forked from lijiext/lammps
Merge remote-tracking branch 'origin/master' into latte
This commit is contained in:
Christoph Junghans
commit
17aeccf19f
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@ -23,13 +23,11 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
|||
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
|
||||
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
||||
|
||||
foreach(STYLE_FILE style_angle.h style_atom.h style_body.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h
|
||||
style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_nbin.h style_npair.h style_nstencil.h
|
||||
style_ntopo.h style_pair.h style_reader.h style_region.h)
|
||||
if(EXISTS ${LAMMPS_SOURCE_DIR}/${STYLE_FILE})
|
||||
message(FATAL_ERROR "There is a ${STYLE_FILE} in ${LAMMPS_SOURCE_DIR}, please clean up the source directory first")
|
||||
endif()
|
||||
endforeach()
|
||||
# remove any style headers in the src dir
|
||||
file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
|
||||
if(SRC_STYLE_FILES)
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||||
file(REMOVE ${SRC_STYLE_FILES})
|
||||
endif()
|
||||
|
||||
enable_language(CXX)
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||||
|
||||
|
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@ -43,10 +41,13 @@ include(CheckCCompilerFlag)
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|||
# User input options #
|
||||
########################################################################
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||||
option(BUILD_SHARED_LIBS "Build shared libs" OFF)
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||||
option(INSTALL_LIB "Install lammps library and header" ON)
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||||
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
|
||||
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
|
||||
endif()
|
||||
include(GNUInstallDirs)
|
||||
|
||||
set(LAMMPS_LINK_LIBS)
|
||||
set(LAMMPS_API_DEFINES)
|
||||
option(ENABLE_MPI "Build MPI version" OFF)
|
||||
if(ENABLE_MPI)
|
||||
find_package(MPI REQUIRED)
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||||
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@ -58,13 +59,15 @@ if(ENABLE_MPI)
|
|||
endif()
|
||||
else()
|
||||
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
|
||||
list(APPEND LIB_SOURCES ${MPI_SOURCES})
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||||
add_library(mpi_stubs STATIC ${MPI_SOURCES})
|
||||
include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
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||||
list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
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||||
endif()
|
||||
|
||||
set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit")
|
||||
set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL)
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||||
add_definitions(-D${LAMMPS_SIZE_LIMIT})
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||||
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
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||||
|
||||
set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
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||||
add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
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||||
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@ -72,6 +75,13 @@ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
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|||
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
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||||
if(LAMMPS_EXCEPTIONS)
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||||
add_definitions(-DLAMMPS_EXCEPTIONS)
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||||
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES -DLAMMPS_EXCEPTIONS")
|
||||
endif()
|
||||
|
||||
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
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||||
mark_as_advanced(LAMMPS_MACHINE)
|
||||
if(LAMMPS_MACHINE)
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||||
set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
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||||
endif()
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||||
|
||||
option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
|
||||
|
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@ -86,10 +96,10 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU
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|||
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
|
||||
REAX REPLICA RIGID SHOCK SNAP SRD)
|
||||
set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
|
||||
USER-ATC USER-AWPMD USER-CGDNA
|
||||
USER-ATC USER-AWPMD USER-CGDNA USER-MESO
|
||||
USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
|
||||
USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
|
||||
USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
|
||||
USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
|
||||
USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
|
||||
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
|
||||
foreach(PKG ${DEFAULT_PACKAGES})
|
||||
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@ -122,6 +132,8 @@ endif()
|
|||
######################################################
|
||||
if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
|
||||
enable_language(Fortran)
|
||||
include(CheckFortranCompilerFlag)
|
||||
check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
|
||||
endif()
|
||||
|
||||
if(ENABLE_KOKKOS OR ENABLE_MSCG)
|
||||
|
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@ -156,18 +168,22 @@ endif()
|
|||
if(ENABLE_MISC)
|
||||
option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
|
||||
if(LAMMPS_XDR)
|
||||
add_definitions(-DLAMMPS_XDR)
|
||||
add_definitions(-DLAMMPS_XDR) # for liblammps
|
||||
endif()
|
||||
endif()
|
||||
|
||||
if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP)
|
||||
find_package(LAPACK)
|
||||
if(LAPACK_FOUND)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${LAPACK_LIBRARIES})
|
||||
else()
|
||||
if(NOT LAPACK_FOUND)
|
||||
enable_language(Fortran)
|
||||
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
|
||||
list(APPEND LIB_SOURCES ${LAPACK_SOURCES})
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||||
add_library(linalg STATIC ${LAPACK_SOURCES})
|
||||
include(CheckFortranCompilerFlag)
|
||||
check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
|
||||
if(FC_HAS_NO_SECOND_UNDERSCORE)
|
||||
target_compile_options(linalg PRIVATE -fno-second-underscore)
|
||||
endif()
|
||||
set(LAPACK_LIBRARIES linalg)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
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@ -227,7 +243,10 @@ if(ENABLE_LATTE)
|
|||
endif()
|
||||
|
||||
if(ENABLE_USER-MOLFILE)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${CMAKE_DL_LIBS})
|
||||
add_library(molfile INTERFACE)
|
||||
target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
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||||
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
|
||||
list(APPEND LAMMPS_LINK_LIBS molfile)
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-NETCDF)
|
||||
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@ -244,7 +263,7 @@ endif()
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|||
|
||||
if(ENABLE_USER-QUIP)
|
||||
find_package(QUIP REQUIRED)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
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||||
list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-QMMM)
|
||||
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@ -253,17 +272,6 @@ if(ENABLE_USER-QMMM)
|
|||
list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-AWPMD)
|
||||
include_directories(${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact
|
||||
${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-H5MD)
|
||||
find_package(HDF5 REQUIRED)
|
||||
list(APPEND LAMMPS_LINK_LIBS ${HDF5_LIBRARIES})
|
||||
include_directories(${HDF5_INCLUDE_DIRS} ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-VTK)
|
||||
find_package(VTK REQUIRED NO_MODULE)
|
||||
include(${VTK_USE_FILE})
|
||||
|
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@ -294,13 +302,11 @@ if(ENABLE_MSCG)
|
|||
WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
|
||||
endif()
|
||||
file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
|
||||
list(APPEND LIB_SOURCES ${MSCG_SOURCES})
|
||||
foreach(MSCG_SOURCE ${MSCG_SOURCES})
|
||||
set_property(SOURCE ${MSCG_SOURCE} APPEND PROPERTY COMPILE_DEFINITIONS
|
||||
DIMENSION=3 _exclude_gromacs=1)
|
||||
endforeach()
|
||||
include_directories(${LAMMPS_LIB_MSCG_BIN_DIR} ${GSL_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
|
||||
add_library(mscg STATIC ${MSCG_SOURCES})
|
||||
list(APPEND LAMMPS_LINK_LIBS mscg)
|
||||
target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
|
||||
target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
|
||||
target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
########################################################################
|
||||
|
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@ -326,7 +332,7 @@ endforeach(FUNC)
|
|||
list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
|
||||
|
||||
######################################
|
||||
# Generate Basic Style files
|
||||
# Generate Basic Style files
|
||||
######################################
|
||||
include(StyleHeaderUtils)
|
||||
RegisterStyles(${LAMMPS_SOURCE_DIR})
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||||
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@ -335,13 +341,27 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
|
|||
# add sources of enabled packages
|
||||
############################################
|
||||
foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
|
||||
if(ENABLE_${PKG})
|
||||
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
|
||||
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
|
||||
|
||||
# ignore PKG files which were manually installed in src folder
|
||||
# headers are ignored during RegisterStyles
|
||||
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
|
||||
file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
|
||||
|
||||
foreach(PKG_FILE in ${${PKG}_SOURCES})
|
||||
get_filename_component(FNAME ${PKG_FILE} NAME)
|
||||
list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME})
|
||||
endforeach()
|
||||
|
||||
foreach(PKG_FILE in ${${PKG}_HEADERS})
|
||||
get_filename_component(FNAME ${PKG_FILE} NAME)
|
||||
DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
|
||||
endforeach()
|
||||
|
||||
if(ENABLE_${PKG})
|
||||
# detects styles in package and adds them to global list
|
||||
RegisterStyles(${${PKG}_SOURCES_DIR})
|
||||
|
||||
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
|
||||
list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
|
||||
include_directories(${${PKG}_SOURCES_DIR})
|
||||
endif()
|
||||
|
|
@ -351,17 +371,53 @@ endforeach()
|
|||
# add lib sources of (simple) enabled packages
|
||||
############################################
|
||||
foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
|
||||
USER-MOLFILE USER-QMMM)
|
||||
USER-QMMM)
|
||||
if(ENABLE_${SIMPLE_LIB})
|
||||
string(REGEX REPLACE "^USER-" "" SIMPLE_LIB "${SIMPLE_LIB}")
|
||||
string(TOLOWER "${SIMPLE_LIB}" INC_DIR)
|
||||
file(GLOB_RECURSE ${SIMPLE_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.F
|
||||
${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.cpp)
|
||||
list(APPEND LIB_SOURCES ${${SIMPLE_LIB}_SOURCES})
|
||||
include_directories(${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR})
|
||||
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
|
||||
string(TOLOWER "${PKG_LIB}" PKG_LIB)
|
||||
