inum),*this);
} else if (neighflag == FULL) {
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, PairReaxComputeLJCoulomb<FULL,1> >(0,inum),*this,ev);
else
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxComputeLJCoulomb<FULL,0> >(0,inum),*this);
}
}
ev_all += ev;
@ -809,8 +793,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALF> >(0,ignum),*this);
else if (neighflag == HALFTHREAD)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsHalf<HALFTHREAD> >(0,ignum),*this);
else //(neighflag == FULL)
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBuildListsFull>(0,ignum),*this);
k_resize_bo.modify<DeviceType>();
k_resize_bo.sync<LMPHostType>();
@ -853,11 +835,7 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
Kokkos::Experimental::contribute(d_total_bo, dup_total_bo); // needed in BondOrder1
// Bond order
if (neighflag == HALF) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
} else if (neighflag == HALFTHREAD) {
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
}
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder1>(0,ignum),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder2>(0,ignum),*this);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, PairReaxBondOrder3>(0,ignum),*this);
@ -1044,14 +1022,14 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// free duplicated memory
if (need_dup) {
dup_f = decltype(dup_f)();
dup_eatom = decltype(dup_eatom)();
dup_vatom = decltype(dup_vatom)();
dup_dDeltap_self = decltype(dup_dDeltap_self)();
dup_total_bo = decltype(dup_total_bo)();
dup_CdDelta = decltype(dup_CdDelta)();
//dup_Cdbo = decltype(dup_Cdbo)();
//dup_Cdbopi = decltype(dup_Cdbopi)();
//dup_Cdbopi2 = decltype(dup_Cdbopi2)();
dup_eatom = decltype(dup_eatom)();
dup_vatom = decltype(dup_vatom)();
}
}
@ -1119,18 +1097,16 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG,
const tagint jtag = tag(j);
const F_FLOAT qj = q(j);
if (NEIGHFLAG != FULL) {
// skip half of the interactions
if (j >= nlocal) {
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x(j,2) < ztmp) continue;
if (x(j,2) == ztmp && x(j,1) < ytmp) continue;
if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue;
}
// skip half of the interactions
if (j >= nlocal) {
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x(j,2) < ztmp) continue;
if (x(j,2) == ztmp && x(j,1) < ytmp) continue;
if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue;
}
}
@ -1215,19 +1191,12 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeLJCoulomb<NEIGHFLAG,
fxtmp += delx*ftotal;
fytmp += dely*ftotal;
fztmp += delz*ftotal;
if (NEIGHFLAG != FULL) {
a_f(j,0) -= delx*ftotal;
a_f(j,1) -= dely*ftotal;
a_f(j,2) -= delz*ftotal;
}
a_f(j,0) -= delx*ftotal;
a_f(j,1) -= dely*ftotal;
a_f(j,2) -= delz*ftotal;
if (NEIGHFLAG == FULL) {
if (eflag) ev.evdwl += 0.5*evdwl;
if (eflag) ev.ecoul += 0.5*ecoul;
} else {
if (eflag) ev.evdwl += evdwl;
if (eflag) ev.ecoul += ecoul;
}
if (eflag) ev.evdwl += evdwl;
if (eflag) ev.ecoul += ecoul;
if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG>(ev,i,j,evdwl+ecoul,-ftotal,delx,dely,delz);
}
@ -1276,18 +1245,16 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<N
