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Merge branch 'master' of https://github.com/lammps/lammps into kk_compute_coord_atom

This commit is contained in:
Stan Moore 2020-04-30 11:34:19 -06:00
parent 63a2f17410 6b8f26e8ad
commit 23c5384b47
19 changed files with 54 additions and 181 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)

24
doc/src/hyper.rst
View File

@ -51,19 +51,17 @@ each timestep. In the bond-boost hyperdynamics context, a "bond" is
not a covalent bond between a pair of atoms in a molecule. Rather it
is simply a pair of nearby atoms as discussed below.
Both global and local HD are described in :ref:`(Voter2013) <Voter2013>` by
Art Voter and collaborators. Similar to parallel replica dynamics
(PRD), global and local HD are methods for performing accelerated
dynamics that are suitable for infrequent-event systems that obey
first-order kinetics. A good overview of accelerated dynamics methods
for such systems in given in :ref:`(Voter2002) <Voter2002hd>` from the same
group. To quote from the review paper: "The dynamical evolution is
characterized by vibrational excursions within a potential basin,
punctuated by occasional transitions between basins." The transition
probability is characterized by p(t) = k\*exp(-kt) where k is the rate
constant. Running multiple replicas gives an effective enhancement in
the timescale spanned by the multiple simulations, while waiting for
an event to occur.
Both global and local HD are described in :ref:`(Voter2013)
<Voter2013>` by Art Voter and collaborators. Similar to parallel
replica dynamics (PRD), global and local HD are methods for performing
accelerated dynamics that are suitable for infrequent-event systems
that obey first-order kinetics. A good overview of accelerated
dynamics methods (AMD) for such systems in given in :ref:`(Voter2002)
<Voter2002hd>` from the same group. To quote from the review paper:
"The dynamical evolution is characterized by vibrational excursions
within a potential basin, punctuated by occasional transitions between
basins. The transition probability is characterized by p(t) =
k\*exp(-kt) where k is the rate constant."
Both HD and PRD produce a time-accurate trajectory that effectively
extends the timescale over which a system can be simulated, but they

23
doc/src/prd.rst
View File

@ -52,19 +52,16 @@ replicas of a system. One or more replicas can be used. The total
number of steps *N* to run can be interpreted in one of two ways; see
discussion of the *time* keyword below.
PRD is described in :ref:`(Voter1998) <Voter1998>` by Art Voter. Similar to
global or local hyperdynamics (HD), PRD is a method for performing
accelerated dynamics that is suitable for infrequent-event systems
that obey first-order kinetics. A good overview of accelerated
dynamics methods for such systems in given in this review paper
:ref:`(Voter2002) <Voter2002prd>` from Art's group. To quote from the
paper: "The dynamical evolution is characterized by vibrational
excursions within a potential basin, punctuated by occasional
transitions between basins." The transition probability is
characterized by p(t) = k\*exp(-kt) where k is the rate constant.
Running multiple replicas gives an effective enhancement in the
timescale spanned by the multiple simulations, while waiting for an
event to occur.
PRD is described in :ref:`(Voter1998) <Voter1998>` by Art Voter.
Similar to global or local hyperdynamics (HD), PRD is a method for
performing accelerated dynamics that is suitable for infrequent-event
systems that obey first-order kinetics. A good overview of
accelerated dynamics methods (AMD) for such systems in given in this
review paper :ref:`(Voter2002) <Voter2002prd>` from Art's group. To
quote from the paper: "The dynamical evolution is characterized by
vibrational excursions within a potential basin, punctuated by
occasional transitions between basins. The transition probability is
characterized by p(t) = k\*exp(-kt) where k is the rate constant."
Both PRD and HD produce a time-accurate trajectory that effectively
extends the timescale over which a system can be simulated, but they

29
doc/src/tad.rst
View File

@ -58,18 +58,21 @@ Run a temperature accelerated dynamics (TAD) simulation. This method
requires two or more partitions to perform NEB transition state
searches.
TAD is described in :ref:`this paper <Voter2000>` by Art Voter. It is a method
that uses accelerated dynamics at an elevated temperature to generate
results at a specified lower temperature. A good overview of
accelerated dynamics methods for such systems is given in :ref:`this review paper <Voter2002>` from the same group. In general, these methods assume
that the long-time dynamics is dominated by infrequent events i.e. the
system is confined to low energy basins for long periods,
punctuated by brief, randomly-occurring transitions to adjacent
basins. TAD is suitable for infrequent-event systems, where in
TAD is described in :ref:`this paper <Voter2000>` by Art Voter. It is
a method that uses accelerated dynamics at an elevated temperature to
generate results at a specified lower temperature. A good overview of
accelerated dynamics methods (AMD) for such systems is given in
:ref:`this review paper <Voter2002>` from the same group. To quote
from the review paper: "The dynamical evolution is characterized by
vibrational excursions within a potential basin, punctuated by
occasional transitions between basins. The transition probability is
characterized by p(t) = k\*exp(-kt) where k is the rate constant."
TAD is a suitable AMD method for infrequent-event systems, where in
addition, the transition kinetics are well-approximated by harmonic
transition state theory (hTST). In hTST, the temperature dependence of
transition rates follows the Arrhenius relation. As a consequence a
set of event times generated in a high-temperature simulation can be
transition state theory (hTST). In hTST, the temperature dependence
of transition rates follows the Arrhenius relation. As a consequence
a set of event times generated in a high-temperature simulation can be
mapped to a set of much longer estimated times in the low-temperature
system. However, because this mapping involves the energy barrier of
the transition event, which is different for each event, the first
@ -79,8 +82,8 @@ events from the current basin. After each event, the simulation is
reflected backwards into the current basin. This is repeated until
the stopping criterion is satisfied, at which point the event with the
earliest low-temperature occurrence time is selected. The stopping
criterion is that the confidence measure be greater than
1-\ *delta*\ . The confidence measure is the probability that no earlier
criterion is that the confidence measure be greater than 1-\ *delta*\
. The confidence measure is the probability that no earlier
low-temperature event will occur at some later time in the
high-temperature simulation. hTST provides an lower bound for this
probability, based on the user-specified minimum pre-exponential

1
src/KOKKOS/npair_kokkos.cpp
View File

@ -55,6 +55,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI,SIZE>::copy_neighbor_info()
newton_pair = force->newton_pair;
k_cutneighsq = neighborKK->k_cutneighsq;
k_cutneighsq.modify<LMPHostType>();
// exclusion info