file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
|
||||
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
|
||||
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
|
||||
if(PKG_LIB STREQUAL awpmd)
|
||||
target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
|
||||
elseif(PKG_LIB STREQUAL h5md)
|
||||
target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
|
||||
else()
|
||||
target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
|
||||
endif()
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
if(ENABLE_USER-AWPMD)
|
||||
target_link_libraries(awpmd ${LAPACK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-ATC)
|
||||
target_link_libraries(atc ${LAPACK_LIBRARIES})
|
||||
endif()
|
||||
|
||||
if(ENABLE_USER-H5MD)
|
||||
find_package(HDF5 REQUIRED)
|
||||
target_link_libraries(h5md ${HDF5_LIBRARIES})
|
||||
target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
|
||||
endif()
|
||||
|
||||
if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE)
|
||||
foreach(FSRC ${meam_SOURCES})
|
||||
string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}")
|
||||
list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX)
|
||||
if(FINDEX GREATER -1)
|
||||
set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore")
|
||||
endif()
|
||||
endforeach()
|
||||
endif()
|
||||
|
||||
if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE)
|
||||
target_compile_options(reax PRIVATE -fno-second-underscore)
|
||||
endif()
|
||||
|
||||
|
||||
######################################################################
|
||||
# packages which selectively include variants based on enabled styles
|
||||
# e.g. accelerator packages
|
||||
|
|
@ -458,62 +514,130 @@ if(ENABLE_USER-INTEL)
|
|||
endif()
|
||||
|
||||
if(ENABLE_GPU)
|
||||
find_package(CUDA REQUIRED)
|
||||
find_program(BIN2C bin2c)
|
||||
if(NOT BIN2C)
|
||||
message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
|
||||
endif()
|
||||
include_directories(${CUDA_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||
set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "Lammps gpu precision size")
|
||||
set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
|
||||
add_definitions(-D_${GPU_PREC})
|
||||
add_definitions(-DNV_KERNEL -DUCL_CUDADR)
|
||||
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
|
||||
|
||||
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
|
||||
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h)
|
||||
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
|
||||
${GPU_SOURCES_DIR}/fix_gpu.h
|
||||
${GPU_SOURCES_DIR}/fix_gpu.cpp)
|
||||
|
||||
set(GPU_API "OpenCL" CACHE STRING "API used by GPU package")
|
||||
set_property(CACHE GPU_API PROPERTY STRINGS OpenCL CUDA)
|
||||
|
||||
set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "LAMMPS GPU precision size")
|
||||
set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
|
||||
|
||||
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
|
||||
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
|
||||
|
||||
if(GPU_API STREQUAL "CUDA")
|
||||
find_package(CUDA REQUIRED)
|
||||
find_program(BIN2C bin2c)
|
||||
if(NOT BIN2C)
|
||||
message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
|
||||
endif()
|
||||
option(CUDPP_OPT "Enable CUDPP_OPT" ON)
|
||||
|
||||
set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture")
|
||||
set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60)
|
||||
|
||||
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
|
||||
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
|
||||
|
||||
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
|
||||
|
||||
if(CUDPP_OPT)
|
||||
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
|
||||
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
|
||||
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
|
||||
endif()
|
||||
|
||||
cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
|
||||
-DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
|
||||
|
||||
cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
|
||||
-DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
|
||||
|
||||
foreach(CU_OBJ ${GPU_GEN_OBJS})
|
||||
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
|
||||
string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
|
||||
add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
|
||||
COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
|
||||
DEPENDS ${CU_OBJ}
|
||||
COMMENT "Generating ${CU_NAME}_cubin.h")
|
||||
list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
|
||||
endforeach()
|
||||
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
|
||||
|
||||
|
||||
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
|
||||
target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
|
||||
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
|
||||
if(CUDPP_OPT)
|
||||
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
|
||||
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
|
||||
endif()
|
||||
|
||||
list(APPEND LAMMPS_LINK_LIBS gpu)
|
||||
|
||||
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
||||
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
|
||||
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
|
||||
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
|
||||
|
||||
|
||||
elseif(GPU_API STREQUAL "OpenCL")
|
||||
find_package(OpenCL REQUIRED)
|
||||
set(OCL_TUNE "GENERIC" CACHE STRING "OpenCL Device Tuning")
|
||||
set_property(CACHE OCL_TUNE PROPERTY STRINGS INTEL FERMI KEPLER CYPRESS GENERIC)
|
||||
|
||||
include(OpenCLUtils)
|
||||
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
|
||||
|
||||
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu)
|
||||
list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
|
||||
|
||||
foreach(GPU_KERNEL ${GPU_LIB_CU})
|
||||
get_filename_component(basename ${GPU_KERNEL} NAME_WE)
|
||||
string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
|
||||
GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
|
||||
list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
|
||||
endforeach()
|
||||
|
||||
GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
|
||||
GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
|
||||
list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h)
|
||||
|
||||
add_library(gpu STATIC ${GPU_LIB_SOURCES})
|
||||
target_link_libraries(gpu ${OpenCL_LIBRARIES})
|
||||
target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
|
||||
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
|
||||
target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
|
||||
|
||||
list(APPEND LAMMPS_LINK_LIBS gpu)
|
||||
|
||||
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
|
||||
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
|
||||
target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
|
||||
target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
|
||||
endif()
|
||||
|
||||
# GPU package
|
||||
FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
|
||||
|
||||
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
|
||||
|
||||
# detects styles which have GPU version
|
||||
RegisterStylesExt(${GPU_SOURCES_DIR} opt GPU_SOURCES)
|
||||
RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
|
||||
|
||||
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
|
||||
|
||||
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
|
||||
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
|
||||
file(GLOB_RECURSE GPU_NOT_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
|
||||
list(REMOVE_ITEM GPU_LIB_CU ${GPU_NOT_LIB_CU})
|
||||
include_directories(${GPU_SOURCES_DIR} ${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
|
||||
if(CUDPP_OPT)
|
||||
include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
|
||||
add_definitions(-DCUDPP_OPT)
|
||||
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
|
||||
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
|
||||
endif()
|
||||
cuda_compile(GPU_OBJS ${GPU_LIB_CU} ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>)
|
||||
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
|
||||
foreach(CU_OBJ ${GPU_OBJS})
|
||||
get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
|
||||
string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
|
||||
add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
|
||||
COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
|
||||
DEPENDS ${CU_OBJ}
|
||||
COMMENT "Generating ${CU_NAME}_cubin.h")
|
||||
list(APPEND LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
|
||||
if(${CU_NAME} STREQUAL "pppm_d") #pppm_d doesn't get linked into the lib
|
||||
set(CU_FORBIDDEN_OBJ "${CU_OBJ}")
|
||||
endif()
|
||||
endforeach()
|
||||
list(REMOVE_ITEM GPU_OBJS "${CU_FORBIDDEN_OBJ}")
|
||||
list(APPEND LIB_SOURCES ${GPU_SOURCES} ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
|
||||
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
|
||||
|
||||
list(APPEND LIB_SOURCES ${GPU_SOURCES})
|
||||
include_directories(${GPU_SOURCES_DIR})
|
||||
endif()
|
||||
|
||||
######################################################
|
||||
# Generate style headers based on global list of
|
||||
# styles registered during package selection
|
||||
# styles registered during package selection
|
||||
######################################################
|
||||
set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
|
||||
|
||||
|
|
@ -527,19 +651,21 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
|
|||
############################################
|
||||
add_library(lammps ${LIB_SOURCES})
|
||||
target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
|
||||
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
|
||||
if(INSTALL_LIB)
|
||||
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
|
||||
if(BUILD_SHARED_LIBS)
|
||||
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
|
||||
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
|
||||
install(FILES ${LAMMPS_SOURCE_DIR}/lammps.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
|
||||
elseif(BUILD_SHARED_LIBS)
|
||||
message(FATAL_ERROR "Shared library has to be installed, use -DINSTALL_LIB=ON to install lammps with a library")
|
||||
install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
|
||||
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)
|
||||
endif()
|
||||
|
||||
add_executable(lmp ${LMP_SOURCES})
|
||||
target_link_libraries(lmp lammps)
|
||||
set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
|
||||
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
if(ENABLE_TESTING)
|
||||
add_test(ShowHelp ${CMAKE_CURRENT_BINARY_DIR}/lmp -help)
|
||||
add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
|
||||
endif()
|
||||
|
||||
##################################
|
||||
|
|
@ -550,3 +676,27 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
|
|||
message(STATUS "Building package: ${PKG}")
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
|
||||
message(STATUS "<<< Build configuration >>>
|
||||
Build type ${CMAKE_BUILD_TYPE}
|
||||
Install path ${CMAKE_INSTALL_PREFIX}
|
||||
Compilers and Flags:
|
||||
C++ Compiler ${CMAKE_CXX_COMPILER}
|
||||
Type ${CMAKE_CXX_COMPILER_ID}
|
||||
C++ Flags ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
|
||||
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
|
||||
if(LANGUAGES MATCHES ".*Fortran.*")
|
||||
message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
|
||||
Type ${CMAKE_Fortran_COMPILER_ID}
|
||||
Fortran Flags ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
|
||||
endif()
|
||||
message(STATUS "Linker flags:
|
||||
Executable ${CMAKE_EXE_LINKER_FLAGS}")
|
||||
if(BUILD_SHARED_LIBS)
|
||||
message(STATUS "Shared libries ${CMAKE_SHARED_LINKER_FLAGS}")
|
||||
else()
|
||||
message(STATUS "Static libries ${CMAKE_STATIC_LINKER_FLAGS}")
|
||||
endif()
|
||||
message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,18 @@
|
|||
function(GenerateOpenCLHeader varname outfile files)
|
||||
message("Creating ${outfile}...")