const tagint jtag = tag(j);
const F_FLOAT qj = q(j);
if (NEIGHFLAG != FULL) {
// skip half of the interactions
if (j >= nlocal) {
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x(j,2) < ztmp) continue;
if (x(j,2) == ztmp && x(j,1) < ytmp) continue;
if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue;
}
// skip half of the interactions
if (j >= nlocal) {
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x(j,2) < ztmp) continue;
if (x(j,2) == ztmp && x(j,1) < ytmp) continue;
if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue;
}
}
@ -1331,19 +1298,12 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeTabulatedLJCoulomb<N
fxtmp += delx*ftotal;
fytmp += dely*ftotal;
fztmp += delz*ftotal;
if (NEIGHFLAG != FULL) {
a_f(j,0) -= delx*ftotal;
a_f(j,1) -= dely*ftotal;
a_f(j,2) -= delz*ftotal;
}
a_f(j,0) -= delx*ftotal;
a_f(j,1) -= dely*ftotal;
a_f(j,2) -= delz*ftotal;
if (NEIGHFLAG == FULL) {
if (eflag) ev.evdwl += 0.5*evdwl;
if (eflag) ev.ecoul += 0.5*ecoul;
} else {
if (eflag) ev.evdwl += evdwl;
if (eflag) ev.ecoul += ecoul;
}
if (eflag) ev.evdwl += evdwl;
if (eflag) ev.ecoul += ecoul;
if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG>(ev,i,j,evdwl+ecoul,-ftotal,delx,dely,delz);
}
@ -1436,10 +1396,8 @@ KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxZero, const int &n) const {
d_total_bo(n) = 0.0;
d_CdDelta(n) = 0.0;
if (neighflag != FULL) {
d_bo_num(n) = 0.0;
d_hb_num(n) = 0.0;
}
d_bo_num(n) = 0.0;
d_hb_num(n) = 0.0;
for (int j = 0; j < 3; j++)
d_dDeltap_self(n,j) = 0.0;
}
@ -1850,261 +1808,6 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxBondOrder1, const int &ii)
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxBuildListsHalf_LessAtomics<NEIGHFLAG>, const int &ii) const {
if (d_resize_bo() || d_resize_hb())
return;
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int itype = type(i);
const tagint itag = tag(i);
const int jnum = d_numneigh[i];
F_FLOAT C12, C34, C56, BO_s, BO_pi, BO_pi2, BO, delij[3];
int j_index,i_index;
d_bo_first[i] = i*maxbo;
const int bo_first_i = d_bo_first[i];
int ihb = -1;
int jhb = -1;
int hb_first_i;
if (cut_hbsq > 0.0) {
ihb = paramssing(itype).p_hbond;
if (ihb == 1) {
d_hb_first[i] = i*maxhb;
hb_first_i = d_hb_first[i];
}
}
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const tagint jtag = tag(j);
d_bo_first[j] = j*maxbo;
d_hb_first[j] = j*maxhb;
const int jtype = type(j);
delij[0] = x(j,0) - xtmp;
delij[1] = x(j,1) - ytmp;
delij[2] = x(j,2) - ztmp;
const F_FLOAT rsq = delij[0]*delij[0] + delij[1]*delij[1] + delij[2]*delij[2];
double cutoffsq;
if(i < nlocal) cutoffsq = MAX(cut_bosq,cut_hbsq);
else cutoffsq = cut_bosq;
if (rsq > cutoffsq) continue;
// hbond list
if (i < nlocal && cut_hbsq > 0.0 && (ihb == 1 || ihb == 2) && rsq <= cut_hbsq) {
jhb = paramssing(jtype).p_hbond;
if (ihb == 1 && jhb == 2) {
if (NEIGHFLAG == HALF) {
j_index = hb_first_i + d_hb_num[i];
d_hb_num[i]++;
} else {
j_index = hb_first_i + Kokkos::atomic_fetch_add(&d_hb_num[i],1);
}
const int jj_index = j_index - hb_first_i;
if (jj_index >= maxhb) {
d_resize_hb() = 1;
return;
}
d_hb_list[j_index] = j;
} else if ( j < nlocal && ihb == 2 && jhb == 1) {
if (NEIGHFLAG == HALF) {
i_index = d_hb_first[j] + d_hb_num[j];
d_hb_num[j]++;
} else {
i_index = d_hb_first[j] + Kokkos::atomic_fetch_add(&d_hb_num[j],1);
}
const int ii_index = i_index - d_hb_first[j];
if (ii_index >= maxhb) {
d_resize_hb() = 1;
return;
}
d_hb_list[i_index] = i;
}
}
if (rsq > cut_bosq) continue;
// bond_list
const F_FLOAT rij = sqrt(rsq);
const F_FLOAT p_bo1 = paramstwbp(itype,jtype).p_bo1;
const F_FLOAT p_bo2 = paramstwbp(itype,jtype).p_bo2;
const F_FLOAT p_bo3 = paramstwbp(itype,jtype).p_bo3;
const F_FLOAT p_bo4 = paramstwbp(itype,jtype).p_bo4;
const F_FLOAT p_bo5 = paramstwbp(itype,jtype).p_bo5;
const F_FLOAT p_bo6 = paramstwbp(itype,jtype).p_bo6;
const F_FLOAT r_s = paramstwbp(itype,jtype).r_s;
const F_FLOAT r_pi = paramstwbp(itype,jtype).r_pi;
const F_FLOAT r_pi2 = paramstwbp(itype,jtype).r_pi2;
if (paramssing(itype).r_s > 0.0 && paramssing(jtype).r_s > 0.0) {
C12 = p_bo1*pow(rij/r_s,p_bo2);
BO_s = (1.0+bo_cut)*exp(C12);
}
else BO_s = C12 = 0.0;
if (paramssing(itype).r_pi > 0.0 && paramssing(jtype).r_pi > 0.0) {
C34 = p_bo3*pow(rij/r_pi,p_bo4);
BO_pi = exp(C34);
}
else BO_pi = C34 = 0.0;
if (paramssing(itype).r_pi2 > 0.0 && paramssing(jtype).r_pi2 > 0.0) {
C56 = p_bo5*pow(rij/r_pi2,p_bo6);
BO_pi2 = exp(C56);
}
else BO_pi2 = C56 = 0.0;
BO = BO_s + BO_pi + BO_pi2;
if (BO < bo_cut) continue;
if (NEIGHFLAG == HALF) {
j_index = bo_first_i + d_bo_num[i];
i_index = d_bo_first[j] + d_bo_num[j];
d_bo_num[i]++;
d_bo_num[j]++;
} else {
j_index = bo_first_i + Kokkos::atomic_fetch_add(&d_bo_num[i],1);
i_index = d_bo_first[j] + Kokkos::atomic_fetch_add(&d_bo_num[j],1);
}
const int jj_index = j_index - bo_first_i;
const int ii_index = i_index - d_bo_first[j];
if (jj_index >= maxbo || ii_index >= maxbo) {
d_resize_bo() = 1;
return;
}
d_bo_list[j_index] = j;
d_bo_list[i_index] = i;
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxBondOrder1_LessAtomics, const int &ii) const {
F_FLOAT C12, C34, C56, BO_s, BO_pi, BO_pi2, BO, delij[3], dBOp_i[3], dln_BOp_pi_i[3], dln_BOp_pi2_i[3];
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int itype = type(i);
const int j_start = d_bo_first[i];
const int j_end = j_start + d_bo_num[i];
F_FLOAT total_bo = 0.0;
for (int jj = j_start; jj < j_end; jj++) {
int j = d_bo_list[jj];
j &= NEIGHMASK;
delij[0] = x(j,0) - xtmp;
delij[1] = x(j,1) - ytmp;
delij[2] = x(j,2) - ztmp;
const F_FLOAT rsq = delij[0]*delij[0] + delij[1]*delij[1] + delij[2]*delij[2];
const F_FLOAT rij = sqrt(rsq);
const int jtype = type(j);
const int j_index = jj - j_start;
// calculate uncorrected BO and total bond order
const F_FLOAT p_bo1 = paramstwbp(itype,jtype).p_bo1;
const F_FLOAT p_bo2 = paramstwbp(itype,jtype).p_bo2;
const F_FLOAT p_bo3 = paramstwbp(itype,jtype).p_bo3;
const F_FLOAT p_bo4 = paramstwbp(itype,jtype).p_bo4;
const F_FLOAT p_bo5 = paramstwbp(itype,jtype).p_bo5;
const F_FLOAT p_bo6 = paramstwbp(itype,jtype).p_bo6;
const F_FLOAT r_s = paramstwbp(itype,jtype).r_s;
const F_FLOAT r_pi = paramstwbp(itype,jtype).r_pi;
const F_FLOAT r_pi2 = paramstwbp(itype,jtype).r_pi2;