|
||||
file(WRITE ${outfile} "const char * ${varname} = \n")
|
||||
math(EXPR ARG_END "${ARGC}-1")
|
||||
|
||||
foreach(IDX RANGE 2 ${ARG_END})
|
||||
list(GET ARGV ${IDX} filename)
|
||||
file(READ ${filename} content)
|
||||
string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}")
|
||||
string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
|
||||
string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
|
||||
string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")
|
||||
string(REGEX REPLACE "\n+" "\n" content "${content}")
|
||||
file(APPEND ${outfile} "${content}")
|
||||
endforeach()
|
||||
|
||||
file(APPEND ${outfile} ";\n")
|
||||
endfunction(GenerateOpenCLHeader)
|
||||
|
|
@ -85,6 +85,35 @@ function(RegisterStyles search_path)
|
|||
FindStyleHeaders(${search_path} REGION_CLASS region_ REGION ) # region ) # domain
|
||||
endfunction(RegisterStyles)
|
||||
|
||||
function(RemovePackageHeader headers pkg_header)
|
||||
get_property(hlist GLOBAL PROPERTY ${headers})
|
||||
list(REMOVE_ITEM hlist ${pkg_header})
|
||||
set_property(GLOBAL PROPERTY ${headers} "${hlist}")
|
||||
endfunction(RemovePackageHeader)
|
||||
|
||||
function(DetectAndRemovePackageHeader fname)
|
||||
RemovePackageHeader(ANGLE ${fname})
|
||||
RemovePackageHeader(ATOM_VEC ${fname})
|
||||
RemovePackageHeader(BODY ${fname})
|
||||
RemovePackageHeader(BOND ${fname})
|
||||
RemovePackageHeader(COMMAND ${fname})
|
||||
RemovePackageHeader(COMPUTE ${fname})
|
||||
RemovePackageHeader(DIHEDRAL ${fname})
|
||||
RemovePackageHeader(DUMP ${fname})
|
||||
RemovePackageHeader(FIX ${fname})
|
||||
RemovePackageHeader(IMPROPER ${fname})
|
||||
RemovePackageHeader(INTEGRATE ${fname})
|
||||
RemovePackageHeader(KSPACE ${fname})
|
||||
RemovePackageHeader(MINIMIZE ${fname})
|
||||
RemovePackageHeader(NBIN ${fname})
|
||||
RemovePackageHeader(NPAIR ${fname})
|
||||
RemovePackageHeader(NSTENCIL ${fname})
|
||||
RemovePackageHeader(NTOPO ${fname})
|
||||
RemovePackageHeader(PAIR ${fname})
|
||||
RemovePackageHeader(READER ${fname})
|
||||
RemovePackageHeader(REGION ${fname})
|
||||
endfunction(DetectAndRemovePackageHeader)
|
||||
|
||||
function(RegisterStylesExt search_path extension sources)
|
||||
FindStyleHeadersExt(${search_path} ANGLE_CLASS ${extension} ANGLE ${sources})
|
||||
FindStyleHeadersExt(${search_path} ATOM_CLASS ${extension} ATOM_VEC ${sources})
|
||||
|
|
|
|||
|
|
@ -0,0 +1,18 @@
|
|||
# pkg-config file for lammps
|
||||
# https://people.freedesktop.org/~dbn/pkg-config-guide.html
|
||||
# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
|
||||
# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
|
||||
# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
|
||||
|
||||
prefix=@CMAKE_INSTALL_FULL_PREFIX@
|
||||
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
|
||||
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
|
||||
|
||||
Name: liblammps@LAMMPS_MACHINE@
|
||||
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
|
||||
URL: http://lammps.sandia.gov
|
||||
Version:
|
||||
Requires:
|
||||
Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
|
||||
Libs.private: -lm
|
||||
Cflags: -I${includedir} @LAMMPS_API_DEFINES@
|
||||
|
|
@ -532,7 +532,7 @@ package"_Section_start.html#start_3.
|
|||
"dump vtk"_dump_vtk.html,
|
||||
"group2ndx"_group2ndx.html,
|
||||
"ndx2group"_group2ndx.html,
|
||||
"temper/grem"_temper_grem.html
|
||||
"temper/grem"_temper_grem.html,
|
||||
"temper/npt"_temper_npt.html :tb(c=3,ea=c)
|
||||
|
||||
:line
|
||||
|
|
|
|||
|
|
@ -2191,7 +2191,7 @@ src/USER-MESO/README
|
|||
"pair_style edpd"_pair_meso.html
|
||||
"pair_style mdpd"_pair_meso.html
|
||||
"pair_style tdpd"_pair_meso.html
|
||||
"fix mvv/dpd"_fix_mvv.html
|
||||
"fix mvv/dpd"_fix_mvv_dpd.html
|
||||
examples/USER/meso
|
||||
http://lammps.sandia.gov/movies.html#mesodpd :ul
|
||||
|
||||
|
|
|
|||
|
|
@ -139,6 +139,11 @@ forces added by this fix in a consistent manner. I.e. there is a
|
|||
decrease in potential energy when atoms move in the direction of the
|
||||
added force.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to the added forces on atoms to the
|
||||
system's virial as part of "thermodynamic output"_thermo_style.html.
|
||||
The default is {virial no}
|
||||
|
||||
The "fix_modify"_fix_modify.html {respa} option is supported by this
|
||||
fix. This allows to set at which level of the "r-RESPA"_run_style.html
|
||||
integrator the fix is adding its forces. Default is the outermost
|
||||
|
|
|
|||
|
|
@ -97,6 +97,11 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
|
|||
fix to add the potential "energy" of the CMAP interactions system's
|
||||
potential energy as part of "thermodynamic output"_thermo_style.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to the interaction between atoms to
|
||||
the system's virial as part of "thermodynamic output"_thermo_style.html.
|
||||
The default is {virial yes}
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15. The scalar is the
|
||||
potential energy discussed above. The scalar value calculated by this
|
||||
|
|
|
|||
|
|
@ -124,6 +124,11 @@ can include the forces added by this fix in a consistent manner.
|
|||
I.e. there is a decrease in potential energy when atoms move in the
|
||||
direction of the added force due to the electric field.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to the added forces on atoms to the
|
||||
system's virial as part of "thermodynamic output"_thermo_style.html.
|
||||
The default is {virial no}
|
||||
|
||||
The "fix_modify"_fix_modify.html {respa} option is supported by this
|
||||
fix. This allows to set at which level of the "r-RESPA"_run_style.html
|
||||
integrator the fix adding its forces. Default is the outermost level.
|
||||
|
|
|
|||
|
|
@ -131,6 +131,11 @@ forces added by this fix in a consistent manner. I.e. there is a
|
|||
decrease in potential energy when atoms move in the direction of the
|
||||
added force.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to the interactions computed by the
|
||||
external program to the system's virial as part of "thermodynamic
|
||||
output"_thermo_style.html. The default is {virial yes}
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
"output commands"_Section_howto.html#howto_15. The scalar is the
|
||||
potential energy discussed above. The scalar stored by this fix
|
||||
|
|
|
|||
|
|
@ -14,10 +14,11 @@ fix_modify fix-ID keyword value ... :pre
|
|||
|
||||
fix-ID = ID of the fix to modify :ulb,l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l
|
||||
keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
|
||||
{temp} value = compute ID that calculates a temperature
|
||||
{press} value = compute ID that calculates a pressure
|
||||
{energy} value = {yes} or {no}
|
||||
{virial} value = {yes} or {no}
|
||||
{respa} value = {1} to {max respa level} or {0} (for outermost level)
|
||||
{dynamic/dof} value = {yes} or {no}
|
||||
yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
|
||||
|
|
@ -52,11 +53,10 @@ define their own compute by default, as described in their
|
|||
documentation. Thus this option allows the user to override the
|
||||
default method for computing P.