if (paramssing(itype).r_s > 0.0 && paramssing(jtype).r_s > 0.0) {
C12 = p_bo1*pow(rij/r_s,p_bo2);
BO_s = (1.0+bo_cut)*exp(C12);
}
else BO_s = C12 = 0.0;
if (paramssing(itype).r_pi > 0.0 && paramssing(jtype).r_pi > 0.0) {
C34 = p_bo3*pow(rij/r_pi,p_bo4);
BO_pi = exp(C34);
}
else BO_pi = C34 = 0.0;
if (paramssing(itype).r_pi2 > 0.0 && paramssing(jtype).r_pi2 > 0.0) {
C56 = p_bo5*pow(rij/r_pi2,p_bo6);
BO_pi2 = exp(C56);
}
else BO_pi2 = C56 = 0.0;
BO = BO_s + BO_pi + BO_pi2;
if (BO < bo_cut) continue;
d_BO(i,j_index) = BO;
d_BO_s(i,j_index) = BO;
d_BO_pi(i,j_index) = BO_pi;
d_BO_pi2(i,j_index) = BO_pi2;
F_FLOAT Cln_BOp_s = p_bo2 * C12 / rij / rij;
F_FLOAT Cln_BOp_pi = p_bo4 * C34 / rij / rij;
F_FLOAT Cln_BOp_pi2 = p_bo6 * C56 / rij / rij;
if (nlocal == 0)
Cln_BOp_s = Cln_BOp_pi = Cln_BOp_pi2 = 0.0;
for (int d = 0; d < 3; d++) dln_BOp_pi_i[d] = -(BO_pi*Cln_BOp_pi)*delij[d];
for (int d = 0; d < 3; d++) dln_BOp_pi2_i[d] = -(BO_pi2*Cln_BOp_pi2)*delij[d];
for (int d = 0; d < 3; d++) dBOp_i[d] = -(BO_s*Cln_BOp_s+BO_pi*Cln_BOp_pi+BO_pi2*Cln_BOp_pi2)*delij[d];
for (int d = 0; d < 3; d++) d_dDeltap_self(i,d) += dBOp_i[d];
d_dln_BOp_pix(i,j_index) = dln_BOp_pi_i[0];
d_dln_BOp_piy(i,j_index) = dln_BOp_pi_i[1];
d_dln_BOp_piz(i,j_index) = dln_BOp_pi_i[2];
d_dln_BOp_pi2x(i,j_index) = dln_BOp_pi2_i[0];
d_dln_BOp_pi2y(i,j_index) = dln_BOp_pi2_i[1];
d_dln_BOp_pi2z(i,j_index) = dln_BOp_pi2_i[2];
d_dBOpx(i,j_index) = dBOp_i[0];
d_dBOpy(i,j_index) = dBOp_i[1];
d_dBOpz(i,j_index) = dBOp_i[2];
d_BO(i,j_index) -= bo_cut;
d_BO_s(i,j_index) -= bo_cut;
total_bo += d_BO(i,j_index);
}
d_total_bo[i] += total_bo;
const F_FLOAT val_i = paramssing(itype).valency;
d_Deltap[i] = d_total_bo[i] - val_i;
d_Deltap_boc[i] = d_total_bo[i] - paramssing(itype).valency_val;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairReaxCKokkos<DeviceType>::operator()(PairReaxBondOrder2, const int &ii) const {
@ -3728,7 +3431,7 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
if (eflag_atom) {
const E_FLOAT epairhalf = 0.5 * epair;
a_eatom[i] += epairhalf;
if (NEIGHFLAG != FULL) a_eatom[j] += epairhalf;
a_eatom[j] += epairhalf;
}
if (VFLAG) {
@ -3740,21 +3443,12 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
const E_FLOAT v5 = dely*delz*fpair;
if (vflag_global) {
if (NEIGHFLAG != FULL) {
ev.v[0] += v0;
ev.v[1] += v1;
ev.v[2] += v2;
ev.v[3] += v3;
ev.v[4] += v4;
ev.v[5] += v5;
} else {
ev.v[0] += 0.5*v0;
ev.v[1] += 0.5*v1;
ev.v[2] += 0.5*v2;
ev.v[3] += 0.5*v3;
ev.v[4] += 0.5*v4;
ev.v[5] += 0.5*v5;
}
ev.v[0] += v0;
ev.v[1] += v1;
ev.v[2] += v2;
ev.v[3] += v3;
ev.v[4] += v4;
ev.v[5] += v5;
}
if (vflag_atom) {
@ -3764,15 +3458,12 @@ void PairReaxCKokkos<DeviceType>::ev_tally(EV_FLOAT_REAX &ev, const int &i, cons
a_vatom(i,3) += 0.5*v3;
a_vatom(i,4) += 0.5*v4;
a_vatom(i,5) += 0.5*v5;
if (NEIGHFLAG != FULL) {
a_vatom(j,0) += 0.5*v0;
a_vatom(j,1) += 0.5*v1;
a_vatom(j,2) += 0.5*v2;
a_vatom(j,3) += 0.5*v3;
a_vatom(j,4) += 0.5*v4;
a_vatom(j,5) += 0.5*v5;
}
a_vatom(j,0) += 0.5*v0;
a_vatom(j,1) += 0.5*v1;
a_vatom(j,2) += 0.5*v2;
a_vatom(j,3) += 0.5*v3;
a_vatom(j,4) += 0.5*v4;
a_vatom(j,5) += 0.5*v5;
}
}
}