|
||||
|
||||
For fixes that calculate a contribution to the potential energy of the
|
||||
system, the {energy} keyword will include that contribution in
|
||||
thermodynamic output of potential energy. This is because the {energy
|
||||
yes} setting must be specified to include the fix's global or per-atom
|
||||
energy in the calculation performed by the "compute
|
||||
The {energy} keyword can be used with fixes that support it.
|
||||
{energy yes} adds a contribution to the potential energy of the
|
||||
system. The fix's global and per-atom
|
||||
energy is included in the calculation performed by the "compute
|
||||
pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html
|
||||
commands. See the "thermo_style"_thermo_style.html command for info
|
||||
on how potential energy is output. For fixes that tally a global
|
||||
|
|
@ -69,6 +69,25 @@ are using it when performing an "energy minimization"_minimize.html
|
|||
and if you want the energy and forces it produces to be part of the
|
||||
optimization criteria.
|
||||
|
||||
The {virial} keyword can be used with fixes that support it.
|
||||
{virial yes} adds a contribution to the virial of the
|
||||
system. The fix's global and per-atom
|
||||
virial is included in the calculation performed by the "compute
|
||||
pressure"_compute_pressure.html or
|
||||
"compute stress/atom"_compute_stress_atom.html
|
||||
commands. See the "thermo_style"_thermo_style.html command for info
|
||||
on how pressure is output.
|
||||
|
||||
NOTE: You must specify the {virial yes} setting for a fix if you
|
||||
are doing "box relaxation"_fix_box_relax.html and
|
||||
if you want virial contribution of the fix to be part of the
|
||||
relaxation criteria, although this seems unlikely.
|
||||
|
||||
NOTE: This option is only supported by fixes that explicitly say
|
||||
so. For some of these (e.g. the
|
||||
"fix shake"_fix_shake.html command) the default setting is
|
||||
{virial yes}, for others it is {virial no}.
|
||||
|
||||
For fixes that set or modify forces, it may be possible to select at
|
||||
which "r-RESPA"_run_style.html level the fix operates via the {respa}
|
||||
keyword. The RESPA level at which the fix is active can be selected.
|
||||
|
|
@ -111,4 +130,4 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
|
|||
[Default:]
|
||||
|
||||
The option defaults are temp = ID defined by fix, press = ID defined
|
||||
by fix, energy = no, respa = 0.
|
||||
by fix, energy = no, virial = different for each fix style, respa = 0.
|
||||
|
|
|
|||
|
|
@ -703,6 +703,11 @@ NVT, NPT, NPH rigid styles to add the energy change induced by the
|
|||
thermostatting to the system's potential energy as part of
|
||||
"thermodynamic output"_thermo_style.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to keeping the objects rigid to the
|
||||
system's virial as part of "thermodynamic output"_thermo_style.html.
|
||||
The default is {virial yes}
|
||||
|
||||
The "fix_modify"_fix_modify.html {temp} and {press} options are
|
||||
supported by the 4 NPT and NPH rigid styles to change the computes
|
||||
used to calculate the instantaneous pressure tensor. Note that the 2
|
||||
|
|
|
|||
|
|
@ -186,6 +186,11 @@ to 1 and recompiling LAMMPS.
|
|||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to keeping the constraints to the
|
||||
system's virial as part of "thermodynamic output"_thermo_style.html.
|
||||
The default is {virial yes}
|
||||
|
||||
No information about these fixes is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to these fixes. No global or per-atom quantities are
|
||||
|
|
|
|||
|
|
@ -101,6 +101,11 @@ See the "read_restart"_read_restart.html command for info on how to
|
|||
re-specify a fix in an input script that reads a restart file, so that
|
||||
the operation of the fix continues in an uninterrupted fashion.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to the added forces on atoms to the
|
||||
system's virial as part of "thermodynamic output"_thermo_style.html.
|
||||
The default is {virial no}
|
||||
|
||||
The "fix_modify"_fix_modify.html {respa} option is supported by
|
||||
this fix. This allows to set at which level of the "r-RESPA"_run_style.html
|
||||
integrator the fix is adding its forces. Default is the outermost level.
|
||||
|
|
|
|||
|
|
@ -252,6 +252,11 @@ fix to add the energy of interaction between atoms and each wall to
|
|||
the system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to the interaction between
|
||||
atoms and each wall to the system's virial as part of "thermodynamic
|
||||
output"_thermo_style.html. The default is {virial no}
|
||||
|
||||
The "fix_modify"_fix_modify.html {respa} option is supported by this
|
||||
fix. This allows to set at which level of the "r-RESPA"_run_style.html
|
||||
integrator the fix is adding its forces. Default is the outermost level.
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@ fix ID group-ID wall/region region-ID style epsilon sigma cutoff :pre
|
|||
ID, group-ID are documented in "fix"_fix.html command
|
||||
wall/region = style name of this fix command
|
||||
region-ID = region whose boundary will act as wall
|
||||
style = {lj93} or {lj126} or {colloid} or {harmonic}
|
||||
style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic}
|
||||
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
|
||||
sigma = size factor for wall-particle interaction (distance units)
|
||||
cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
|
||||
|
|
@ -112,6 +112,10 @@ For style {lj126}, the energy E is given by the 12/6 potential:
|
|||
|
||||
:c,image(Eqs/pair_lj.jpg)
|
||||
|
||||
For style {wall/lj1043}, the energy E is given by the 10/4/3 potential:
|
||||
|
||||
:c,image(Eqs/fix_wall_lj1043.jpg)
|
||||
|
||||
For style {colloid}, the energy E is given by an integrated form of
|
||||
the "pair_style colloid"_pair_colloid.html potential:
|
||||
|
||||
|
|
@ -128,49 +132,8 @@ surface no longer interact. The energy of the wall potential is
|
|||
shifted so that the wall-particle interaction energy is 0.0 at the
|
||||
cutoff distance.
|
||||
|
||||
For the {lj93} and {lj126} styles, {epsilon} and {sigma} are the usual
|
||||
Lennard-Jones parameters, which determine the strength and size of the
|
||||
particle as it interacts with the wall. Epsilon has energy units.
|
||||
Note that this {epsilon} and {sigma} may be different than any
|
||||
{epsilon} or {sigma} values defined for a pair style that computes
|
||||
particle-particle interactions.
|
||||
|
||||
The {lj93} interaction is derived by integrating over a 3d
|
||||
half-lattice of Lennard-Jones 12/6 particles. The {lj126} interaction
|
||||
is effectively a harder, more repulsive wall interaction.
|
||||
|
||||
For the {colloid} style, {epsilon} is effectively a Hamaker constant
|
||||
with energy units for the colloid-wall interaction, {R} is the radius
|
||||
of the colloid particle, {D} is the distance from the surface of the
|
||||
colloid particle to the wall (r-R), and {sigma} is the size of a
|
||||
constituent LJ particle inside the colloid particle. Note that the
|
||||
cutoff distance Rc in this case is the distance from the colloid
|
||||
particle center to the wall.
|
||||
|
||||
The {colloid} interaction is derived by integrating over constituent
|
||||
LJ particles of size {sigma} within the colloid particle and a 3d
|
||||
half-lattice of Lennard-Jones 12/6 particles of size {sigma} in the
|
||||
wall.
|
||||
|
||||
For the {wall/harmonic} style, {epsilon} is effectively the spring
|
||||
constant K, and has units (energy/distance^2). The input parameter
|
||||
{sigma} is ignored. The minimum energy position of the harmonic
|
||||
spring is at the {cutoff}. This is a repulsive-only spring since the
|
||||
interaction is truncated at the {cutoff}
|
||||
|
||||
NOTE: For all of the styles, you must insure that r is always > 0 for
|
||||
all particles in the group, or LAMMPS will generate an error. This
|
||||
means you cannot start your simulation with particles on the region
|
||||
surface (r = 0) or with particles on the wrong side of the region
|
||||
surface (r < 0). For the {wall/lj93} and {wall/lj126} styles, the
|
||||
energy of the wall/particle interaction (and hence the force on the
|
||||
particle) blows up as r -> 0. The {wall/colloid} style is even more
|
||||
restrictive, since the energy blows up as D = r-R -> 0. This means
|
||||
the finite-size particles of radius R must be a distance larger than R
|
||||
from the region surface. The {harmonic} style is a softer potential
|
||||
and does not blow up as r -> 0, but you must use a large enough
|
||||
{epsilon} that particles always reamin on the correct side of the
|
||||
region surface (r > 0).