14
src/KOKKOS/pair_reaxc_kokkos.h
View File

@ -64,9 +64,6 @@ struct PairReaxBuildListsFull{};
template<int NEIGHFLAG>
struct PairReaxBuildListsHalf{};
template<int NEIGHFLAG>
struct PairReaxBuildListsHalf_LessAtomics{};
struct PairReaxZero{};
struct PairReaxZeroEAtom{};
@ -75,8 +72,6 @@ struct PairReaxZeroVAtom{};
struct PairReaxBondOrder1{};
struct PairReaxBondOrder1_LessAtomics{};
struct PairReaxBondOrder2{};
struct PairReaxBondOrder3{};
@ -164,10 +159,6 @@ class PairReaxCKokkos : public PairReaxC {
KOKKOS_INLINE_FUNCTION
void operator()(PairReaxBuildListsHalf<NEIGHFLAG>, const int&) const;
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(PairReaxBuildListsHalf_LessAtomics<NEIGHFLAG>, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(PairReaxZero, const int&) const;
@ -180,9 +171,6 @@ class PairReaxCKokkos : public PairReaxC {
KOKKOS_INLINE_FUNCTION
void operator()(PairReaxBondOrder1, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(PairReaxBondOrder1_LessAtomics, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(PairReaxBondOrder2, const int&) const;
@ -437,7 +425,7 @@ class PairReaxCKokkos : public PairReaxC {
typename AT::t_ffloat_2d_dl d_sum_ovun;
typename AT::t_ffloat_2d_dl d_dBOpx, d_dBOpy, d_dBOpz;
int neighflag,newton_pair, maxnumneigh, maxhb, maxbo;
int neighflag, newton_pair, maxnumneigh, maxhb, maxbo;
int nlocal,nall,eflag,vflag;
F_FLOAT cut_nbsq, cut_hbsq, cut_bosq, bo_cut, thb_cut, thb_cutsq;
F_FLOAT bo_cut_bond;