|
||||
For a full description of these wall styles, see fix_style
|
||||
"wall"_fix_wall.html
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
|
@ -182,6 +145,11 @@ fix to add the energy of interaction between atoms and the wall to the
|
|||
system's potential energy as part of "thermodynamic
|
||||
output"_thermo_style.html.
|
||||
|
||||
The "fix_modify"_fix_modify.html {virial} option is supported by this
|
||||
fix to add the contribution due to the interaction between
|
||||
atoms and each wall to the system's virial as part of "thermodynamic
|
||||
output"_thermo_style.html. The default is {virial no}
|
||||
|
||||
The "fix_modify"_fix_modify.html {respa} option is supported by this
|
||||
fix. This allows to set at which level of the "r-RESPA"_run_style.html
|
||||
integrator the fix is adding its forces. Default is the outermost level.
|
||||
|
|
|
|||
|
|
@ -308,7 +308,7 @@ int colvarbias_restraint_centers_moving::update_centers(cvm::real lambda)
|
|||
colvarvalue const c_new = colvarvalue::interpolate(initial_centers[i],
|
||||
target_centers[i],
|
||||
lambda);
|
||||
centers_incr[i] = (c_new).dist2_grad(colvar_centers[i]);
|
||||
centers_incr[i] = 0.5 * c_new.dist2_grad(colvar_centers[i]);
|
||||
colvar_centers[i] = c_new;
|
||||
variables(i)->wrap(colvar_centers[i]);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -140,8 +140,13 @@ class UCL_Device {
|
|||
inline void push_command_queue() {
|
||||
cl_int errorv;
|
||||
_cq.push_back(cl_command_queue());
|
||||
_cq.back()=clCreateCommandQueue(_context,_cl_device,
|
||||
CL_QUEUE_PROFILING_ENABLE,&errorv);
|
||||
|
||||
#ifdef CL_VERSION_2_0
|
||||
cl_queue_properties props[] = {CL_QUEUE_PROPERTIES, CL_QUEUE_PROFILING_ENABLE, 0};
|
||||
_cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props, &errorv);
|
||||
#else
|
||||
_cq.back()=clCreateCommandQueue(_context, _cl_device, CL_QUEUE_PROFILING_ENABLE, &errorv);
|
||||
#endif
|
||||
if (errorv!=CL_SUCCESS) {
|
||||
std::cerr << "Could not create command queue on device: " << name()
|
||||
<< std::endl;
|
||||
|
|
|
|||
|
|
@ -217,7 +217,7 @@ __kernel void k_sw(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int nbor, nbor_end, i, numj;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
|
||||
n_stride,nbor_end,nbor);
|
||||
|
||||
|
|
@ -428,7 +428,7 @@ __kernel void k_sw_three_center(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
@ -570,7 +570,7 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end, k_end;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
@ -724,7 +724,7 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end, k_end;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
|
|||
|
|
@ -272,7 +272,7 @@ __kernel void k_tersoff_zeta(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int nbor_j, nbor_end, i, numj;
|
||||
const int* nbor_mem=dev_packed;
|
||||
const __global int* nbor_mem=dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
@ -433,7 +433,7 @@ __kernel void k_tersoff_repulsive(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int nbor, nbor_end, i, numj;
|
||||
const int* nbor_mem=dev_packed;
|
||||
const __global int* nbor_mem=dev_packed;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
|
||||
n_stride,nbor_end,nbor);
|
||||
|
||||
|
|
@ -545,7 +545,7 @@ __kernel void k_tersoff_three_center(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end;
|
||||
const int* nbor_mem=dev_packed;
|
||||
const __global int* nbor_mem=dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
@ -732,7 +732,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end, k_end;
|
||||
const int* nbor_mem=dev_packed;
|
||||
const __global int* nbor_mem=dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
@ -977,7 +977,7 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end, k_end;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
|
|||
|
|
@ -436,7 +436,7 @@ __kernel void k_vashishta_three_center(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
@ -580,7 +580,7 @@ __kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end, k_end;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
@ -735,7 +735,7 @@ __kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (ii<inum) {
|
||||
int i, numj, nbor_j, nbor_end, k_end;
|
||||
const int* nbor_mem = dev_packed;
|
||||
const __global int* nbor_mem = dev_packed;
|
||||
int offset_j=offset/t_per_atom;
|
||||
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset_j,i,numj,
|
||||
n_stride,nbor_end,nbor_j);
|
||||
|
|
|
|||
|
|
@ -46,6 +46,7 @@
|
|||
|
||||
/colvarproxy_lammps.cpp
|
||||
/colvarproxy_lammps.h
|
||||
/colvarproxy_lammps_version.h
|
||||
/fix_colvars.cpp
|
||||
/fix_colvars.h
|
||||
/dump_molfile.cpp
|
||||
|
|
|
|||
|
|
@ -81,6 +81,7 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
|
|||
double r3,rinv3,r2inv3,r4inv3;
|
||||
double rad,rad2,rad4,rad8,diam,new_coeff2;
|
||||
double eoffset;
|
||||
double vn;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
@ -151,6 +152,12 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
|
|||
ewall[0] -= eoffset;
|
||||
|
||||
ewall[m+1] += fwall;
|
||||
|
||||
if (evflag) {
|
||||
if (side < 0) vn = -fwall*delta;
|
||||
else vn = fwall*delta;
|
||||
v_tally(dim, i, vn);
|
||||
}
|
||||
}
|
||||
|
||||
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ FixWallLJ93Kokkos<DeviceType>::FixWallLJ93Kokkos(LAMMPS *lmp, int narg, char **a
|
|||
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
|
||||
datamask_read = EMPTY_MASK;
|
||||
datamask_modify = EMPTY_MASK;
|
||||
virial_flag = 0
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -55,6 +55,7 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
|
|||
extscalar = 1;
|
||||
respa_level_support = 1;
|
||||
ilevel_respa = 0;
|
||||
virial_flag = 1;
|
||||
|
||||
qe2f = force->qe2f;
|
||||
xstr = ystr = zstr = NULL;
|
||||
|
|
@ -257,6 +258,11 @@ void FixEfield::post_force(int vflag)
|
|||
imageint *image = atom->image;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// energy and virial setup
|
||||
|
||||
if (vflag) v_setup(vflag);
|
||||
else evflag = 0;
|
||||
|
||||
// reallocate efield array if necessary
|
||||
|
||||
if (varflag == ATOM && atom->nmax > maxatom) {
|
||||
|
|
@ -281,6 +287,7 @@ void FixEfield::post_force(int vflag)
|
|||
|
||||
double **x = atom->x;
|
||||
double fx,fy,fz;
|
||||
double v[6];
|
||||
|
||||
// constant efield
|
||||
|
||||
|
|
@ -306,6 +313,15 @@ void FixEfield::post_force(int vflag)
|
|||
fsum[1] += fx;
|
||||
fsum[2] += fy;
|
||||
fsum[3] += fz;
|
||||
if (evflag) {
|
||||
v[0] = fx*unwrap[0];
|
||||
v[1] = fy*unwrap[1];
|
||||
v[2] = fz*unwrap[2];
|
||||
v[3] = fx*unwrap[1];
|
||||
v[4] = fx*unwrap[2];
|
||||
v[5] = fy*unwrap[2];
|
||||
v_tally(i, v);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -76,6 +76,7 @@ FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) :
|
|||
restart_peratom = 1;
|
||||
peatom_flag = 1;
|
||||
virial_flag = 1;
|
||||
thermo_virial = 1;
|
||||
peratom_freq = 1;
|
||||
scalar_flag = 1;
|
||||
global_freq = 1;
|
||||
|
|
|
|||
|
|
@ -423,9 +423,6 @@ atom_vec_granular.h
|
|||
# deleted on Fri Nov 19 12:53:07 2010 -0500
|
||||
fix_pour_omp.cpp
|
||||
fix_pour_omp.h
|
||||
# deleted on Thu Aug 19 23:20:14 2010 +0000
|
||||
fix_qeq.cpp
|
||||
fix_qeq.h
|
||||
# deleted on Thu Jun 17 01:34:38 2010 +0000
|
||||
compute_vsum.cpp
|
||||
compute_vsum.h
|
||||
|
|
|
|||
|
|
@ -74,6 +74,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
|
|||
time_integrate = 1;
|
||||
rigid_flag = 1;
|
||||
virial_flag = 1;
|
||||
thermo_virial = 1;
|
||||
create_attribute = 1;
|
||||
dof_flag = 1;
|
||||
enforce2d_flag = 1;
|
||||
|
|
|
|||
|
|
@ -78,6 +78,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
|
|||
time_integrate = 1;
|
||||
rigid_flag = 1;
|
||||
virial_flag = 1;
|
||||
thermo_virial = 1;
|
||||
create_attribute = 1;
|
||||
dof_flag = 1;
|
||||
enforce2d_flag = 1;
|
||||
|
|
|
|||
|
|
@ -60,6 +60,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
|
|||
MPI_Comm_size(world,&nprocs);
|
||||
|
||||
virial_flag = 1;
|
||||
thermo_virial = 1;
|
||||
create_attribute = 1;
|
||||
dof_flag = 1;
|
||||
|
||||
|
|
|
|||
|
|
@ -255,11 +255,10 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR,
|
|||
ito = inum; \
|
||||
}
|
||||
|
||||
#define IP_PRE_omp_range(ifrom, ip, ito, tid, inum, nthreads) \
|
||||
#define IP_PRE_omp_range(ifrom, ito, tid, inum, nthreads) \
|
||||
{ \
|
||||
ifrom = 0; \
|
||||
ito = inum; \
|
||||
ip = 1; \
|
||||
}
|
||||
|
||||
#define IP_PRE_omp_stride_id(ifrom, ip, ito, tid, inum, nthr) \
|
||||
|
|
|
|||
|
|
@ -58,6 +58,7 @@ FixSMD::FixSMD(LAMMPS *lmp, int narg, char **arg) :
|
|||
extvector = 1;
|
||||
respa_level_support = 1;
|
||||
ilevel_respa = 0;
|
||||
virial_flag = 1;
|
||||
|
||||
int argoffs=3;
|
||||
if (strcmp(arg[argoffs],"cvel") == 0) {
|
||||
|
|
@ -181,6 +182,11 @@ void FixSMD::setup(int vflag)
|
|||
|
||||
void FixSMD::post_force(int vflag)
|
||||
{
|
||||
// energy and virial setup
|
||||
|
||||
if (vflag) v_setup(vflag);
|
||||
else evflag = 0;
|
||||
|
||||
if (styleflag & SMD_TETHER) smd_tether();
|
||||
else smd_couple();
|
||||
|
||||
|
|
@ -238,12 +244,15 @@ void FixSMD::smd_tether()
|
|||
// apply restoring force to atoms in group
|
||||
// f = -k*(r-r0)*mass/masstotal
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int *type = atom->type;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
double massfrac;
|
||||
double unwrap[3],v[6];
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
ftotal[0] = ftotal[1] = ftotal[2] = 0.0;
|
||||
|
|
@ -259,6 +268,16 @@ void FixSMD::smd_tether()
|
|||
ftotal[0] -= fx*massfrac;
|
||||
ftotal[1] -= fy*massfrac;
|
||||
ftotal[2] -= fz*massfrac;
|
||||
if (evflag) {
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
v[0] = fx*massfrac*unwrap[0];
|
||||
v[1] = fy*massfrac*unwrap[1];
|
||||
v[2] = fz*massfrac*unwrap[2];
|
||||
v[3] = fx*massfrac*unwrap[1];
|
||||
v[4] = fx*massfrac*unwrap[2];
|
||||
v[5] = fy*massfrac*unwrap[2];
|
||||
v_tally(i, v);
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
|
|
@ -270,6 +289,16 @@ void FixSMD::smd_tether()
|
|||
ftotal[0] -= fx*massfrac;
|
||||
ftotal[1] -= fy*massfrac;
|
||||
ftotal[2] -= fz*massfrac;
|
||||
if (evflag) {
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
v[0] = fx*massfrac*unwrap[0];
|
||||
v[1] = fy*massfrac*unwrap[1];
|
||||
v[2] = fz*massfrac*unwrap[2];
|
||||
v[3] = fx*massfrac*unwrap[1];
|
||||
v[4] = fx*massfrac*unwrap[2];
|
||||
v[5] = fy*massfrac*unwrap[2];
|
||||
v_tally(i, v);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -218,10 +218,10 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
|
|||
if (limit && !compress) limitfirst = 1;
|
||||
iarg += 2;
|
||||
if (limit) {
|
||||
if (iarg+1 > narg)
|
||||
if (iarg > narg)
|
||||
error->all(FLERR,"Illegal compute chunk/atom command");
|
||||
if (strcmp(arg[iarg+1],"max") == 0) limitstyle = LIMITMAX;
|
||||
else if (strcmp(arg[iarg+1],"exact") == 0) limitstyle = LIMITEXACT;
|
||||
if (strcmp(arg[iarg],"max") == 0) limitstyle = LIMITMAX;
|
||||
else if (strcmp(arg[iarg],"exact") == 0) limitstyle = LIMITEXACT;
|
||||
else error->all(FLERR,"Illegal compute chunk/atom command");
|
||||
iarg++;
|
||||
}
|
||||
|
|
|
|||
87
src/fix.cpp
87
src/fix.cpp
|
|
@ -31,7 +31,7 @@ int Fix::instance_total = 0;
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Fix::Fix(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix::Fix(LAMMPS *lmp, int narg, char **arg) :
|
||||
Pointers(lmp),
|
||||
id(NULL), style(NULL), extlist(NULL), vector_atom(NULL), array_atom(NULL),
|
||||
vector_local(NULL), array_local(NULL), eatom(NULL), vatom(NULL)
|
||||
|
|
@ -61,6 +61,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) :
|
|||
force_reneighbor = 0;
|
||||
box_change_size = box_change_shape = box_change_domain = 0;
|
||||
thermo_energy = 0;
|
||||
thermo_virial = 0;
|
||||
rigid_flag = 0;
|
||||
peatom_flag = 0;
|
||||
virial_flag = 0;
|
||||
|
|
@ -140,8 +141,20 @@ void Fix::modify_params(int narg, char **arg)
|
|||
} else if (strcmp(arg[iarg],"energy") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
|
||||
if (strcmp(arg[iarg+1],"no") == 0) thermo_energy = 0;
|
||||
else if (strcmp(arg[iarg+1],"yes") == 0) thermo_energy = 1;
|
||||
else error->all(FLERR,"Illegal fix_modify command");
|
||||
else if (strcmp(arg[iarg+1],"yes") == 0) {
|
||||
if (!(THERMO_ENERGY & setmask()))
|
||||
error->all(FLERR,"Illegal fix_modify command");
|
||||
thermo_energy = 1;
|
||||
} else error->all(FLERR,"Illegal fix_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"virial") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
|
||||
if (strcmp(arg[iarg+1],"no") == 0) thermo_virial = 0;
|
||||
else if (strcmp(arg[iarg+1],"yes") == 0) {
|
||||
if (virial_flag == 0)
|
||||
error->all(FLERR,"Illegal fix_modify command");
|
||||
thermo_virial = 1;
|
||||
} else error->all(FLERR,"Illegal fix_modify command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"respa") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
|
||||
|
|
@ -214,15 +227,22 @@ void Fix::ev_setup(int eflag, int vflag)
|
|||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
setup for virial computation
|
||||
see integrate::ev_set() for values of vflag (0-6)
|
||||
fixes call this if use v_tally()
|
||||
if thermo_virial is on:
|
||||
setup for virial computation
|
||||
see integrate::ev_set() for values of vflag (0-6)
|
||||
fixes call this if use v_tally()
|
||||
else: set evflag=0
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Fix::v_setup(int vflag)
|
||||
{
|
||||
int i,n;
|
||||
|
||||
if (!thermo_virial) {
|
||||
evflag = 0;
|
||||
return;
|
||||
}
|
||||
|
||||
evflag = 1;
|
||||
|
||||
vflag_global = vflag % 4;
|
||||
|
|
@ -316,3 +336,58 @@ void Fix::v_tally(int n, int *list, double total, double *v)
|
|||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
tally virial into global and per-atom accumulators
|
||||
i = local index of atom
|
||||
v = total virial for the interaction
|
||||
increment global virial by v
|
||||
increment per-atom virial by v
|
||||