15
src/KOKKOS/pair_table_kokkos.cpp
View File

@ -136,12 +136,6 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
f.contribute();
} else if (neighflag == N2) {
PairComputeFunctor<PairTableKokkos<DeviceType>,N2,false,S_TableCompute<DeviceType,TABSTYLE> >
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
f.contribute();
}
} else {
if (neighflag == FULL) {
@ -162,12 +156,6 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
f.contribute();
} else if (neighflag == N2) {
PairComputeFunctor<PairTableKokkos<DeviceType>,N2,true,S_TableCompute<DeviceType,TABSTYLE> >
f(this,(NeighListKokkos<DeviceType>*) list);
if (eflag || vflag) Kokkos::parallel_reduce(list->inum,f,ev);
else Kokkos::parallel_for(list->inum,f);
f.contribute();
}
}
@ -525,9 +513,6 @@ void PairTableKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/kk");
}

10
src/KOKKOS/pair_table_kokkos.h
View File

@ -41,7 +41,7 @@ template<class DeviceType>
class PairTableKokkos : public PairTable {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
@ -139,38 +139,30 @@ class PairTableKokkos : public PairTable {
friend class PairComputeFunctor<PairTableKokkos,FULL,true,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,true,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,true,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,N2,true,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,FULL,false,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,false,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,false,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,N2,false,S_TableCompute<DeviceType,LOOKUP> >;
friend class PairComputeFunctor<PairTableKokkos,FULL,true,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,true,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,true,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,N2,true,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,FULL,false,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,false,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,false,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,N2,false,S_TableCompute<DeviceType,LINEAR> >;
friend class PairComputeFunctor<PairTableKokkos,FULL,true,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,true,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,true,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,N2,true,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,FULL,false,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,false,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,false,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,N2,false,S_TableCompute<DeviceType,SPLINE> >;
friend class PairComputeFunctor<PairTableKokkos,FULL,true,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,true,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,true,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,N2,true,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,FULL,false,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,HALF,false,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,false,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,N2,false,S_TableCompute<DeviceType,BITMAP> >;
friend void pair_virial_fdotr_compute<PairTableKokkos>(PairTableKokkos*);
};

5
src/KOKKOS/pair_table_rx_kokkos.cpp
View File

@ -665,8 +665,6 @@ void PairTableRXKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
nspecies, isite1, isite2, fractionalWeighting,
mixWtSite1old, mixWtSite2old, mixWtSite1, mixWtSite2);
if (neighflag == N2) error->all(FLERR,"pair table/rx/kk can't handle N2 yet\n");
NeighListKokkos<DeviceType>* l =
dynamic_cast<NeighListKokkos<DeviceType>*>(list);
@ -1282,9 +1280,6 @@ void PairTableRXKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/kk");
}

2
src/KOKKOS/pair_table_rx_kokkos.h
View File

@ -30,7 +30,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairTableRXKokkos : public PairTable {
public:
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
typedef DeviceType device_type;
PairTableRXKokkos(class LAMMPS *);

4
src/KOKKOS/pair_yukawa_kokkos.h
View File

@ -103,19 +103,15 @@ class PairYukawaKokkos : public PairYukawa {
friend class PairComputeFunctor<PairYukawaKokkos,FULL,true>;
friend class PairComputeFunctor<PairYukawaKokkos,HALF,true>;
friend class PairComputeFunctor<PairYukawaKokkos,HALFTHREAD,true>;
friend class PairComputeFunctor<PairYukawaKokkos,N2,true>;
friend class PairComputeFunctor<PairYukawaKokkos,FULL,false>;
friend class PairComputeFunctor<PairYukawaKokkos,HALF,false>;
friend class PairComputeFunctor<PairYukawaKokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairYukawaKokkos,N2,false>;
friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,FULL,void>(
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,HALF,void>(
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,HALFTHREAD,void>(
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,N2,void>(
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairYukawaKokkos,void>(
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
friend void pair_virial_fdotr_compute<PairYukawaKokkos>(PairYukawaKokkos*);