this method can be used when fix computes forces in post_force()
|
||||
and the force depends on a distance to some external object
|
||||
e.g. fix wall/lj93: compute virial only on owned atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Fix::v_tally(int i, double *v)
|
||||
{
|
||||
|
||||
if (vflag_global) {
|
||||
virial[0] += v[0];
|
||||
virial[1] += v[1];
|
||||
virial[2] += v[2];
|
||||
virial[3] += v[3];
|
||||
virial[4] += v[4];
|
||||
virial[5] += v[5];
|
||||
}
|
||||
|
||||
if (vflag_atom) {
|
||||
vatom[i][0] += v[0];
|
||||
vatom[i][1] += v[1];
|
||||
vatom[i][2] += v[2];
|
||||
vatom[i][3] += v[3];
|
||||
vatom[i][4] += v[4];
|
||||
vatom[i][5] += v[5];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
tally virial component into global and per-atom accumulators
|
||||
n = index of virial component (0-5)
|
||||
i = local index of atom
|
||||
vn = nth component of virial for the interaction
|
||||
increment nth component of global virial by vn
|
||||
increment nth component of per-atom virial by vn
|
||||
this method can be used when fix computes forces in post_force()
|
||||
and the force depends on a distance to some external object
|
||||
e.g. fix wall/lj93: compute virial only on owned atoms
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Fix::v_tally(int n, int i, double vn)
|
||||
{
|
||||
|
||||
if (vflag_global)
|
||||
virial[n] += vn;
|
||||
|
||||
if (vflag_atom)
|
||||
vatom[i][n] += vn;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -36,6 +36,7 @@ class Fix : protected Pointers {
|
|||
|
||||
bigint next_reneighbor; // next timestep to force a reneighboring
|
||||
int thermo_energy; // 1 if fix_modify enabled ThEng, 0 if not
|
||||
int thermo_virial; // 1 if fix_modify enabled ThVir, 0 if not
|
||||
int nevery; // how often to call an end_of_step fix
|
||||
int rigid_flag; // 1 if Fix integrates rigid bodies, 0 if not
|
||||
int peatom_flag; // 1 if Fix contributes per-atom eng, 0 if not
|
||||
|
|
@ -223,6 +224,8 @@ class Fix : protected Pointers {
|
|||
void ev_tally(int, int *, double, double, double *);
|
||||
void v_setup(int);
|
||||
void v_tally(int, int *, double, double *);
|
||||
void v_tally(int, double *);
|
||||
void v_tally(int, int, double);
|
||||
|
||||
// union data struct for packing 32-bit and 64-bit ints into double bufs
|
||||
// see atom_vec.h for documentation
|
||||
|
|
|
|||
|
|
@ -51,6 +51,7 @@ FixAddForce::FixAddForce(LAMMPS *lmp, int narg, char **arg) :
|
|||
extvector = 1;
|
||||
respa_level_support = 1;
|
||||
ilevel_respa = 0;
|
||||
virial_flag = 1;
|
||||
|
||||
xstr = ystr = zstr = NULL;
|
||||
|
||||
|
|
@ -237,10 +238,16 @@ void FixAddForce::post_force(int vflag)
|
|||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
imageint *image = atom->image;
|
||||
double v[6];
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
if (update->ntimestep % nevery) return;
|
||||
|
||||
// energy and virial setup
|
||||
|
||||
if (vflag) v_setup(vflag);
|
||||
else evflag = 0;
|
||||
|
||||
if (lmp->kokkos)
|
||||
atom->sync_modify(Host, (unsigned int) (F_MASK | MASK_MASK),
|
||||
(unsigned int) F_MASK);
|
||||
|
|
@ -283,6 +290,15 @@ void FixAddForce::post_force(int vflag)
|
|||
f[i][0] += xvalue;
|
||||
f[i][1] += yvalue;
|
||||
f[i][2] += zvalue;
|
||||
if (evflag) {
|
||||
v[0] = xvalue * unwrap[0];
|
||||
v[1] = yvalue * unwrap[1];
|
||||
v[2] = zvalue * unwrap[2];
|
||||
v[3] = xvalue * unwrap[1];
|
||||
v[4] = xvalue * unwrap[2];
|
||||
v[5] = yvalue * unwrap[2];
|
||||
v_tally(i,v);
|
||||
}
|
||||
}
|
||||
|
||||
// variable force, wrap with clear/add
|
||||
|
|
@ -290,6 +306,7 @@ void FixAddForce::post_force(int vflag)
|
|||
// wrap with clear/add
|
||||
|
||||
} else {
|
||||
double unwrap[3];
|
||||
|
||||
modify->clearstep_compute();
|
||||
|
||||
|
|
@ -307,20 +324,39 @@ void FixAddForce::post_force(int vflag)
|
|||
|
||||
modify->addstep_compute(update->ntimestep + 1);
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
|
||||
if (estyle == ATOM) foriginal[0] += sforce[i][3];
|
||||
domain->unmap(x[i],image[i],unwrap);
|
||||
if (xstyle == ATOM) xvalue = sforce[i][0];
|
||||
if (ystyle == ATOM) yvalue = sforce[i][1];
|
||||
if (zstyle == ATOM) zvalue = sforce[i][2];
|
||||
|
||||
if (estyle == ATOM) {
|
||||
foriginal[0] += sforce[i][3];
|
||||
} else {
|
||||
if (xstyle) foriginal[0] -= xvalue*unwrap[0];
|
||||
if (ystyle) foriginal[0] -= yvalue*unwrap[1];
|
||||
if (zstyle) foriginal[0] -= zvalue*unwrap[2];
|
||||
}
|
||||
foriginal[1] += f[i][0];
|
||||
foriginal[2] += f[i][1];
|
||||
foriginal[3] += f[i][2];
|
||||
if (xstyle == ATOM) f[i][0] += sforce[i][0];
|
||||
else if (xstyle) f[i][0] += xvalue;
|
||||
if (ystyle == ATOM) f[i][1] += sforce[i][1];
|
||||
else if (ystyle) f[i][1] += yvalue;
|
||||
if (zstyle == ATOM) f[i][2] += sforce[i][2];
|
||||
else if (zstyle) f[i][2] += zvalue;
|
||||
|
||||
if (xstyle) f[i][0] += xvalue;
|
||||
if (ystyle) f[i][1] += yvalue;
|
||||
if (zstyle) f[i][2] += zvalue;
|
||||
if (evflag) {
|
||||
v[0] = xstyle ? xvalue*unwrap[0] : 0.0;
|
||||
v[1] = ystyle ? yvalue*unwrap[1] : 0.0;
|
||||
v[2] = zstyle ? zvalue*unwrap[2] : 0.0;
|
||||
v[3] = xstyle ? xvalue*unwrap[1] : 0.0;
|
||||
v[4] = xstyle ? xvalue*unwrap[2] : 0.0;
|
||||
v[5] = ystyle ? yvalue*unwrap[2] : 0.0;
|
||||
v_tally(i, v);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -37,6 +37,7 @@ FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
|
|||
scalar_flag = 1;
|
||||
global_freq = 1;
|
||||
virial_flag = 1;
|
||||
thermo_virial = 1;
|
||||
extscalar = 1;
|
||||
|
||||
if (strcmp(arg[3],"pf/callback") == 0) {
|
||||
|
|
|
|||
|
|
@ -45,6 +45,7 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
|
|||
extvector = 1;
|
||||
respa_level_support = 1;
|
||||
ilevel_respa = 0;
|
||||
virial_flag = 1;
|
||||
|
||||
// parse args
|
||||
|
||||
|
|
@ -298,7 +299,12 @@ void FixWall::pre_force(int vflag)
|
|||
|
||||
void FixWall::post_force(int vflag)
|
||||
{
|
||||
|
||||
// energy and virial setup
|
||||
|
||||
eflag = 0;
|
||||
if (vflag) v_setup(vflag);
|
||||
else evflag = 0;
|
||||
for (int m = 0; m <= nwall; m++) ewall[m] = 0.0;
|
||||
|
||||
// coord = current position of wall
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@ FixWallHarmonic::FixWallHarmonic(LAMMPS *lmp, int narg, char **arg) :
|
|||
void FixWallHarmonic::wall_particle(int m, int which, double coord)
|
||||
{
|
||||
double delta,dr,fwall;
|
||||
double vn;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
@ -60,6 +61,12 @@ void FixWallHarmonic::wall_particle(int m, int which, double coord)
|
|||
f[i][dim] -= fwall;
|
||||
ewall[0] += epsilon[m]*dr*dr;
|
||||
ewall[m+1] += fwall;
|
||||
|
||||
if (evflag) {
|
||||
if (side < 0) vn = -fwall*delta;
|
||||
else vn = fwall*delta;
|
||||
v_tally(dim, i, vn);
|
||||
}
|
||||
}
|
||||
|
||||
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
|
||||
|
|
|
|||
|
|
@ -52,6 +52,7 @@ void FixWallLJ1043::precompute(int m)
|
|||
void FixWallLJ1043::wall_particle(int m, int which, double coord)
|
||||
{
|
||||
double delta,rinv,r2inv,r4inv,r10inv,fwall;
|
||||
double vn;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
@ -79,5 +80,11 @@ void FixWallLJ1043::wall_particle(int m, int which, double coord)
|
|||
ewall[0] += coeff1[m]*r10inv - coeff2[m]*r4inv -
|
||||
coeff3[m]*pow(delta+coeff4[m],-3.0) - offset[m];
|
||||
ewall[m+1] += fwall;
|
||||
|
||||
if (evflag) {
|
||||
if (side < 0) vn = -fwall*delta;
|
||||
else vn = fwall*delta;
|
||||
v_tally(dim, i, vn);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -48,6 +48,7 @@ void FixWallLJ126::precompute(int m)
|
|||
void FixWallLJ126::wall_particle(int m, int which, double coord)
|
||||
{
|
||||
double delta,rinv,r2inv,r6inv,fwall;
|
||||
double vn;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
@ -76,6 +77,12 @@ void FixWallLJ126::wall_particle(int m, int which, double coord)
|
|||
f[i][dim] -= fwall;
|
||||
ewall[0] += r6inv*(coeff3[m]*r6inv - coeff4[m]) - offset[m];
|
||||
ewall[m+1] += fwall;
|
||||
|
||||
if (evflag) {
|
||||
if (side < 0) vn = -fwall*delta;
|
||||
else vn = fwall*delta;
|
||||
v_tally(dim, i, vn);
|
||||
}
|
||||
}
|
||||
|
||||
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
|
||||
|
|
|
|||
|
|
@ -49,6 +49,7 @@ void FixWallLJ93::precompute(int m)
|
|||
void FixWallLJ93::wall_particle(int m, int which, double coord)
|
||||
{
|
||||
double delta,rinv,r2inv,r4inv,r10inv,fwall;
|
||||
double vn;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
@ -79,6 +80,12 @@ void FixWallLJ93::wall_particle(int m, int which, double coord)
|
|||
ewall[0] += coeff3[m]*r4inv*r4inv*rinv -
|
||||
coeff4[m]*r2inv*rinv - offset[m];
|
||||
ewall[m+1] += fwall;
|
||||
|
||||
if (evflag) {
|
||||
if (side < 0) vn = -fwall*delta;
|
||||
else vn = fwall*delta;
|
||||
v_tally(dim, i, vn);
|
||||
}
|
||||
}
|
||||
|
||||
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
|
||||
|
|
|
|||
|
|
@ -25,11 +25,13 @@
|
|||
#include "output.h"
|
||||
#include "respa.h"
|
||||
#include "error.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
using namespace MathConst;
|
||||
|
||||
enum{LJ93,LJ126,COLLOID,HARMONIC};
|
||||
enum{LJ93,LJ126,LJ1043,COLLOID,HARMONIC};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
|
@ -47,6 +49,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
|
|||
extvector = 1;
|
||||
respa_level_support = 1;
|
||||
ilevel_respa = 0;
|
||||
virial_flag = 1;
|
||||
|
||||
// parse args
|
||||
|
||||
|
|
@ -59,6 +62,7 @@ FixWallRegion::FixWallRegion(LAMMPS *lmp, int narg, char **arg) :
|
|||
|
||||
if (strcmp(arg[4],"lj93") == 0) style = LJ93;
|
||||
else if (strcmp(arg[4],"lj126") == 0) style = LJ126;
|
||||
else if (strcmp(arg[4],"lj1043") == 0) style = LJ1043;
|
||||
else if (strcmp(arg[4],"colloid") == 0) style = COLLOID;
|
||||
else if (strcmp(arg[4],"harmonic") == 0) style = HARMONIC;
|
||||
else error->all(FLERR,"Illegal fix wall/region command");
|
||||
|
|
@ -143,6 +147,20 @@ void FixWallRegion::init()
|
|||
double r2inv = 1.0/(cutoff*cutoff);
|
||||
double r6inv = r2inv*r2inv*r2inv;
|
||||
offset = r6inv*(coeff3*r6inv - coeff4);
|
||||
} else if (style == LJ1043) {
|
||||
coeff1 = MY_2PI * 2.0/5.0 * epsilon * pow(sigma,10.0);
|
||||
coeff2 = MY_2PI * epsilon * pow(sigma,4.0);
|
||||
coeff3 = MY_2PI * pow(2.0,1/2.0) / 3 * epsilon * pow(sigma,3.0);
|
||||
coeff4 = 0.61 / pow(2.0,1/2.0) * sigma;
|
||||
coeff5 = coeff1 * 10.0;
|
||||
coeff6 = coeff2 * 4.0;
|
||||
coeff7 = coeff3 * 3.0;
|
||||
|
||||
double rinv = 1.0/cutoff;
|
||||
double r2inv = rinv*rinv;
|
||||
double r4inv = r2inv*r2inv;
|
||||
offset = coeff1*r4inv*r4inv*r2inv - coeff2*r4inv -
|
||||
coeff3*pow(cutoff+coeff4,-3.0);
|
||||
} else if (style == COLLOID) {
|
||||
coeff1 = -4.0/315.0 * epsilon * pow(sigma,6.0);
|
||||
coeff2 = -2.0/3.0 * epsilon;
|
||||
|
|
@ -186,6 +204,7 @@ void FixWallRegion::post_force(int vflag)
|
|||
{
|
||||
int i,m,n;
|
||||
double rinv,fx,fy,fz,tooclose;
|
||||
double delx, dely, delz, v[6];
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
|
|
@ -198,13 +217,18 @@ void FixWallRegion::post_force(int vflag)
|
|||
|
||||
int onflag = 0;
|
||||
|
||||
// energy and virial setup
|
||||
|
||||
eflag = 0;
|
||||
if (vflag) v_setup(vflag);
|
||||
else evflag = 0;
|
||||
|
||||
// region->match() insures particle is in region or on surface, else error
|
||||
// if returned contact dist r = 0, is on surface, also an error
|
||||
// in COLLOID case, r <= radius is an error
|
||||
// initilize ewall after region->prematch(),
|
||||
// so a dynamic region can access last timestep values
|
||||
|
||||
eflag = 0;
|
||||
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
|
||||
|
||||
for (i = 0; i < nlocal; i++)
|
||||
|
|
@ -226,19 +250,32 @@ void FixWallRegion::post_force(int vflag)
|
|||
|
||||
if (style == LJ93) lj93(region->contact[m].r);
|
||||
else if (style == LJ126) lj126(region->contact[m].r);
|
||||
else if (style == LJ1043) lj1043(region->contact[m].r);
|
||||
else if (style == COLLOID) colloid(region->contact[m].r,radius[i]);
|
||||
else harmonic(region->contact[m].r);
|
||||
|
||||
ewall[0] += eng;
|
||||
fx = fwall * region->contact[m].delx * rinv;
|
||||
fy = fwall * region->contact[m].dely * rinv;
|
||||
fz = fwall * region->contact[m].delz * rinv;
|
||||
delx = region->contact[m].delx;
|
||||
dely = region->contact[m].dely;
|
||||
delz = region->contact[m].delz;
|
||||
fx = fwall * delx * rinv;
|
||||
fy = fwall * dely * rinv;
|
||||
fz = fwall * delz * rinv;
|
||||
f[i][0] += fx;
|
||||
f[i][1] += fy;
|
||||
f[i][2] += fz;
|
||||
ewall[1] -= fx;
|
||||
ewall[2] -= fy;
|
||||
ewall[3] -= fz;
|
||||
ewall[0] += eng;
|
||||
if (evflag) {
|
||||
v[0] = fx*delx;
|
||||
v[1] = fy*dely;
|
||||
v[2] = fz*delz;
|
||||
v[3] = fx*dely;
|
||||
v[4] = fx*delz;
|
||||
v[5] = fy*delz;
|
||||
v_tally(i, v);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -319,6 +356,23 @@ void FixWallRegion::lj126(double r)
|
|||
eng = r6inv*(coeff3*r6inv - coeff4) - offset;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
LJ 10/4/3 interaction for particle with wall
|
||||
compute eng and fwall = magnitude of wall force
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallRegion::lj1043(double r)
|
||||
{
|
||||
double rinv = 1.0/r;
|
||||
double r2inv = rinv*rinv;
|
||||
double r4inv = r2inv*r2inv;
|
||||
double r10inv = r4inv*r4inv*r2inv;
|
||||
fwall = coeff5*r10inv*rinv - coeff6*r4inv*rinv -
|
||||
coeff7*pow(r+coeff4,-4.0);
|
||||
eng = coeff1*r10inv - coeff2*r4inv -
|
||||
coeff3*pow(r+coeff4,-3.0) - offset;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
colloid interaction for finite-size particle of rad with wall
|
||||
compute eng and fwall = magnitude of wall force
|
||||
|
|
|
|||
|
|
@ -47,10 +47,12 @@ class FixWallRegion : public Fix {
|
|||
char *idregion;
|
||||
|
||||
double coeff1,coeff2,coeff3,coeff4,offset;
|
||||
double coeff5,coeff6,coeff7;
|
||||
double eng,fwall;
|
||||
|
||||
void lj93(double);
|
||||
void lj126(double);
|
||||
void lj1043(double);
|
||||
void colloid(double, double);
|
||||
void harmonic(double);
|
||||
};
|
||||
|
|
|
|||
Loading…
Reference in New Issue