3
src/KOKKOS/pair_zbl_kokkos.cpp
View File

@ -103,9 +103,6 @@ void PairZBLKokkos<DeviceType>::init_style()
} else if (neighflag == HALF || neighflag == HALFTHREAD) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
} else if (neighflag == N2) {
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 0;
} else {
error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/kk");
}

10
src/KOKKOS/pppm_kokkos.cpp
View File

@ -106,7 +106,7 @@ PPPMKokkos<DeviceType>::PPPMKokkos(LAMMPS *lmp) : PPPM(lmp)
// see JCP 109, pg 7698 for derivation of coefficients
// higher order coefficients may be computed if needed
acons = typename Kokkos::DualView<F_FLOAT[8][7],Kokkos::LayoutRight,LMPDeviceType>::t_host("pppm:acons");
acons = typename Kokkos::DualView<F_FLOAT[8][7],Kokkos::LayoutRight,DeviceType>::t_host("pppm:acons");
acons(1,0) = 2.0 / 3.0;
acons(2,0) = 1.0 / 50.0;
acons(2,1) = 5.0 / 294.0;
@ -2581,7 +2581,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_fieldforce_peratom, const int &i
------------------------------------------------------------------------- */
template<class DeviceType>
void PPPMKokkos<DeviceType>::pack_forward_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
void PPPMKokkos<DeviceType>::pack_forward_kspace_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());
@ -2637,7 +2637,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_pack_forward2, const int &i) con
------------------------------------------------------------------------- */
template<class DeviceType>
void PPPMKokkos<DeviceType>::unpack_forward_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
void PPPMKokkos<DeviceType>::unpack_forward_kspace_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());
@ -2694,7 +2694,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_unpack_forward2, const int &i) c
------------------------------------------------------------------------- */
template<class DeviceType>
void PPPMKokkos<DeviceType>::pack_reverse_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
void PPPMKokkos<DeviceType>::pack_reverse_kspace_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());
@ -2724,7 +2724,7 @@ void PPPMKokkos<DeviceType>::operator()(TagPPPM_pack_reverse, const int &i) cons
------------------------------------------------------------------------- */
template<class DeviceType>
void PPPMKokkos<DeviceType>::unpack_reverse_kspace_kokkos(int flag, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
void PPPMKokkos<DeviceType>::unpack_reverse_kspace_kokkos(int flag, FFT_DAT::tdual_FFT_SCALAR_1d &k_buf, int nlist, DAT::tdual_int_2d &k_list, int index)
{
typename AT::t_int_2d_um d_list = k_list.view<DeviceType>();
d_list_index = Kokkos::subview(d_list,index,Kokkos::ALL());

8
src/KOKKOS/pppm_kokkos.h
View File

@ -403,10 +403,10 @@ class PPPMKokkos : public PPPM, public KokkosBaseFFT {
// grid communication
void pack_forward_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
void unpack_forward_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
void pack_reverse_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
void unpack_reverse_kspace_kokkos(int, Kokkos::DualView<FFT_SCALAR*,Kokkos::LayoutRight,LMPDeviceType> &, int, DAT::tdual_int_2d &, int);
void pack_forward_kspace_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int);
void unpack_forward_kspace_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int);
void pack_reverse_kspace_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int);
void unpack_reverse_kspace_kokkos(int, FFT_DAT::tdual_FFT_SCALAR_1d &, int, DAT::tdual_int_2d &, int);
// triclinic